Bio

Bio


Dr. Khavari only sees U.S. veteran patients at the VA Palo Alto Healthcare System

Clinical Focus


  • Cancer > Cutaneous (Dermatologic) Oncology
  • Dermatology
  • General Dermatology

Academic Appointments


Administrative Appointments


  • Chair Department of Dermatology, Stanford University School of Medicine (2010 - Present)
  • Co-Director, Stanford Program in Epithelial Biology (1999 - Present)

Professional Education


  • Fellowship:Stanford University School of Medicine Registrar (1994) CA
  • Board Certification: Dermatology, American Board of Dermatology (1992)
  • Residency:Stanford University School of Medicine Registrar (1991) CA
  • Internship:Yale-New Haven Hospital (1989) CT
  • Medical Education:Yale School Of Medicine Office of Student Affairs (1988) CT
  • Residency:Yale - New Haven Hospital (1990) CT

Research & Scholarship

Current Research and Scholarly Interests


Our experimental focus is on the mammalian setting, including mouse genetics, human genetics, single cell studies, and new human tissue platforms. The latter encompass human skin regenerated on immune deficient mice as well as organotypic constructs with epithelial and stromal cells embedded within architecturally faithful mesenchyma in vitro. These new models, which we term Multi-Functional Human Tissue Genetics, allow up to 10 alleles or more to be altered simultaneously, permitting genetic experiments with an unprecedented degree of rapidity and complexity.

Stem cell biology and differentiation

In stratified epithelia proliferative basal cells adherent to the underlying basement membrane undergo cell cycle arrest then outward migration and terminal differentiation. This process is mediated by 2 mutually exclusive programs of gene expression: 1) an undifferentiated program supporting proliferation by stem cells within the basal layer and 2) a differentiation program instructing growth arrest and differentiation-associated programmed cell death in suprabasal layers. The control of this transition from epithelial stem cell to differentiated corneocyte, which is abnormal in epidermal cancers, is not well understood. We are currently pursuing studies of the dominant signaling and gene regulatory networks that control this process, including the Ras/MAPK cascade, which is required for stem cell-mediated self-renewal and the p53 transcription factor family member, p63, which is required for epidermal differentiation.

Epigenetic regulation by histone modifying proteins and noncoding RNA

In addition to classical gene regulatory networks noted above, we have recently identified a central role for additional biologic mechanisms, namely gene regulation by chromatin regulators and by noncoding RNAs. Epigenetic control of gene expression lasts through multiple cell divisions without alterations in primary DNA sequence and can occur via mechanisms that include histone modification and DNA methylation. Noncoding RNA sequences can regulate gene expression via interactions with epigenetic and other control mechanisms. The function of histone modifying epigenetic regulators and noncoding RNA as central mediators of epithelial stem cell renewal and differentiation represent major emerging areas of study in the lab.

Cancer

Skin malignancies, including epidermal squamous cell carcinoma (SCC), alone account for nearly as many cancers as all other tissues combined. Progress in understanding epithelial carcinogenesis has been hindered in the past by a lack of models that faithfully recapitulate the 3-dimensional architecture of tumor-stroma co-evolution. To address this and to also study the oncogenic potential of unregulated function of dominant regulators of epithelial homeostasis noted above, we developed Multi-Functional Human Tissue Genetics noted above which, when combined with skin tissue regeneration on immune deficient mice, has permitted the molecular reconstruction of events sufficient to trigger human cancer. These models are being used to systematically elucidate proteins required for cutaneous carcinogenesis and to test their potential role as therapeutic targets.

Molecular Therapeutics

Epithelial tissues in general and skin in particular offer an attractive site for development of new approaches in molecular therapeutics. A family of human genetic skin diseases is characterized by defective epithelial gene expression. Among the most severe of these are subtypes of epidermolysis bullosa (EB) and lamellar ichthyosis (LI). We have developed approaches for high efficiency gene transfer to EB and LI patient skin tissue that are corrective at biochemical, histologic, clinical and functional levels. In addition to EB subtypes and LI, similar corrective efforts have also been undertaken with a number of other genetic skin disorders.

Clinical Trials


  • Characteristics of Patients With Recessive Dystrophic Epidermolysis Bullosa Recruiting

    Recessive dystrophic epidermolysis bullosa (RDEB) is a disease caused by genetic mutations in the gene for type VII collagen. Patients with RDEB develop large, severely painful blisters and open wounds from minor trauma to their skin. We are screening subjects with RDEB to evaluate characteristics of the subjects and their cells in order to develop new strategies of therapy and determine whether subjects could be candidates for treatment studies.

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  • Analysis of Cutaneous and Hematologic Disorders by High-Throughput Nucleic Acid Sequencing Not Recruiting

    The goal of this study is to identify genetic changes associated with the initiation, progression, and treatment response of response of cutaneous and hematologic disorders using recently developed high-throughput sequencing technologies. The improved understanding of the genetic changes associated with cutaneous and hematologic disorders may lead to improved diagnostic, prognostic and therapeutic options for these disorders.

    Stanford is currently not accepting patients for this trial. For more information, please contact Alexander Ungewickell, 650-723-6661.

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  • Characteristics of Adult Patients With Recessive Dystrophic Epidermolysis Bullosa Not Recruiting

    Recessive dystrophic epidermolysis bullosa (RDEB) is a severe inherited blistering disease caused by the absence of type VII collagen. Patients with RDEB develop large, severely painful blisters and open wounds from minor trauma to their skin. We are screening RDEB subjects to determine additional characteristics of patients who survive to adulthood.

    Stanford is currently not accepting patients for this trial. For more information, please contact Emily Gorell, MS, 650-721-7166.

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  • Gene Transfer for Recessive Dystrophic Epidermolysis Bullosa Not Recruiting

    This trial will create a skin graft, which the investigators call "LEAES," using the patient's own skin cells that have been genetically engineered in the lab to express a missing protein called type VII collagen. The corrected cells will be transplanted back to the patient.

    Stanford is currently not accepting patients for this trial. For more information, please contact Yana Dutt-Singkh, 650-721-7166.

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  • Pilot Trial to Evaluate the Effect of Vitamin D on Melanocyte Biomarkers Not Recruiting

    The purpose of this study is to determine the signaling pathways and changes in gene expression in melanocytes of subjects with a history of non-melanoma skin cancer who are exposed to oral vitamin D. If vitamin D is found to inhibit a signaling pathway involved in the development of melanoma such as BRAF, a protein involved in cell proliferation, then oral vitamin D could be explored further as a chemoprevention for melanoma skin cancer.

    Stanford is currently not accepting patients for this trial. For more information, please contact Irene Bailey, 650-498-7061.

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Teaching

2019-20 Courses


Stanford Advisees


Graduate and Fellowship Programs


Publications

All Publications


  • Methods to study RNA-protein interactions. Nature methods Ramanathan, M., Porter, D. F., Khavari, P. A. 2019; 16 (3): 225–34

    Abstract

    Noncoding RNA sequences, including long noncoding RNAs, small nucleolar RNAs, and untranslated mRNA regions, accomplish many of their diverse functions through direct interactions with RNA-binding proteins (RBPs). Recent efforts have identified hundreds of new RBPs that lack known RNA-binding domains, thus underscoring the complexity and diversity of RNA-protein complexes. Recent progress has expanded the number of methods for studying RNA-protein interactions in two general categories: approaches that characterize proteins bound to an RNA of interest (RNA-centric), and those that examine RNAs bound to a protein of interest (protein-centric). Each method has unique strengths and limitations, which makes it important to select optimal approaches for the biological question being addressed. Here we review methods for the study of RNA-protein interactions, with a focus on their suitability for specific applications.

    View details for PubMedID 30804549

  • The Functional Proximal Proteome of Oncogenic Ras Includes mTORC2. Molecular cell Kovalski, J. R., Bhaduri, A., Zehnder, A. M., Neela, P. H., Che, Y., Wozniak, G. G., Khavari, P. A. 2019

    Abstract

    Proximity-dependent biotin labeling (BioID) may identify new targets for cancers driven by difficult-to-drug oncogenes such as Ras. Therefore, BioID was used with wild-type (WT) and oncogenic mutant (MT) H-,K-, and N-Ras, identifying known interactors, including Raf and PI3K, as well as a common set of 130 novel proteins proximal to all Ras isoforms. A CRISPR screen of these proteins for Ras dependence identified mTOR, which was also found proximal to MT Ras in human tumors. Oncogenic Ras directly bound two mTOR complex 2 (mTORC2) components, mTOR and MAPKAP1, to promote mTORC2 kinase activity at the plasma membrane. mTORC2 enabled the Ras pro-proliferative cell cycletranscriptional program, and perturbing the Ras-mTORC2 interaction impaired Ras-dependent neoplasia invivo. Combining proximity-dependent proteomics with CRISPR screening identified a new set of functional Ras-associated proteins, defined mTORC2 as a new direct Ras effector, and offers a strategy for finding new proteins that cooperate with dominant oncogenes.

    View details for PubMedID 30639242

  • Coupled Single-Cell CRISPR Screening and Epigenomic Profiling Reveals Causal Gene Regulatory Networks. Cell Rubin, A. J., Parker, K. R., Satpathy, A. T., Qi, Y., Wu, B., Ong, A. J., Mumbach, M. R., Ji, A. L., Kim, D. S., Cho, S. W., Zarnegar, B. J., Greenleaf, W. J., Chang, H. Y., Khavari, P. A. 2018

    Abstract

    Here, we present Perturb-ATAC, a method that combines multiplexed CRISPR interference or knockout with genome-wide chromatin accessibility profiling in single cells based on the simultaneous detection of CRISPR guide RNAs and open chromatin sites by assay of transposase-accessible chromatin with sequencing (ATAC-seq). We applied Perturb-ATAC to transcription factors (TFs), chromatin-modifying factors, and noncoding RNAs (ncRNAs) in 4,300 single cells, encompassing more than 63 genotype-phenotype relationships. Perturb-ATAC in human Blymphocytes uncovered regulators of chromatin accessibility, TF occupancy, and nucleosome positioning and identified a hierarchy of TFs that govern B cell state, variation, and disease-associated cis-regulatory elements. Perturb-ATAC in primary human epidermal cells revealed three sequential modules of cis-elements that specify keratinocyte fate. Combinatorial deletion of all pairs of these TFsuncovered their epistatic relationships and highlighted genomic co-localization as a basis for synergistic interactions. Thus, Perturb-ATAC is a powerful strategy to dissect gene regulatory networks in development and disease.

    View details for PubMedID 30580963

  • RNA-protein interaction detection in living cells. Nature methods Ramanathan, M., Majzoub, K., Rao, D. S., Neela, P. H., Zarnegar, B. J., Mondal, S., Roth, J. G., Gai, H., Kovalski, J. R., Siprashvili, Z., Palmer, T. D., Carette, J. E., Khavari, P. A. 2018

    Abstract

    RNA-protein interactions play numerous roles in cellular function and disease. Here we describe RNA-protein interaction detection (RaPID), which uses proximity-dependent protein labeling, based on the BirA* biotin ligase, to rapidly identify the proteins that bind RNA sequences of interest in living cells. RaPID displays utility in multiple applications, including in evaluating protein binding to mutant RNA motifs in human genetic disorders, in uncovering potential post-transcriptional networks in breast cancer, and in discovering essential host proteins that interact with Zika virus RNA. To improve the BirA*-labeling component of RaPID, moreover, a new mutant BirA* was engineered from Bacillus subtilis, termed BASU, that enables >1,000-fold faster kinetics and >30-fold increased signal-to-noise ratio over the prior standard Escherichia coli BirA*, thereby enabling direct study of RNA-protein interactions in living cells on a timescale as short as 1 min.

    View details for PubMedID 29400715

  • Lineage-specific dynamic and pre-established enhancer-promoter contacts cooperate in terminal differentiation. Nature genetics Rubin, A. J., Barajas, B. C., Furlan-Magaril, M., Lopez-Pajares, V., Mumbach, M. R., Howard, I., Kim, D. S., Boxer, L. D., Cairns, J., Spivakov, M., Wingett, S. W., Shi, M., Zhao, Z., Greenleaf, W. J., Kundaje, A., Snyder, M., Chang, H. Y., Fraser, P., Khavari, P. A. 2017; 49 (10): 1522–28

    Abstract

    Chromosome conformation is an important feature of metazoan gene regulation; however, enhancer-promoter contact remodeling during cellular differentiation remains poorly understood. To address this, genome-wide promoter capture Hi-C (CHi-C) was performed during epidermal differentiation. Two classes of enhancer-promoter contacts associated with differentiation-induced genes were identified. The first class ('gained') increased in contact strength during differentiation in concert with enhancer acquisition of the H3K27ac activation mark. The second class ('stable') were pre-established in undifferentiated cells, with enhancers constitutively marked by H3K27ac. The stable class was associated with the canonical conformation regulator cohesin, whereas the gained class was not, implying distinct mechanisms of contact formation and regulation. Analysis of stable enhancers identified a new, essential role for a constitutively expressed, lineage-restricted ETS-family transcription factor, EHF, in epidermal differentiation. Furthermore, neither class of contacts was observed in pluripotent cells, suggesting that lineage-specific chromatin structure is established in tissue progenitor cells and is further remodeled in terminal differentiation.

    View details for PubMedID 28805829

  • CSNK1a1 Regulates PRMT1 to Maintain the Progenitor State in Self-Renewing Somatic Tissue. Developmental cell Bao, X., Siprashvili, Z., Zarnegar, B. J., Shenoy, R. M., Rios, E. J., Nady, N., Qu, K., Mah, A., Webster, D. E., Rubin, A. J., Wozniak, G. G., Tao, S., Wysocka, J., Khavari, P. A. 2017; 43 (2): 227–39.e5

    Abstract

    Somatic progenitors sustain tissue self-renewal while suppressing premature differentiation. Protein arginine methyltransferases (PRMTs) affect many processes; however, their role in progenitor function is incompletely understood. PRMT1 was found to be the most highly expressed PRMT in epidermal progenitors and the most downregulated PRMT during differentiation. In targeted mouse knockouts and in long-term regenerated human mosaic epidermis in vivo, epidermal PRMT1 loss abolished progenitor self-renewal and led to premature differentiation. Mass spectrometry of the PRMT1 protein interactome identified the CSNK1a1 kinase, which also proved essential for progenitor maintenance. CSNK1a1 directly bound and phosphorylated PRMT1 to control its genomic targeting to PRMT1-sustained proliferation genes as well as PRMT1-suppressed differentiation genes. Among the latter were GRHL3, whose derepression was required for the premature differentiation seen with PRMT1 and CSNK1a1 loss. Maintenance of the progenitors thus requires cooperation by PRMT1 and CSNK1a1 to sustain proliferation gene expression and suppress premature differentiation driven by GRHL3.

    View details for PubMedID 28943242

  • irCLIP platform for efficient characterization of protein-RNA interactions NATURE METHODS Zarnegar, B. J., Flynn, R. A., Shen, Y., Do, B. T., Chang, H. Y., Khavari, P. A. 2016; 13 (6): 489-?

    Abstract

    The complexity of transcriptome-wide protein-RNA interaction networks is incompletely understood. While emerging studies are greatly expanding the known universe of RNA-binding proteins, methods for the discovery and characterization of protein-RNA interactions remain resource intensive and technically challenging. Here we introduce a UV-C crosslinking and immunoprecipitation platform, irCLIP, which provides an ultraefficient, fast, and nonisotopic method for the detection of protein-RNA interactions using far less material than standard protocols.

    View details for DOI 10.1038/NMETH.3840

    View details for PubMedID 27111506

  • The noncoding RNAs SNORD50A and SNORD50B bind K-Ras and are recurrently deleted in human cancer. Nature genetics Siprashvili, Z., Webster, D. E., Johnston, D., Shenoy, R. M., Ungewickell, A. J., Bhaduri, A., Flockhart, R., Zarnegar, B. J., Che, Y., Meschi, F., Puglisi, J. D., Khavari, P. A. 2016; 48 (1): 53-58

    Abstract

    Small nucleolar RNAs (snoRNAs) are conserved noncoding RNAs best studied as ribonucleoprotein (RNP) guides in RNA modification. To explore their role in cancer, we compared 5,473 tumor-normal genome pairs to identify snoRNAs with frequent copy number loss. The SNORD50A-SNORD50B snoRNA locus was deleted in 10-40% of 12 common cancers, where its loss was associated with reduced survival. A human protein microarray screen identified direct SNORD50A and SNORD50B RNA binding to K-Ras. Loss of SNORD50A and SNORD50B increased the amount of GTP-bound, active K-Ras and hyperactivated Ras-ERK1/ERK2 signaling. Loss of these snoRNAs also increased binding by farnesyltransferase to K-Ras and increased K-Ras prenylation, suggesting that KRAS mutation might synergize with SNORD50A and SNORD50B loss in cancer. In agreement with this hypothesis, CRISPR-mediated deletion of SNORD50A and SNORD50B in KRAS-mutant tumor cells enhanced tumorigenesis, and SNORD50A and SNORD50B deletion and oncogenic KRAS mutation co-occurred significantly in multiple human tumor types. SNORD50A and SNORD50B snoRNAs thus directly bind and inhibit K-Ras and are recurrently deleted in human cancer.

    View details for DOI 10.1038/ng.3452

    View details for PubMedID 26595770

  • Network Analysis Identifies Mitochondria! Regulation of Epidermal Differentiation by MPZL3 and FDXR DEVELOPMENTAL CELL Bhaduri, A., Ungewickell, A., Boxer, L. D., Lopez-Pajares, V., Zarnegar, B. J., Khavari, P. A. 2015; 35 (4): 444-457

    Abstract

    Current gene expression network approaches commonly focus on transcription factors (TFs), biasing network-based discovery efforts away from potentially important non-TF proteins. We developed proximity analysis, a network reconstruction method that uses topological constraints of scale-free, small-world biological networks to reconstruct relationships in eukaryotic systems, independent of subcellular localization. Proximity analysis identified MPZL3 as a highly connected hub that is strongly induced during epidermal differentiation. MPZL3 was essential for normal differentiation, acting downstream of p63, ZNF750, KLF4, and RCOR1, each of which bound near the MPZL3 gene and controlled its expression. MPZL3 protein localized to mitochondria, where it interacted with FDXR, which was itself also found to be essential for differentiation. Together, MPZL3 and FDXR increased reactive oxygen species (ROS) to drive epidermal differentiation. ROS-induced differentiation is dependent upon promotion of FDXR enzymatic activity by MPZL3. ROS induction by the MPZL3 and FDXR mitochondrial proteins is therefore essential for epidermal differentiation.

    View details for DOI 10.1016/j.devcel.2015.10.023

    View details for PubMedID 26609959

  • Genomic analysis of mycosis fungoides and Sézary syndrome identifies recurrent alterations in TNFR2. Nature genetics Ungewickell, A., Bhaduri, A., Rios, E., Reuter, J., Lee, C. S., Mah, A., Zehnder, A., Ohgami, R., Kulkarni, S., Armstrong, R., Weng, W., Gratzinger, D., Tavallaee, M., Rook, A., Snyder, M., Kim, Y., Khavari, P. A. 2015; 47 (9): 1056-1060

    Abstract

    Mycosis fungoides and Sézary syndrome comprise the majority of cutaneous T cell lymphomas (CTCLs), disorders notable for their clinical heterogeneity that can present in skin or peripheral blood. Effective treatment options for CTCL are limited, and the genetic basis of these T cell lymphomas remains incompletely characterized. Here we report recurrent point mutations and genomic gains of TNFRSF1B, encoding the tumor necrosis factor receptor TNFR2, in 18% of patients with mycosis fungoides and Sézary syndrome. Expression of the recurrent TNFR2 Thr377Ile mutant in T cells leads to enhanced non-canonical NF-κB signaling that is sensitive to the proteasome inhibitor bortezomib. Using an integrative genomic approach, we additionally discovered a recurrent CTLA4-CD28 fusion, as well as mutations in downstream signaling mediators of these receptors.

    View details for DOI 10.1038/ng.3370

    View details for PubMedID 26258847

  • A LncRNA-MAF:MAFB Transcription Factor Network Regulates Epidermal Differentiation DEVELOPMENTAL CELL Lopez-Pajares, V., Qu, K., Zhang, J., Webster, D. E., Barajas, B. C., Siprashvili, Z., Zarnegar, B. J., Boxer, L. D., Rios, E. J., Tao, S., Kretz, M., Khavari, P. A. 2015; 32 (6): 693-706

    Abstract

    Progenitor differentiation requires remodeling of genomic expression; however, in many tissues, such as epidermis, the spectrum of remodeled genes and the transcription factors (TFs) that control them are not fully defined. We performed kinetic transcriptome analysis during regeneration of differentiated epidermis and identified gene sets enriched in progenitors (594 genes), in early (159 genes), and in late differentiation (387 genes). Module mapping of 1,046 TFs identified MAF and MAFB as necessary and sufficient for progenitor differentiation. MAF:MAFB regulated 393 genes altered in this setting. Integrative analysis identified ANCR and TINCR lncRNAs as essential upstream MAF:MAFB regulators. ChIP-seq analysis demonstrated MAF:MAFB binding to known epidermal differentiation TF genes whose expression they controlled, including GRHL3, ZNF750, KLF4, and PRDM1. Each of these TFs rescued expression of specific MAF:MAFB target gene subsets in the setting of MAF:MAFB loss, indicating they act downstream of MAF:MAFB. A lncRNA-TF network is thus essential for epidermal differentiation.

    View details for DOI 10.1016/j.devcel.2015.01.028

    View details for PubMedID 25805135

  • Advances in skin grafting and treatment of cutaneous wounds SCIENCE Sun, B. K., Siprashvili, Z., Khavari, P. A. 2014; 346 (6212): 941-945

    Abstract

    The ability of the skin to repair itself after injury is vital to human survival and is disrupted in a spectrum of disorders. The process of cutaneous wound healing is complex, requiring a coordinated response by immune cells, hematopoietic cells, and resident cells of the skin. We review the classic paradigms of wound healing and evaluate how recent discoveries have enriched our understanding of this process. We evaluate current and experimental approaches to treating cutaneous wounds, with an emphasis on cell-based therapies and skin transplantation.

    View details for DOI 10.1126/science.1253836

    View details for Web of Science ID 000345696000031

  • Recurrent point mutations in the kinetochore gene KNSTRN in cutaneous squamous cell carcinoma NATURE GENETICS Lee, C. S., Bhaduri, A., Mah, A., Johnson, W. L., Ungewickell, A., Aros, C. J., Nguyen, C. B., Rios, E. J., Siprashvili, Z., Straight, A., Kim, J., Aasi, S. Z., Khavari, P. A. 2014; 46 (10): 1060-1062

    Abstract

    Here we report the discovery of recurrent mutations concentrated at an ultraviolet signature hotspot in KNSTRN, which encodes a kinetochore protein, in 19% of cutaneous squamous cell carcinomas (SCCs). Cancer-associated KNSTRN mutations, most notably those encoding p.Ser24Phe, disrupt chromatid cohesion in normal cells, occur in SCC precursors, correlate with increased aneuploidy in primary tumors and enhance tumorigenesis in vivo. These findings suggest a role for KNSTRN mutagenesis in SCC development.

    View details for DOI 10.1038/ng.3091

    View details for Web of Science ID 000342554100007

    View details for PubMedCentralID PMC4324615

  • IQGAP1 scaffold-kinase interaction blockade selectively targets RAS-MAP kinase-driven tumors. Nature medicine Jameson, K. L., Mazur, P. K., Zehnder, A. M., Zhang, J., Zarnegar, B., Sage, J., Khavari, P. A. 2013; 19 (5): 626-630

    Abstract

    Upregulation of the ERK1 and ERK2 (ERK1/2) MAP kinase (MAPK) cascade occurs in >30% of cancers, often through mutational activation of receptor tyrosine kinases or other upstream genes, including KRAS and BRAF. Efforts to target endogenous MAPKs are challenged by the fact that these kinases are required for viability in mammals. Additionally, the effectiveness of new inhibitors of mutant BRAF has been diminished by acquired tumor resistance through selection for BRAF-independent mechanisms of ERK1/2 induction. Furthermore, recently identified ERK1/2-inducing mutations in MEK1 and MEK2 (MEK1/2) MAPK genes in melanoma confer resistance to emerging therapeutic MEK inhibitors, underscoring the challenges facing direct kinase inhibition in cancer. MAPK scaffolds, such as IQ motif-containing GTPase activating protein 1 (IQGAP1), assemble pathway kinases to affect signal transmission, and disrupting scaffold function therefore offers an orthogonal approach to MAPK cascade inhibition. Consistent with this, we found a requirement for IQGAP1 in RAS-driven tumorigenesis in mouse and human tissue. In addition, the ERK1/2-binding IQGAP1 WW domain peptide disrupted IQGAP1-ERK1/2 interactions, inhibited RAS- and RAF-driven tumorigenesis, bypassed acquired resistance to the BRAF inhibitor vemurafenib (PLX-4032) and acted as a systemically deliverable therapeutic to significantly increase the lifespan of tumor-bearing mice. Scaffold-kinase interaction blockade acts by a mechanism distinct from direct kinase inhibition and may be a strategy to target overactive oncogenic kinase cascades in cancer.

    View details for DOI 10.1038/nm.3165

    View details for PubMedID 23603816

  • ACTL6a enforces the epidermal progenitor state by suppressing SWI/SNF-dependent induction of KLF4. Cell stem cell Bao, X., Tang, J., Lopez-Pajares, V., Tao, S., Qu, K., Crabtree, G. R., Khavari, P. A. 2013; 12 (2): 193-203

    Abstract

    Somatic progenitors suppress differentiation to maintain tissue self-renewal. The mammalian SWI/SNF chromatin-remodeling complex regulates nucleosome packaging to control differentiation in embryonic and adult stem cells. Catalytic Brg1 and Brm subunits are required for these processes; however, the roles of SWI/SNF regulatory subunits are not fully understood. Here, we show that ACTL6a/BAF53A modulates the SWI/SNF complex to suppress differentiation in epidermis. Conditional loss of ACTL6a resulted in terminal differentiation, cell-cycle exit, and hypoplasia, whereas ectopic expression of ACTL6a promoted the progenitor state. A significant portion of genes regulated by ACTL6a were found to also be targets of KLF4, a known activator of epidermal differentiation. Mechanistically, we show that ACTL6a prevents SWI/SNF complex binding to promoters of KLF4 and other differentiation genes and that SWI/SNF catalytic subunits are required for full induction of KLF4 targets. Thus, ACTL6a controls the epidermal progenitor state by sequestering SWI/SNF to prevent activation of differentiation programs.

    View details for DOI 10.1016/j.stem.2012.12.014

    View details for PubMedID 23395444

  • Control of somatic tissue differentiation by the long non-coding RNA TINCR. Nature Kretz, M., Siprashvili, Z., Chu, C., Webster, D. E., Zehnder, A., Qu, K., Lee, C. S., Flockhart, R. J., Groff, A. F., Chow, J., Johnston, D., Kim, G. E., Spitale, R. C., Flynn, R. A., Zheng, G. X., Aiyer, S., Raj, A., Rinn, J. L., Chang, H. Y., Khavari, P. A. 2013; 493 (7431): 231-235

    Abstract

    Several of the thousands of human long non-coding RNAs (lncRNAs) have been functionally characterized; however, potential roles for lncRNAs in somatic tissue differentiation remain poorly understood. Here we show that a 3.7-kilobase lncRNA, terminal differentiation-induced ncRNA (TINCR), controls human epidermal differentiation by a post-transcriptional mechanism. TINCR is required for high messenger RNA abundance of key differentiation genes, many of which are mutated in human skin diseases, including FLG, LOR, ALOXE3, ALOX12B, ABCA12, CASP14 and ELOVL3. TINCR-deficient epidermis lacked terminal differentiation ultrastructure, including keratohyalin granules and intact lamellar bodies. Genome-scale RNA interactome analysis revealed that TINCR interacts with a range of differentiation mRNAs. TINCR-mRNA interaction occurs through a 25-nucleotide 'TINCR box' motif that is strongly enriched in interacting mRNAs and required for TINCR binding. A high-throughput screen to analyse TINCR binding capacity to approximately 9,400 human recombinant proteins revealed direct binding of TINCR RNA to the staufen1 (STAU1) protein. STAU1-deficient tissue recapitulated the impaired differentiation seen with TINCR depletion. Loss of UPF1 and UPF2, both of which are required for STAU1-mediated RNA decay, however, did not have differentiation effects. Instead, the TINCR-STAU1 complex seems to mediate stabilization of differentiation mRNAs, such as KRT80. These data identify TINCR as a key lncRNA required for somatic tissue differentiation, which occurs through lncRNA binding to differentiation mRNAs to ensure their expression.

    View details for DOI 10.1038/nature11661

    View details for PubMedID 23201690

  • ZNF750 Is a p63 Target Gene that Induces KLF4 to Drive Terminal Epidermal Differentiation DEVELOPMENTAL CELL Sen, G. L., Boxer, L. D., Webster, D. E., Bussat, R. T., Qu, K., Zarnegar, B. J., Johnston, D., Siprashvili, Z., Khavari, P. A. 2012; 22 (3): 669-677

    Abstract

    Disrupted epidermal differentiation characterizes numerous diseases that impact >25% of the population. In a search for dominant mediators of differentiation, we defined a requirement for ZNF750 in terminal epidermal differentiation. ZNF750 controlled genes mutated in numerous human skin diseases, including FLG, LOR, LCE3B, ALOXE3, and SPINK5. ZNF750 induced progenitor differentiation via an evolutionarily conserved C2H2 zinc finger motif. The epidermal master regulator, p63, bound the ZNF750 promoter and was necessary for its induction. ZNF750 restored differentiation to p63-deficient tissue, suggesting that it acts downstream of p63. A search for functionally important ZNF750 targets via analysis of ZNF750-regulated genes identified KLF4, a transcription factor that activates late epidermal differentiation. ZNF750 binds to KLF4 at multiple sites flanking the transcriptional start site and controls its expression. ZNF750 thus directly links a tissue-specifying factor, p63, to an effector of terminal differentiation, KLF4, and represents a potential future target for disorders of this process.

    View details for DOI 10.1016/j.devcel.2011.12.001

    View details for Web of Science ID 000301701600020

    View details for PubMedID 22364861

    View details for PubMedCentralID PMC3306457

  • DNMT1 maintains progenitor function in self-renewing somatic tissue NATURE Sen, G. L., Reuter, J. A., Webster, D. E., Zhu, L., Khavari, P. A. 2010; 463 (7280): 563-U189

    Abstract

    Progenitor cells maintain self-renewing tissues throughout life by sustaining their capacity for proliferation while suppressing cell cycle exit and terminal differentiation. DNA methylation provides a potential epigenetic mechanism for the cellular memory needed to preserve the somatic progenitor state through repeated cell divisions. DNA methyltransferase 1 (DNMT1) maintains DNA methylation patterns after cellular replication. Although dispensable for embryonic stem cell maintenance, the role for DNMT1 in maintaining the progenitor state in constantly replenished somatic tissues, such as mammalian epidermis, is unclear. Here we show that DNMT1 is essential for epidermal progenitor cell function. DNMT1 protein was found enriched in undifferentiated cells, where it was required to retain proliferative stamina and suppress differentiation. In tissue, DNMT1 depletion led to exit from the progenitor cell compartment, premature differentiation and eventual tissue loss. Genome-wide analysis showed that a significant portion of epidermal differentiation gene promoters were methylated in self-renewing conditions but were subsequently demethylated during differentiation. Furthermore, UHRF1 (refs 9, 10), a component of the DNA methylation machinery that targets DNMT1 to hemi-methylated DNA, is also necessary to suppress premature differentiation and sustain proliferation. In contrast, Gadd45A and B, which promote active DNA demethylation, are required for full epidermal differentiation gene induction. These data demonstrate that proteins involved in the dynamic regulation of DNA methylation patterns are required for progenitor maintenance and self-renewal in mammalian somatic tissue.

    View details for DOI 10.1038/nature08683

    View details for PubMedID 20081831

  • HiChIRP reveals RNA-associated chromosome conformation. Nature methods Mumbach, M. R., Granja, J. M., Flynn, R. A., Roake, C. M., Satpathy, A. T., Rubin, A. J., Qi, Y., Jiang, Z., Shams, S., Louie, B. H., Guo, J. K., Gennert, D. G., Corces, M. R., Khavari, P. A., Atianand, M. K., Artandi, S. E., Fitzgerald, K. A., Greenleaf, W. J., Chang, H. Y. 2019

    Abstract

    Modular domains of long non-coding RNAs can serve as scaffolds to bring distant regions of the linear genome into spatial proximity. Here, we present HiChIRP, a method leveraging bio-orthogonal chemistry and optimized chromosome conformation capture conditions, which enables interrogation of chromatin architecture focused around a specific RNA of interest down to approximately ten copies per cell. HiChIRP of three nuclear RNAs reveals insights into promoter interactions (7SK), telomere biology (telomerase RNA component) and inflammatory gene regulation (lincRNA-EPS).

    View details for DOI 10.1038/s41592-019-0407-x

    View details for PubMedID 31133759

  • Impact of a patient-derived hepatitis C viral RNA genome with a mutated microRNA binding site PLOS PATHOGENS Mata, M., Neben, S., Majzoub, K., Carette, J., Ramanathan, M., Khavari, P. A., Sarnow, P. 2019; 15 (5)
  • Characterization of novel MAPK interactor with potential in therapeutic development Jiang, T. E., Che, Y., Seelman, A., Guenin, C., Khavari, P. ELSEVIER SCIENCE INC. 2019: S69
  • Uncovering causative, noncoding genetic variants in cutaneous diseases Wozniak, G., Shen, Y., Rubin, A., Neela, P., Khavari, P. ELSEVIER SCIENCE INC. 2019: S68
  • Dissecting intratumoral heterogeneity and microenvironment interactions in SCC through single-cell RNA-sequencing Ji, A., Rubin, A., Reynolds, D., Guo, M., Bhaduri, A., George, B., Hollmig, S., Aasi, S., Khavari, P. ELSEVIER SCIENCE INC. 2019: S24
  • Small non-coding RNA SNORA12 effects MAPK1 signaling Siprashvili, Z., Shenoy, R. M., Elcavage, L., Khavari, P. A. ELSEVIER SCIENCE INC. 2019: S21
  • Unraveling keratinocyte gene regulatory networks with single-cell cripsr screening and epigenomic profiling Ramanathan, M., Rubin, A., Parker, K., Satpathy, A., Greenleaf, W., Chang, H., Khavari, P. ELSEVIER SCIENCE INC. 2019: S63
  • Profiling of rotavirus 3UTR-binding proteins reveals the ATP synthase subunit ATP5B as a host factor that supports late-stage virus replication JOURNAL OF BIOLOGICAL CHEMISTRY Ren, L., Ding, S., Song, Y., Li, B., Ramanathan, M., Co, J., Amieva, M. R., Khavari, P. A., Greenberg, H. B. 2019; 294 (15): 5993–6006
  • Methods to study RNA-protein interactions (vol 16, pg 225, 2019) NATURE METHODS Ramanathan, M., Porter, D. F., Khavari, P. A. 2019; 16 (4): 351
  • Author Correction: Methods to study RNA-protein interactions. Nature methods Ramanathan, M., Porter, D. F., Khavari, P. A. 2019

    Abstract

    In the version of this paper originally published, three references were accidentally omitted: Schwartz, J. C. et al. Cell Rep. 5, 918-925 (2013); Tundup, S. et al. FEBS Lett. 580, 1285-1293 (2006); and Itri, F. et al. Biochem. Biophys. Res. Commun. 492, 67-73 (2017). The PDF and HTML versions of the paper now include these as references 58, 59, and 60, respectively, and subsequent references have been renumbered accordingly.

    View details for PubMedID 30850752

  • Methods to study RNA-protein interactions NATURE METHODS Ramanathan, M., Porter, D. F., Khavari, P. A. 2019; 16 (3): 225–34
  • The Functional Proximal Proteome of Oncogenic Ras Includes mTORC2 MOLECULAR CELL Kovalski, J. R., Bhaduri, A., Zehnder, A. M., Neela, P. H., Che, Y., Wozniak, G. G., Khavari, P. A. 2019; 73 (4): 830-+
  • Profiling of rotavirus 3'UTR-binding proteins reveals the ATP synthase subunit ATP5B as a host factor that supports late-stage virus replication. The Journal of biological chemistry Ren, L., Ding, S., Song, Y., Li, B., Ramanathan, M., Co, J., Amieva, M. R., Khavari, P. A., Greenberg, H. B. 2019

    Abstract

    Genome replication and virion assembly of segmented RNA viruses are highly coordinated events, tightly regulated by sequence and structural elements in the UTRs of viral RNA. This process is poorly defined and likely requires the participation of host proteins in concert with viral proteins. In this study, we employed a proteomics-based approach, named RNA-protein interaction detection (RaPID), to comprehensively screen for host proteins that bind to a conserved motif within the rotavirus (RV) 3' terminus. Using this assay, we identified ATP5B, a core subunit of the mitochondrial ATP synthase, as having high affinity to the RV 3'UTR consensus sequences. During RV infection, ATP5B bound to the RV 3'UTR and co-localized with viral RNA and viroplasm. Functionally, siRNA-mediated genetic depletion of ATP5B or other ATP synthase subunits such as ATP5A1 and ATP5O reduced the production of infectious viral progeny without significant alteration of intracellular viral RNA levels or RNA translation. Chemical inhibition of ATP synthase diminished RV yield in both conventional cell culture and in human intestinal enteroids, indicating that ATP5B positively regulates late-stage RV maturation in primary intestinal epithelial cells. Collectively, our results shed light on the role of host proteins in RV genome assembly and particle formation and identify ATP5B as a novel pro-RV RNA-binding protein, contributing to our understanding of how host ATP synthases may galvanize virus growth and pathogenesis.

    View details for PubMedID 30770472

  • Coupled Single-Cell CRISPR Screening and Epigenomic Profiling Reveals Causal Gene Regulatory Networks CELL Rubin, A. J., Parker, K. R., Satpathy, A. T., Qi, Y., Wu, B., Ong, A. J., Mumbach, M. R., Ji, A. L., Kim, D. S., Cho, S., Zarnegar, B. J., Greenleaf, W. J., Chang, H. Y., Khavari, P. A. 2019; 176 (1-2): 361-+
  • Impact of a patient-derived hepatitis C viral RNA genome with a mutated microRNA binding site. PLoS pathogens Mata, M., Neben, S., Majzoub, K., Carette, J., Ramanathan, M., Khavari, P. A., Sarnow, P. 2019; 15 (5): e1007467

    Abstract

    Hepatitis C virus (HCV) depends on liver-specific microRNA miR-122 for efficient viral RNA amplification in liver cells. This microRNA interacts with two different conserved sites at the very 5' end of the viral RNA, enhancing miR-122 stability and promoting replication of the viral RNA. Treatment of HCV patients with oligonucleotides that sequester mir-122 resulted in profound loss of viral RNA in phase II clinical trials. However, some patients accumulated in their sera a viral RNA genome that contained a single cytidine to uridine mutation at the third nucleotide from the 5' genomic end. It is shown here that this C3U variant indeed displayed higher rates of replication than that of wild-type HCV when miR-122 abundance is low in liver cells. However, when miR-122 abundance is high, binding of miR-122 to site 1, most proximal to the 5' end in the C3U variant RNA, is impaired without disrupting the binding of miR-122 to site 2. As a result, C3U RNA displays a much lower rate of replication than wild-type mRNA when miR-122 abundance is high in the liver. This phenotype was accompanied by binding of a different set of cellular proteins to the 5' end of the C3U RNA genome. In particular, binding of RNA helicase DDX6 was important for displaying the C3U RNA replication phenotype in liver cells. These findings suggest that sequestration of miR-122 leads to a resistance-associated mutation that has only been observed in treated patients so far, and raises the question about the function of the C3U variant in the peripheral blood.

    View details for PubMedID 31075158

  • KRAS regulation by small non-coding RNAs and SNARE proteins. Nature communications Che, Y., Siprashvili, Z., Kovalski, J. R., Jiang, T., Wozniak, G., Elcavage, L., Khavari, P. A. 2019; 10 (1): 5118

    Abstract

    KRAS receives and relays signals at the plasma membrane (PM) where it transmits extracellular growth factor signals to downstream effectors. SNORD50A/B were recently found to bind KRAS and inhibit its tumorigenic action by unknown mechanisms. KRAS proximity protein labeling was therefore undertaken in SNORD50A/B wild-type and knockout cells, revealing that SNORD50A/B RNAs shape the composition of proteins proximal to KRAS, notably by inhibiting KRAS proximity to the SNARE vesicular transport proteins SNAP23, SNAP29, and VAMP3. To remain enriched on the PM, KRAS undergoes cycles of endocytosis, solubilization, and vesicular transport to the PM. Here we report that SNAREs are essential for the final step of this process, with KRAS localization to the PM facilitated by SNAREs but antagonized by SNORD50A/B. Antagonism between SNORD50A/B RNAs and specific SNARE proteins thus controls KRAS localization, signaling, and tumorigenesis, and disrupting SNARE-enabled KRAS function represents a potential therapeutic opportunity in KRAS-driven cancer.

    View details for DOI 10.1038/s41467-019-13106-4

    View details for PubMedID 31712554

  • Retinoic acid and BMP4 cooperate with p63 to alter chromatin dynamics during surface epithelial commitment NATURE GENETICS Pattison, J. M., Melo, S. P., Piekos, S. N., Torkelson, J. L., Bashkirova, E., Mumbach, M. R., Rajasingh, C., Zhen, H., Li, L., Liaw, E., Alber, D., Rubin, A. J., Shankar, G., Bao, X., Chang, H. Y., Khavari, P. A., Oro, A. E. 2018; 50 (12): 1658-+
  • Retinoic acid and BMP4 cooperate with p63 to alter chromatin dynamics during surface epithelial commitment. Nature genetics Pattison, J. M., Melo, S. P., Piekos, S. N., Torkelson, J. L., Bashkirova, E., Mumbach, M. R., Rajasingh, C., Zhen, H. H., Li, L., Liaw, E., Alber, D., Rubin, A. J., Shankar, G., Bao, X., Chang, H. Y., Khavari, P. A., Oro, A. E. 2018

    Abstract

    Human embryonic stem cell (hESC) differentiation promises advances in regenerative medicine1-3, yet conversion of hESCs into transplantable cells or tissues remains poorly understood. Using our keratinocyte differentiation system, we employ a multi-dimensional genomics approach to interrogate the contributions of inductive morphogens retinoic acid and bone morphogenetic protein 4 (BMP4) and the epidermal master regulator p63 (encoded by TP63)4,5 during surface ectoderm commitment. In contrast to other master regulators6-9, p63 effects major transcriptional changes only after morphogens alter chromatin accessibility, establishing an epigenetic landscape for p63 to modify. p63 distally closes chromatin accessibility and promotes accumulation of H3K27me3 (trimethylated histone H3 lysine 27). Cohesin HiChIP10 visualizations of chromosome conformation show that p63 and the morphogens contribute to dynamic long-range chromatin interactions, as illustrated by TFAP2C regulation11. Our study demonstrates the unexpected dependency of p63 on morphogenetic signaling and provides novel insights into how a master regulator can specify diverse transcriptional programs based on the chromatin landscape induced by exposure to specific morphogens.

    View details for PubMedID 30397335

  • Cancer-Associated Long Noncoding RNA SMRT-2 Controls Epidermal Differentiation JOURNAL OF INVESTIGATIVE DERMATOLOGY Lee, C. S., Mah, A., Aros, C. J., Lopez-Pajares, V., Bhaduri, A., Webster, D. E., Kretz, M., Khavari, P. A. 2018; 138 (6): 1445–49

    View details for PubMedID 29360484

  • Single-cell RNA-sequencing reveals SCC intratumoral heterogeneity Ji, A., Rubin, A., Hollmig, S., Aasi, S., Khavari, P. ELSEVIER SCIENCE INC. 2018: S31
  • Targeting pathogenic interactions between Rac1 and NCK1 in psoriasis Winge, M. G., Nasrallah, M., Fuhriman, J. M., Ramanathan, M., Azameera, A., Nguyen, N., Inayathullah, M., Rajadas, J., Khavari, P., Butte, A., Marinkovich, M. ELSEVIER SCIENCE INC. 2018: S161
  • Phase I / II Clinical Trial for Recessive Dystrophic Epidermolysis Bullosa Using EB-101 (COL7A1 Gene-Corrected Autologous Keratinocytes) Tang, J. Y., Marinkovich, M. P., Siprashvili, Z., Nguyen, N. T., Gorell, E. S., Loutit, K., Dutt-Singkh, Y., Barriga, M., Solis, D., Khuu, P., Furukawa, L., Lorenz, H. P., Leung, T. H., Keene, D. R., Rieger, K. E., Khavari, P. A., Lane, A. T. CELL PRESS. 2018: 158
  • KRAS regulation by small non-coding RNAs and SNARE proteins Che, Y., Khavari, P. ELSEVIER SCIENCE INC. 2018: S27
  • Dynamic morphogen-p63 chromatin interactions that guide epigenetic changes and p63 activity in surface ectoderm commitment Pattison, J., Melo, S., Piekos, S., Torkelson, J., Mumbach, M. R., Rubin, A., Li, L., Zhen, H., Chang, H., Khavari, P., Oro, A. E. ELSEVIER SCIENCE INC. 2018: S243
  • Metabolomic analysis reveals an essential role for glucose in epidermal differentiation Lopez-Pajares, V., Bhaduri, A., Garcia, O., Guerrero, A., Gowrishankar, G., Che, Y., Sanchez, A., Boxer, L., Gambhir, S., Khavari, P. ELSEVIER SCIENCE INC. 2018: S123
  • Small non-coding RNAs control the MAPK/ERK pathway Siprashvili, Z., Shenoy, R., Elcavage, L., Khavari, P. ELSEVIER SCIENCE INC. 2018: S27
  • Decoding regulatory sequence across skin differentiation with deep learning Kim, D., Risca, V., Chappell, J., Shi, M., Zhao, Z., Jung, N., Chang, H., Snyder, M., Greenleaf, W., Kundaje, A., Khavari, P. ELSEVIER SCIENCE INC. 2018: S135
  • Transcript-indexed ATAC-seq for precision immune profiling. Nature medicine Satpathy, A. T., Saligrama, N., Buenrostro, J. D., Wei, Y., Wu, B., Rubin, A. J., Granja, J. M., Lareau, C. A., Li, R., Qi, Y., Parker, K. R., Mumbach, M. R., Serratelli, W. S., Gennert, D. G., Schep, A. N., Corces, M. R., Khodadoust, M. S., Kim, Y. H., Khavari, P. A., Greenleaf, W. J., Davis, M. M., Chang, H. Y. 2018

    Abstract

    T cells create vast amounts of diversity in the genes that encode their T cell receptors (TCRs), which enables individual clones to recognize specific peptide-major histocompatibility complex (MHC) ligands. Here we combined sequencing of the TCR-encoding genes with assay for transposase-accessible chromatin with sequencing (ATAC-seq) analysis at the single-cell level to provide information on the TCR specificity and epigenomic state of individual T cells. By using this approach, termed transcript-indexed ATAC-seq (T-ATAC-seq), we identified epigenomic signatures in immortalized leukemic T cells, primary human T cells from healthy volunteers and primary leukemic T cells from patient samples. In peripheral blood CD4+ T cells from healthy individuals, we identified cis and trans regulators of naive and memory T cell states and found substantial heterogeneity in surface-marker-defined T cell populations. In patients with a leukemic form of cutaneous T cell lymphoma, T-ATAC-seq enabled identification of leukemic and nonleukemic regulatory pathways in T cells from the same individual by allowing separation of the signals that arose from the malignant clone from the background T cell noise. Thus, T-ATAC-seq is a new tool that enables analysis of epigenomic landscapes in clonal T cells and should be valuable for studies of T cell malignancy, immunity and immunotherapy.

    View details for PubMedID 29686426

  • The functions and unique features of long intergenic non-coding RNA. Nature reviews. Molecular cell biology Ransohoff, J. D., Wei, Y., Khavari, P. A. 2018; 19 (3): 143–57

    Abstract

    Long intergenic non-coding RNA (lincRNA) genes have diverse features that distinguish them from mRNA-encoding genes and exercise functions such as remodelling chromatin and genome architecture, RNA stabilization and transcription regulation, including enhancer-associated activity. Some genes currently annotated as encoding lincRNAs include small open reading frames (smORFs) and encode functional peptides and thus may be more properly classified as coding RNAs. lincRNAs may broadly serve to fine-tune the expression of neighbouring genes with remarkable tissue specificity through a diversity of mechanisms, highlighting our rapidly evolving understanding of the non-coding genome.

    View details for PubMedID 29138516

  • Research Techniques Made Simple: Emerging Methods to Elucidate Protein Interactions through Spatial Proximity JOURNAL OF INVESTIGATIVE DERMATOLOGY Che, Y., Khavari, P. A. 2017; 137 (12): E197–E203

    Abstract

    Interactions between proteins are essential for fundamental cellular processes, and the diversity of such interactions enables the vast variety of functions essential for life. A persistent goal in biological research is to develop assays that can faithfully capture different types of protein interactions to allow their study. A major step forward in this direction came with a family of methods that delineates spatial proximity of proteins as an indirect measure of protein-protein interaction. A variety of enzyme- and DNA ligation-based methods measure protein co-localization in space, capturing novel interactions that were previously too transient or low affinity to be identified. Here we review some of the methods that have been successfully used to measure spatially proximal protein-protein interactions.

    View details for PubMedID 29169465

  • Phase I/IIa clinical trial for recessive dystrophic epidermolysis bullosa using EB-101 (COL7A1 gene-corrected autologous keratinocytes) Siprashvili, Z., Nguyen, N. T., Gorell, E. S., Loutit, K., Dutt-Singkh, Y., Nazaroff, J., Khuu, P., Furukawa, L., Lorenz, H. P., Leung, T. H., Keene, D. R., Rieger, K. E., Khavari, P. A., Lane, A. T., Tang, J. Y., Marinkovich, M. P. MARY ANN LIEBERT, INC. 2017: A10
  • Phase I/IIa clinical trial for recessive dystrophic epidermolysis bullosa using genetically corrected autologous keratinocytes Siprashvili, Z., Nguyen, N., Gorell, E., Loutit, K., Dutt-Singkh, Y., Nazaroff, J., Khuu, P., Furukawa, L., Lorenz, H., Leung, T., Keene, D., Rieger, K., Khavari, P. A., Lane, A., Tang, J. Y., Marinkovich, M. ELSEVIER SCIENCE INC. 2017: S89
  • K-RAS oncogene activation is regulated by a snoRNA/SNARE protein axis that controls its subcellular transport Che, Y., Siprashvili, Z., Kovalski, J., Khavari, P. A. ELSEVIER SCIENCE INC. 2017: S20
  • RNA-protein interaction detection (RaPID) in living cells uncovers post-transcriptional regulation in carcinogenesis Ramanathan, M., Majzoub, K., Roth, J., Gai, H., Palmer, T., Carette, J., Khavari, P. A. ELSEVIER SCIENCE INC. 2017: S21
  • The SNORD86 small non-coding RNA binds and regulates Rac1 Rios, E., Bhaduri, A., Siprashvili, Z., Zarnegar, B., Khavari, P. A. ELSEVIER SCIENCE INC. 2017: S21
  • Discovery of differential RNA binding and regulation by the APOL4 protein to disease-linked psoriasis CDSN gene variants using RaPID Ransohoff, J. D., Ramanathan, M., Khavari, P. A. ELSEVIER SCIENCE INC. 2017: S71
  • Dynamic and stable enhancer-promoter contacts regulate epidermal terminal differentiation Lopez-Pajares, V., Rubin, A., Barajas, B., Furlan-Magaril, M., Mumbach, M., Greenleaf, W., Kundaje, A., Snyder, M., Chang, H., Fraser, P., Khavari, P. A. ELSEVIER SCIENCE INC. 2017: S80
  • Attenuated netrin-1 receptor mediated regulation of tiam1 is required for rac1 mutant melanoma progression Winge, M. G., Kovalski, J., Nguyen, N. T., Wu, D., Zehnder, A., Khavari, P. A., Marinkovich, M. ELSEVIER SCIENCE INC. 2017: S139
  • Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements. Nature genetics Mumbach, M. R., Satpathy, A. T., Boyle, E. A., Dai, C., Gowen, B. G., Cho, S. W., Nguyen, M. L., Rubin, A. J., Granja, J. M., Kazane, K. R., Wei, Y., Nguyen, T., Greenside, P. G., Corces, M. R., Tycko, J., Simeonov, D. R., Suliman, N., Li, R., Xu, J., Flynn, R. A., Kundaje, A., Khavari, P. A., Marson, A., Corn, J. E., Quertermous, T., Greenleaf, W. J., Chang, H. Y. 2017

    Abstract

    The challenge of linking intergenic mutations to target genes has limited molecular understanding of human diseases. Here we show that H3K27ac HiChIP generates high-resolution contact maps of active enhancers and target genes in rare primary human T cell subtypes and coronary artery smooth muscle cells. Differentiation of naive T cells into T helper 17 cells or regulatory T cells creates subtype-specific enhancer-promoter interactions, specifically at regions of shared DNA accessibility. These data provide a principled means of assigning molecular functions to autoimmune and cardiovascular disease risk variants, linking hundreds of noncoding variants to putative gene targets. Target genes identified with HiChIP are further supported by CRISPR interference and activation at linked enhancers, by the presence of expression quantitative trait loci, and by allele-specific enhancer loops in patient-derived primary cells. The majority of disease-associated enhancers contact genes beyond the nearest gene in the linear genome, leading to a fourfold increase in the number of potential target genes for autoimmune and cardiovascular diseases.

    View details for PubMedID 28945252

  • An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nature methods Corces, M. R., Trevino, A. E., Hamilton, E. G., Greenside, P. G., Sinnott-Armstrong, N. A., Vesuna, S., Satpathy, A. T., Rubin, A. J., Montine, K. S., Wu, B., Kathiria, A., Cho, S. W., Mumbach, M. R., Carter, A. C., Kasowski, M., Orloff, L. A., Risca, V. I., Kundaje, A., Khavari, P. A., Montine, T. J., Greenleaf, W. J., Chang, H. Y. 2017

    Abstract

    We present Omni-ATAC, an improved ATAC-seq protocol for chromatin accessibility profiling that works across multiple applications with substantial improvement of signal-to-background ratio and information content. The Omni-ATAC protocol generates chromatin accessibility profiles from archival frozen tissue samples and 50-μm sections, revealing the activities of disease-associated DNA elements in distinct human brain structures. The Omni-ATAC protocol enables the interrogation of personal regulomes in tissue context and translational studies.

    View details for PubMedID 28846090

  • HiChIP: efficient and sensitive analysis of protein-directed genome architecture. Nature methods Mumbach, M. R., Rubin, A. J., Flynn, R. A., Dai, C., Khavari, P. A., Greenleaf, W. J., Chang, H. Y. 2016; 13 (11): 919-922

    Abstract

    Genome conformation is central to gene control but challenging to interrogate. Here we present HiChIP, a protein-centric chromatin conformation method. HiChIP improves the yield of conformation-informative reads by over 10-fold and lowers the input requirement over 100-fold relative to that of ChIA-PET. HiChIP of cohesin reveals multiscale genome architecture with greater signal-to-background ratios than those of in situ Hi-C.

    View details for DOI 10.1038/nmeth.3999

    View details for PubMedID 27643841

  • Safety and Wound Outcomes Following Genetically Corrected Autologous Epidermal Grafts in Patients With Recessive Dystrophic Epidermolysis Bullosa. JAMA Siprashvili, Z., Nguyen, N. T., Gorell, E. S., Loutit, K., Khuu, P., Furukawa, L. K., Lorenz, H. P., Leung, T. H., Keene, D. R., Rieger, K. E., Khavari, P., Lane, A. T., Tang, J. Y., Marinkovich, M. P. 2016; 316 (17): 1808-1817

    Abstract

    Recessive dystrophic epidermolysis bullosa (RDEB) is a devastating, often fatal, inherited blistering disorder caused by mutations in the COL7A1 gene encoding type VII collagen. Support and palliation are the only current therapies.To evaluate the safety and wound outcomes following genetically corrected autologous epidermal grafts in patients with RDEB.Single-center phase 1 clinical trial conducted in the United States of 4 patients with severe RDEB with a measured area of wounds suitable for grafting of at least 100 cm2. Patients with undetectable type VII collagen keratinocyte expression were excluded.Autologous keratinocytes isolated from biopsy samples collected from 4 patients with RDEB were transduced with good manufacturing practice-grade retrovirus carrying full-length human COL7A1 and assembled into epidermal sheet grafts. Type VII collagen gene-corrected grafts (approximately 35 cm2) were transplanted onto 6 wounds in each of the patients (n = 24 grafts).The primary safety outcomes were recombination competent retrovirus, cancer, and autoimmune reaction. Molecular correction was assessed as type VII collagen expression measured by immunofluorescence and immunoelectron microscopy. Wound healing was assessed using serial photographs taken at 3, 6, and 12 months after grafting.The 4 patients (mean age, 23 years [range, 18-32 years]) were all male with an estimated body surface area affected with RDEB of 4% to 30%. All 24 grafts were well tolerated without serious adverse events. Type VII collagen expression at the dermal-epidermal junction was demonstrated on the graft sites by immunofluorescence microscopy in 9 of 10 biopsy samples (90%) at 3 months, in 8 of 12 samples (66%) at 6 months, and in 5 of 12 samples (42%) at 12 months, including correct type VII collagen localization to anchoring fibrils. Wounds with recombinant type VII collagen graft sites displayed 75% or greater healing at 3 months (21 intact graft sites of 24 wound sites; 87%), 6 months (16/24; 67%), and 12 months (12/24; 50%) compared with baseline wound sites.In this preliminary study of 4 patients with RDEB, there was wound healing in some type VII collagen gene-corrected grafts, but the response was variable among patients and among grafted sites and generally declined over 1 year. Long-term follow-up is necessary for these patients, and controlled trials are needed with a broader range of patients to better understand the potential long-term efficacy of genetically corrected autologous epidermal grafts.clinicaltrials.gov Identifier: NCT01263379.

    View details for DOI 10.1001/jama.2016.15588

    View details for PubMedID 27802546

  • Factors That May Promote an Effective Local Research Environment JOURNAL OF INVESTIGATIVE DERMATOLOGY Wang, K., Lee, C. S., Marinkovich, M., Chang, H. Y., Oro, A. E., Khavari, P. A. 2016; 136 (8): 1529–31

    View details for PubMedID 27450496

  • RAC1 activation drives pathologic interactions between the epidermis and immune cells JOURNAL OF CLINICAL INVESTIGATION Winge, M. C., Ohyama, B., Dey, C. N., Boxer, L. M., Li, W., Ehsani-Chimeh, N., Truong, A. K., Wu, D., Armstrong, A. W., Makino, T., Davidson, M., Starcevic, D., Kislat, A., Nguyen, N. T., Hashimoto, T., Homey, B., Khavari, P. A., Bradley, M., Waterman, E. A., Marinkovich, M. P. 2016; 126 (7): 2661-2677

    Abstract

    Interactions between the epidermis and the immune system govern epidermal tissue homeostasis. These epidermis-immune interactions are altered in the inflammatory disease psoriasis; however, the pathways that underlie this aberrant immune response are not well understood. Here, we determined that Ras-related C3 botulinum toxin substrate 1 (RAC1) is a key mediator of epidermal dysfunction. RAC1 activation was consistently elevated in psoriatic epidermis and primary psoriatic human keratinocytes (PHKCs) exposed to psoriasis-related stimuli, but not in skin from patients with basal or squamous cell carcinoma. Expression of a constitutively active form of RAC1 (RACV12) in mice resulted in the development of lesions similar to those of human psoriasis that required the presence of an intact immune system. RAC1V12-expressing mice and human psoriatic skin showed similar RAC1-dependent signaling as well as transcriptional overlap of differentially expressed epidermal and immune pathways. Coculture of PHKCs with immunocytes resulted in the upregulation of RAC1-dependent proinflammatory cytokines, an effect that was reproduced by overexpressing RAC1 in normal human keratinocytes. In keratinocytes, modulating RAC1 activity altered differentiation, proliferation, and inflammatory pathways, including STAT3, NFκB, and zinc finger protein 750 (ZNF750). Finally, RAC1 inhibition in xenografts composed of human PHKCs and immunocytes abolished psoriasiform hyperplasia and inflammation in vivo. These studies implicate RAC1 as a potential therapeutic target for psoriasis and as a key orchestrator of pathologic epidermis-immune interactions.

    View details for DOI 10.1172/JCI85738

    View details for Web of Science ID 000379094800028

    View details for PubMedID 27294528

    View details for PubMedCentralID PMC4922704

  • Phase I clinical trial for Recessive Dystrophic Epidermolysis Bullosa using genetically corrected autologous keratinocytes Siprashvili, Z., Nguyen, N. T., Gorell, E. S., Loutit, K., Khuu, P., Furukawa, L. K., Lorenz, H. P., Leung, T. H., Keene, D., Rieger, K., Khavari, P. A., Lane, A., Tang, J., Marinkovich, P. ELSEVIER SCIENCE INC. 2016: S65
  • Small non-coding snoRNAs control Ras superfamily GTPases in stem cell differentiation and cancer Zarnegar, B., Rios, E., Siprashvili, Z., Khavari, P. A. ELSEVIER SCIENCE INC. 2016: S17
  • Regulation of epidermal differentiation by MAF and MAFB Lopez-Pajares, V., Barajas, B. C., Rubin, A., Khavari, P. A. ELSEVIER SCIENCE INC. 2016: S59
  • 7SK-BAF axis controls pervasive transcription at enhancers. Nature structural & molecular biology Flynn, R. A., Do, B. T., Rubin, A. J., Calo, E., Lee, B., Kuchelmeister, H., Rale, M., Chu, C., Kool, E. T., Wysocka, J., Khavari, P. A., Chang, H. Y. 2016; 23 (3): 231-238

    Abstract

    RNA functions at enhancers remain mysterious. Here we show that the 7SK small nuclear RNA (snRNA) inhibits enhancer transcription by modulating nucleosome position. 7SK occupies enhancers and super enhancers genome wide in mouse and human cells, and it is required to limit enhancer-RNA initiation and synthesis in a manner distinct from promoter pausing. Clustered elements at super enhancers uniquely require 7SK to prevent convergent transcription and DNA-damage signaling. 7SK physically interacts with the BAF chromatin-remodeling complex, recruits BAF to enhancers and inhibits enhancer transcription by modulating chromatin structure. In turn, 7SK occupancy at enhancers coincides with that of Brd4 and is exquisitely sensitive to the bromodomain inhibitor JQ1. Thus, 7SK uses distinct mechanisms to counteract the diverse consequences of pervasive transcription that distinguish super enhancers, enhancers and promoters.

    View details for DOI 10.1038/nsmb.3176

    View details for PubMedID 26878240

  • Unbiased proteomic-genomic investigation of MHC class I peptide ligands reveals unconventional translation origins Scharf, A. D., Flockhart, R. J., Olsson, N. E., Devabhaktuni, A., Zhang, J., Zhao, X., Khavari, P., Elias, J. E. PERGAMON-ELSEVIER SCIENCE LTD. 2015: 135–36
  • CALML5 is a ZNF750-and TINCR-induced protein that binds stratifin to regulate epidermal differentiation GENES & DEVELOPMENT Sun, B. K., Boxer, L. D., Ransohoff, J. D., Siprashvili, Z., Qu, K., Lopez-Pajares, V., Hollmig, S. T., Khavari, P. A. 2015; 29 (21): 2225-2230

    Abstract

    Outward migration of epidermal progenitors occurs with induction of hundreds of differentiation genes, but the identities of all regulators required for this process are unknown. We used laser capture microdissection followed by RNA sequencing to identify calmodulin-like 5 (CALML5) as the most enriched gene in differentiating outer epidermis. CALML5 mRNA was up-regulated by the ZNF750 transcription factor and then stabilized by the long noncoding RNA TINCR. CALML5 knockout impaired differentiation, abolished keratohyalin granules, and disrupted epidermal barrier function. Mass spectrometry identified SFN (stratifin/14-3-3σ) as a CALML5-binding protein. CALML5 interacts with SFN in suprabasal epidermis, cocontrols 13% of late differentiation genes, and modulates interaction of SFN to some of its binding partners. A ZNF750-TINCR-CALML5-SFN network is thus essential for epidermal differentiation.

    View details for DOI 10.1101/gad.267708.115

    View details for PubMedID 26545810

  • DeltaNp63 expression is reduced in aged and photoexposed human epidermis, and down regulated in reconstructed epidermis by aged dermal fibroblasts secretome Boulgana, R., Leblanc-Noblesse, E., Juan, M., Sobilo, L., Bernois, A., Lopez-Pajares, V., Zarnegar, B., Khavari, P., Schnebert, S., Dumas, M. NATURE PUBLISHING GROUP. 2015: S47
  • DNMT1 expression is down-regulated in human keratinocytes during differentiation and senescence and by the secretome of aged dermal fibroblasts Boulgana, R., Soyer, M., Jeronimo-Monteiro, V., Leblanc-Noblesse, E., Marteau, C., Lopez-Pajares, V., Zarnegar, B., Khavari, P., Schnebert, S., Dumas, M. NATURE PUBLISHING GROUP. 2015: S47
  • ZNF750 expression is reduced in photoexposed sites of the epidermis, by replicative senescence, retinoic acid, and increased by calcium treatment Boulgana, R., Soyer, M., Leblanc-Noblesse, E., Jeronimo-Monteiro, V., Bernois, A., Lopez-Pajares, V., Zarnegar, B., Khavari, P., Schnebert, S., Dumas, M. NATURE PUBLISHING GROUP. 2015: S47
  • IQGAP1, an ERK1/2 MAPK scaffold, is an oncogenic target in canine melanoma Zehnder, A., Lee, B., Neela, P., Khavari, P. AMER ASSOC CANCER RESEARCH. 2015
  • Phase I clinical trial for recessive dystrophic epidermolysis bullosa using genetically corrected autologous keratinocytes Siprashvili, Z., Nguyen, N. T., Gorell, E., Loutit, K., Khuu, P., Furukawa, L. K., Lorenz, H. P., Leung, T. H., Keene, D. R., Khavari, P., Lane, A., Tang, J. Y., Marinkovich, M. NATURE PUBLISHING GROUP. 2015: S72
  • Network analysis identifies MPZL3 as an essential regulator of epidermal differentiation that binds FDXR to induce reactive oxygen species Bhaduri, A., Ungewickell, A., Khavari, P. NATURE PUBLISHING GROUP. 2015: S59
  • Calmodulin-like 5 interacts with 14-3-3-sigma/stratifin to regulate late epidermal differentiation Sun, B., Ransohoff, J., Qu, K., Lopez-Pajares, V., Boxer, L. D., Khavari, P. NATURE PUBLISHING GROUP. 2015: S67
  • The BAF/SWI/SNF complex controls genome accessibility to p63 during epidermal differentiation Bao, X., Rubin, A., Qu, K., Zhang, J., Giresi, P., Chang, H., Khavari, P. NATURE PUBLISHING GROUP. 2015: S77
  • Identification of the KNSTRN proteome by APEX2 targeting Lee, C., Mah, A., Nguyen, C., Khavari, P. NATURE PUBLISHING GROUP. 2015: S25
  • A novel therapeutic inhibits Rac1 mediated invasion and metastasis in a newly described in vivo model of human melanoma Winge, M. C., Kovalski, J., Nguyen, N. T., Wu, D., Zehnder, A., Khavari, P., Marinkovich, M. NATURE PUBLISHING GROUP. 2015: S71
  • Dissecting noncoding and pathogen RNA-protein interactomes RNA-A PUBLICATION OF THE RNA SOCIETY Flynn, R. A., Martin, L., Spitale, R. C., Do, B. T., Sagan, S. M., Zarnegar, B., Qu, K., Khavari, P. A., Quake, S. R., Sarnow, P., Chang, H. Y. 2015; 21 (1): 135-143

    Abstract

    RNA-protein interactions are central to biological regulation. Cross-linking immunoprecipitation (CLIP)-seq is a powerful tool for genome-wide interrogation of RNA-protein interactomes, but current CLIP methods are limited by challenging biochemical steps and fail to detect many classes of noncoding and nonhuman RNAs. Here we present FAST-iCLIP, an integrated pipeline with improved CLIP biochemistry and an automated informatic pipeline for comprehensive analysis across protein coding, noncoding, repetitive, retroviral, and nonhuman transcriptomes. FAST-iCLIP of Poly-C binding protein 2 (PCBP2) showed that PCBP2-bound CU-rich motifs in different topologies to recognize mRNAs and noncoding RNAs with distinct biological functions. FAST-iCLIP of PCBP2 in hepatitis C virus-infected cells enabled a joint analysis of the PCBP2 interactome with host and viral RNAs and their interplay. These results show that FAST-iCLIP can be used to rapidly discover and decipher mechanisms of RNA-protein recognition across the diversity of human and pathogen RNAs.

    View details for DOI 10.1261/rna.047803.114

    View details for PubMedID 25411354

  • A novel ATAC-seq approach reveals lineage-specific reinforcement of the open chromatin landscape via cooperation between BAF and p63. Genome biology Bao, X., Rubin, A. J., Qu, K., Zhang, J., Giresi, P. G., Chang, H. Y., Khavari, P. A. 2015; 16 (1): 284-?

    Abstract

    Open chromatin regions are correlated with active regulatory elements in development and are dysregulated in diseases. The BAF (SWI/SNF) complex is essential for development, and has been demonstrated to remodel reconstituted chromatin in vitro and to control the accessibility of a few individual regions in vivo. However, it remains unclear where and how BAF controls the open chromatin landscape to regulate developmental processes, such as human epidermal differentiation.Using a novel "on-plate" ATAC-sequencing approach for profiling open chromatin landscapes with a low number of adherent cells, we demonstrate that the BAF complex is essential for maintaining 11.6 % of open chromatin regions in epidermal differentiation. These BAF-dependent open chromatin regions are highly cell-type-specific and are strongly enriched for binding sites for p63, a master epidermal transcription factor. The DNA sequences of p63 binding sites intrinsically favor nucleosome formation and are inaccessible in other cell types without p63 to prevent ectopic activation. In epidermal cells, BAF and p63 mutually recruit each other to maintain 14,853 open chromatin regions. We further demonstrate that BAF and p63 cooperatively position nucleosomes away from p63 binding sites and recruit transcriptional machinery to control tissue differentiation.BAF displays high specificity in controlling the open chromatin landscape during epidermal differentiation by cooperating with the master transcription factor p63 to maintain lineage-specific open chromatin regions.

    View details for DOI 10.1186/s13059-015-0840-9

    View details for PubMedID 26683334

  • Inhibiting Oncogenic RAS in Multiple Myeloma By Targeting Scaffold-ERK Interactions Inhibiting Oncogenic RAS in Multiple Myeloma By Targeting Scaffold-ERK Interactions Gocke, C. B., Wang, Q., McMillan, R., Penchev, V., Sage, J., Khavari, P. A., Matsui, W. AMER SOC HEMATOLOGY. 2014
  • Advances in skin grafting and treatment of cutaneous wounds. Science Sun, B. K., Siprashvili, Z., Khavari, P. A. 2014; 346 (6212): 941-945

    Abstract

    The ability of the skin to repair itself after injury is vital to human survival and is disrupted in a spectrum of disorders. The process of cutaneous wound healing is complex, requiring a coordinated response by immune cells, hematopoietic cells, and resident cells of the skin. We review the classic paradigms of wound healing and evaluate how recent discoveries have enriched our understanding of this process. We evaluate current and experimental approaches to treating cutaneous wounds, with an emphasis on cell-based therapies and skin transplantation.

    View details for DOI 10.1126/science.1253836

    View details for PubMedID 25414301

  • Recurrent point mutations in the kinetochore gene KNSTRN in cutaneous squamous cell carcinoma. Nature genetics Lee, C. S., Bhaduri, A., Mah, A., Johnson, W. L., Ungewickell, A., Aros, C. J., Nguyen, C. B., Rios, E. J., Siprashvili, Z., Straight, A., Kim, J., Aasi, S. Z., Khavari, P. A. 2014; 46 (10): 1060-1062

    Abstract

    Here we report the discovery of recurrent mutations concentrated at an ultraviolet signature hotspot in KNSTRN, which encodes a kinetochore protein, in 19% of cutaneous squamous cell carcinomas (SCCs). Cancer-associated KNSTRN mutations, most notably those encoding p.Ser24Phe, disrupt chromatid cohesion in normal cells, occur in SCC precursors, correlate with increased aneuploidy in primary tumors and enhance tumorigenesis in vivo. These findings suggest a role for KNSTRN mutagenesis in SCC development.

    View details for DOI 10.1038/ng.3091

    View details for PubMedID 25194279

  • ZNF750 interacts with KLF4 and RCOR1, KDM1A, and CTBP1/2 chromatin regulators to repress epidermal progenitor genes and induce differentiation genes GENES & DEVELOPMENT Boxer, L. D., Barajas, B., Tao, S., Zhang, J., Khavari, P. A. 2014; 28 (18): 2013-2026

    Abstract

    ZNF750 controls epithelial homeostasis by inhibiting progenitor genes while inducing differentiation genes, a role underscored by pathogenic ZNF750 mutations in cancer and psoriasis. How ZNF750 accomplishes these dual gene regulatory impacts is unknown. Here, we characterized ZNF750 as a transcription factor that binds both the progenitor and differentiation genes that it controls at a CCNNAGGC DNA motif. ZNF750 interacts with the pluripotency transcription factor KLF4 and chromatin regulators RCOR1, KDM1A, and CTBP1/2 through conserved PLNLS sequences. ChIP-seq (chromatin immunoprecipitation [ChIP] followed by high-throughput sequencing) and gene depletion revealed that KLF4 colocalizes ∼10 base pairs from ZNF750 at differentiation target genes to facilitate their activation but is unnecessary for ZNF750-mediated progenitor gene repression. In contrast, KDM1A colocalizes with ZNF750 at progenitor genes and facilitates their repression but is unnecessary for ZNF750-driven differentiation. ZNF750 thus controls differentiation in concert with RCOR1 and CTBP1/2 by acting with either KDM1A to repress progenitor genes or KLF4 to induce differentiation genes.

    View details for DOI 10.1101/gad.246579.114

    View details for Web of Science ID 000342277800005

    View details for PubMedCentralID PMC4173152

  • ZNF750 interacts with KLF4 and RCOR1, KDM1A, and CTBP1/2 chromatin regulators to repress epidermal progenitor genes and induce differentiation genes. Genes & development Boxer, L. D., Barajas, B., Tao, S., Zhang, J., Khavari, P. A. 2014; 28 (18): 2013-2026

    Abstract

    ZNF750 controls epithelial homeostasis by inhibiting progenitor genes while inducing differentiation genes, a role underscored by pathogenic ZNF750 mutations in cancer and psoriasis. How ZNF750 accomplishes these dual gene regulatory impacts is unknown. Here, we characterized ZNF750 as a transcription factor that binds both the progenitor and differentiation genes that it controls at a CCNNAGGC DNA motif. ZNF750 interacts with the pluripotency transcription factor KLF4 and chromatin regulators RCOR1, KDM1A, and CTBP1/2 through conserved PLNLS sequences. ChIP-seq (chromatin immunoprecipitation [ChIP] followed by high-throughput sequencing) and gene depletion revealed that KLF4 colocalizes ∼10 base pairs from ZNF750 at differentiation target genes to facilitate their activation but is unnecessary for ZNF750-mediated progenitor gene repression. In contrast, KDM1A colocalizes with ZNF750 at progenitor genes and facilitates their repression but is unnecessary for ZNF750-driven differentiation. ZNF750 thus controls differentiation in concert with RCOR1 and CTBP1/2 by acting with either KDM1A to repress progenitor genes or KLF4 to induce differentiation genes.

    View details for DOI 10.1101/gad.246579.114

    View details for PubMedID 25228645

    View details for PubMedCentralID PMC4173152

  • Activating HRAS Mutation in Nevus Spilus. journal of investigative dermatology Sarin, K. Y., McNiff, J. M., Kwok, S., Kim, J., Khavari, P. A. 2014; 134 (6): 1766-1768

    View details for DOI 10.1038/jid.2014.6

    View details for PubMedID 24390138

  • Enhancer-targeted genome editing selectively blocks innate resistance to oncokinase inhibition GENOME RESEARCH Webster, D. E., Barajas, B., Bussat, R. T., Yan, K. J., Neela, P. H., Flockhart, R. J., Kovalski, J., Zehnder, A., Khavari, P. A. 2014; 24 (5): 751-760

    Abstract

    Thousands of putative enhancers are characterized in the human genome, yet few have been shown to have a functional role in cancer progression. Inhibiting oncokinases, such as EGFR, ALK, ERBB2, and BRAF, is a mainstay of current cancer therapy but is hindered by innate drug resistance mediated by up-regulation of the HGF receptor, MET. The mechanisms mediating such genomic responses to targeted therapy are unknown. Here, we identify lineage-specific enhancers at the MET locus for multiple common tumor types, including a melanoma lineage-specific enhancer 63 kb downstream from the MET TSS. This enhancer displays inducible chromatin looping with the MET promoter to up-regulate MET expression upon BRAF inhibition. Epigenomic analysis demonstrated that the melanocyte-specific transcription factor, MITF, mediates this enhancer function. Targeted genomic deletion (<7 bp) of the MITF motif within the MET enhancer suppressed inducible chromatin looping and innate drug resistance, while maintaining MITF-dependent, inhibitor-induced melanoma cell differentiation. Epigenomic analysis can thus guide functional disruption of regulatory DNA to decouple pro- and anti-oncogenic functions of a dominant transcription factor and block innate resistance to oncokinase therapy.

    View details for DOI 10.1101/gr.166231.113

    View details for PubMedID 24443471

  • A IncRNA-MAF:MAFB transcription factor network regulates epidermal differentiation Lopez-Pajares, V., Qu, K., Zhang, J., Webster, D., Barajas, B., Zarnegar, B., Boxer, L., Kretz, M., Khavari, P. NATURE PUBLISHING GROUP. 2014: S44
  • The protein arginine methyltransferase PRMT1 acts with the CSNK1a1 kinase to enforce the epidermal progenitor state in vivo Bao, X., Zarnegar, B., Mah, A., Qu, K., Tao, S., Khavari, P. NATURE PUBLISHING GROUP. 2014: S66
  • ZNF750 binding to KLF4 and specific epigenetic regulators controls epidermal differentiation Boxer, L. D., Barajas, B., Zhang, J., Zarnegar, B., Khavari, P. NATURE PUBLISHING GROUP. 2014: S68
  • Calmodulin-like 5 is a downstream effector of the TINCR long noncoding RNA and is required for late epidermal differentiation Sun, B., Zhang, J., Qu, K., Lopez-Pajares, V., Khavari, P. A. NATURE PUBLISHING GROUP. 2014: S71
  • Recurrent point mutations in KNSTRN and disruption of multiple notch signaling genes in cutaneous squamous cell carcinoma Lee, C., Bhaduri, A., Mah, A., Ungewickell, A., Aros, C., Nguyen, C., Siprashvili, Z., Johnson, W., Straight, A., Kim, J., Aasi, S., Khavari, P. NATURE PUBLISHING GROUP. 2014: S35
  • Phase 1 clinical trial of genetically corrected autologous epidermal keratinocytes for recessive dystrophic epidermolysis bullosa Siprashvili, Z., Nguyen, N. T., Gorell, E., Khuu, P., Furukawa, L., Lorenz, H. P., Leung, T. H., Keene, D. R., Khavari, P., Marinkovich, M., Lane, A. T. NATURE PUBLISHING GROUP. 2014: S75
  • Quantitative analysis of mammalian translation initiation sites by FACS-seq. Molecular systems biology Noderer, W. L., Flockhart, R. J., Bhaduri, A., Diaz de Arce, A. J., Zhang, J., Khavari, P. A., Wang, C. L. 2014; 10: 748-?

    Abstract

    An approach combining fluorescence-activated cell sorting and high-throughput DNA sequencing (FACS-seq) was employed to determine the efficiency of start codon recognition for all possible translation initiation sites (TIS) utilizing AUG start codons. Using FACS-seq, we measured translation from a genetic reporter library representing all 65,536 possible TIS sequences spanning the -6 to +5 positions. We found that the motif RYMRMVAUGGC enhanced start codon recognition and translation efficiency. However, dinucleotide interactions, which cannot be conveyed by a single motif, were also important for modeling TIS efficiency. Our dataset combined with modeling allowed us to predict genome-wide translation initiation efficiency for all mRNA transcripts. Additionally, we screened somatic TIS mutations associated with tumorigenesis to identify candidate driver mutations consistent with known tumor expression patterns. Finally, we implemented a quantitative leaky scanning model to predict alternative initiation sites that produce truncated protein isoforms and compared predictions with ribosome footprint profiling data. The comprehensive analysis of the TIS sequence space enables quantitative predictions of translation initiation based on genome sequence.

    View details for DOI 10.15252/msb.20145136

    View details for PubMedID 25170020

  • Activating HRAS Mutation in Agminated Spitz Nevi Arising in a Nevus Spilus. JAMA dermatology Sarin, K. Y., Sun, B. K., Bangs, C. D., Cherry, A., Swetter, S. M., Kim, J., Khavari, P. A. 2013; 149 (9): 1077-1081

    Abstract

    IMPORTANCE Spitz nevi are benign melanocytic proliferations that can sometimes be clinically and histopathologically difficult to distinguish from melanoma. Agminated Spitz nevi have been reported to arise spontaneously, in association with an underlying nevus spilus, or after radiation or chemotherapy. However, to our knowledge, the genetic mechanism for this eruption has not been described. OBSERVATIONS We report a case of agminated Spitz nevi arising in a nevus spilus and use exome sequencing to identify a clonal activating point mutation in HRAS (GenBank 3265) (c.37G→C) in the Spitz nevi and underlying nevus spilus. We also identify a secondary copy number increase involving HRAS on chromosome 11p, which occurs during the development of the Spitz nevi. CONCLUSIONS AND RELEVANCE Our results reveal an activating HRAS mutation in a nevus spilus that predisposes to the formation of Spitz nevi. In addition, we demonstrate a copy number increase in HRAS as a "second hit" during the formation of agminated Spitz nevi, which suggests that both multiple Spitz nevi and solitary Spitz nevi may arise through similar molecular pathways. In addition, we describe a unique investigative approach for the discovery of genetic alterations in Spitz nevi.

    View details for DOI 10.1001/jamadermatol.2013.4745

    View details for PubMedID 23884457

  • Genomic Profiling of a Human Organotypic Model of AEC Syndrome Reveals ZNF750 as an Essential Downstream Target of Mutant TP63 AMERICAN JOURNAL OF HUMAN GENETICS Zarnegar, B. J., Webster, D. E., Lopez-Pajares, V., Hunt, B. V., Qu, K., Yan, K. J., Berk, D. R., Sen, G. L., Khavari, P. A. 2012; 91 (3): 435-443

    Abstract

    The basis for impaired differentiation in TP63 mutant ankyloblepharon-ectodermal dysplasia-clefting (AEC) syndrome is unknown. Human epidermis harboring AEC TP63 mutants recapitulated this impairment, along with downregulation of differentiation activators, including HOPX, GRHL3, KLF4, PRDM1, and ZNF750. Gene-set enrichment analysis indicated that disrupted expression of epidermal differentiation programs under the control of ZNF750 and KLF4 accounted for the majority of disrupted epidermal differentiation resulting from AEC mutant TP63. Chromatin immunoprecipitation (ChIP) analysis and ChIP-sequencing of TP63 binding in differentiated keratinocytes revealed ZNF750 as a direct target of wild-type and AEC mutant TP63. Restoring ZNF750 to AEC model tissue rescued activator expression and differentiation, indicating that AEC TP63-mediated ZNF750 inhibition contributes to differentiation defects in AEC. Incorporating disease-causing mutants into regenerated human tissue can thus dissect pathomechanisms and identify targets that reverse disease features.

    View details for DOI 10.1016/j.ajhg.2012.07.007

    View details for Web of Science ID 000308683100004

    View details for PubMedCentralID PMC3511987

  • Transcriptome sequencing in squamous cell carcinoma identifies novel skin malignancy regulated transcripts Lee, C., Ungewickell, A., Bhaduri, A., Qu, K., Webster, D., Aros, C., Mah, A., Kretz, M., Khavari, P. A. NATURE PUBLISHING GROUP. 2012: S29
  • BAF53A enforces the epidermal progenitor state by re-targeting the SWI/SNF/BAF chromatin remodeling complex away from differentiation gene promoters 75th Annual Meeting of the Society-for-Investigative-Dermatology Bao, X., Tang, J., Tao, S., Qu, K., Crabtree, G. R., Khavari, P. A. NATURE PUBLISHING GROUP. 2012: S63–S63
  • Scaffold-Kinase interaction blockade selectively inhibits Ras-MAPK tumorigenesis 75th Annual Meeting of the Society-for-Investigative-Dermatology Jameson, K. L., Zehnder, A., Khavari, P. A. NATURE PUBLISHING GROUP. 2012: S30–S30
  • ZNF750 is a p63 target that induces KLF4 to drive epidermal differentiation 75th Annual Meeting of the Society-for-Investigative-Dermatology Sen, G. L., Boxer, L., Webster, D., Bussat, R., Qu, K., Zarnegar, B., Johnston, D., Siprashvili, Z., Khavari, P. A. NATURE PUBLISHING GROUP. 2012: S74–S74
  • Transcriptome sequencing in Sezary Syndrome identifies novel Sezary cell-associated transcripts 75th Annual Meeting of the Society-for-Investigative-Dermatology Lee, C., Ungewickell, A., Bhaduri, A., Qu, K., Webster, D., Armstrong, R., Weng, W., Aros, C., MAH, A., Kretz, M., Kim, Y. H., Khavari, P. A. NATURE PUBLISHING GROUP. 2012: S29–S29
  • BAF53A enforces the epidermal progenitor state by re-targeting the SWI/SNF/BAF chromatin remodeling complex away from differentiation gene promoters Bao, X., Tang, J., Lopez-Pajares, V., Tao, S., Qu, K., Crabtree, G. R., Khavari, P. A. AMER SOC CELL BIOLOGY. 2012
  • BAF53A enforces the epidermal progenitor state by re-targeting the SWI/SNF/BAF chromatin remodeling complex away from differentiation gene promoters Bao, X., Tang, J., Lopez-Pajares, V., Tao, S., Qu, K., Crabtree, G. R., Khavari, P. A. AMER SOC CELL BIOLOGY. 2012
  • High throughput RNA sequencing of Sezary syndrome and cutaneous squamous cell carcinoma 71st Annual Meeting of the Society-for-Investigative-Dermatology Lee, C., Qu, K., Webster, D., Kretz, M., MAH, A., Ungewickell, A., Armstrong, R., Weng, W., Kim, Y., Chang, H., Khavari, P. NATURE PUBLISHING GROUP. 2011: S22–S22
  • Epidermal tissue differentiation and lipid barrier function requires the long non-coding RNA Linc19A Kretz, M., Webster, D., Siprashvili, Z., Zehnder, A., Lee, C., Flockhart, R., Chow, J., Kim, G., Rinn, J., Chang, H., Khavari, P. NATURE PUBLISHING GROUP. 2011: S66
  • Maintenance of the epidermal progenitor state requires the long non-coding RNA Linc8D 71st Annual Meeting of the Society-for-Investigative-Dermatology Lee, C., Kretz, M., Webster, D., Flockhart, R., Qu, K., MAH, A., Aros, C., Chang, H., Rinn, J., Khavari, P. NATURE PUBLISHING GROUP. 2011: S136–S136
  • DNMT1 maintains epidermal progenitor function Annual Meeting of the Society-for-Investigative-Dermatology Sen, G. L., Reuter, J. A., Webster, D. E., Zhu, L., Khavari, P. NATURE PUBLISHING GROUP. 2010: S87–S87
  • New cancer models assessed via quantitative transcriptome analysis Ridky, T. W., Chow, J. M., Wong, D. J., Khavari, P. A. NATURE PUBLISHING GROUP. 2010: S31
  • Invasive three-dimensional organotypic neoplasia from multiple normal human epithelia Nature Medicine Ridky TW, Khavari PA 2010; 16: 1450-1455
  • Modeling Inducible Human Tissue Neoplasia Identifies an Extracellular Matrix Interaction Network Involved in Cancer Progression CANCER CELL Reuter, J. A., Ortiz-Urda, S., Kretz, M., Garcia, J., Scholl, F. A., Pasmooij, A. M., Cassarino, D., Chang, H. Y., Khavari, P. A. 2009; 15 (6): 477-488

    Abstract

    To elucidate mechanisms of cancer progression, we generated inducible human neoplasia in three-dimensionally intact epithelial tissue. Gene expression profiling of both epithelia and stroma at specific time points during tumor progression revealed sequential enrichment of genes mediating discrete biologic functions in each tissue compartment. A core cancer progression signature was distilled using the increased signaling specificity of downstream oncogene effectors and subjected to network modeling. Network topology predicted that tumor development depends on specific extracellular matrix-interacting network hubs. Blockade of one such hub, the beta1 integrin subunit, disrupted network gene expression and attenuated tumorigenesis in vivo. Thus, integrating network modeling and temporal gene expression analysis of inducible human neoplasia provides an approach to prioritize and characterize genes functioning in cancer progression.

    View details for DOI 10.1016/j.ccr.2009.04.002

    View details for Web of Science ID 000266686500006

    View details for PubMedID 19477427

    View details for PubMedCentralID PMC3050547

  • Identification of the core gene expression signature and key cell-signaling pathways associated with Ras driven squamous cell carcinoma invasion Ridky, T. W., Wong, D., Khavari, P. A. NATURE PUBLISHING GROUP. 2009: S29
  • Ras driven genetically defined invasive human carcinomas generated from primary human epidermal, head and neck, cervical, esophageal, prostate, and breast epithelial cells established within in a three-dimensional organotypic human tissue platform Ridky, T. W., Chow, J., Khavari, P. A. NATURE PUBLISHING GROUP. 2009: S29
  • Mammalian epithelial development, homeostasis and Raf-induced hyperplasia rely on Mek1/2 MAPK kinases Scholl, F. A., Dumesic, P. A., Barragan, D. I., Harada, K., Bissonauth, V., Charron, J., Khavari, P. A. NATURE PUBLISHING GROUP. 2007: S76
  • Laminin-5 Beta 3 chain promotes epidermal carcinogenesis through type VII collagen binding and pi3k activation Sakai, N., Waterman, E. A., Nguyen, N. E., Horst, B. A., Veitch, D. P., Dey, C. N., Ortiz-Urda, S., Khavari, P. A., Marinkovich, M. NATURE PUBLISHING GROUP. 2006: 24
  • Effects of altered calcium ATPase function on epidermal carcinogenesis Kimmel, R. A., Ridky, T. W., Khavari, P. NATURE PUBLISHING GROUP. 2006: 19
  • Sustained survival and production of recombinant protein by genetically engineered human fibroblasts after intradermal injection Siprashvili, Z., Ridky, T. W., Khavari, P. NATURE PUBLISHING GROUP. 2006: 85
  • TNFR1 signaling to JNK opposes NF-kB to promotes epidermal neoplasia 67th Annual Meeting of the Society-for-Investigative-Dermatology Zhang, J. Y., Tao, S., Ridky, T. W., Khavari, P. NATURE PUBLISHING GROUP. 2006: 92–92
  • Invasive human melanocytic neoplasia in a 3-dimensional model using defined genetic elements 35th Annual Meeting of the European-Society-for-Dermatological-Research Adams, A., Chudnovsky, Y., Khavari, P. NATURE PUBLISHING GROUP. 2005: A58–A58
  • Use of human tissue to assess the oncogenic activity of melanoma-associated mutations NATURE GENETICS Chudnovsky, Y., Adams, A. E., Robbins, P. B., Lin, Q., Khavari, P. A. 2005; 37 (7): 745-749

    Abstract

    Multiple genetic alterations occur in melanoma, a lethal skin malignancy of increasing incidence. These include mutations that activate Ras and two of its effector cascades, Raf and phosphoinositide 3-kinase (PI3K). Induction of Ras and Raf can be caused by active N-Ras and B-Raf mutants as well as by gene amplification. Activation of PI3K pathway components occurs by PTEN loss and by AKT3 amplification. Melanomas also commonly show impairment of the p16(INK4A)-CDK4-Rb and ARF-HDM2-p53 tumor suppressor pathways. CDKN2A mutations can produce p16(INK4A) and ARF protein loss. Rb bypass can also occur through activating CDK4 mutations as well as by CDK4 amplification. In addition to ARF deletion, p53 pathway disruption can result from dominant negative TP53 mutations. TERT amplification also occurs in melanoma. The extent to which these mutations can induce human melanocytic neoplasia is unknown. Here we characterize pathways sufficient to generate human melanocytic neoplasia and show that genetically altered human tissue facilitates functional analysis of mutations observed in human tumors.

    View details for DOI 10.1038/ng1586

    View details for Web of Science ID 000230196400022

    View details for PubMedID 15951821

    View details for PubMedCentralID PMC3063773

  • Type VII collagen is required for cellular invasiveness in epidermal carcinogenesis 66th Annual Meeting of the Society-for-Investigative-Dermatology Ortiz-Urda, S., Garcia, J., Marinkovich, M., Khavari, P. NATURE PUBLISHING GROUP. 2005: A25–A25
  • The structural integrity of individual keratin filament networks is dispensable for epidermal tumorigenesis Ridky, T. W., Yang, E., Leachman, S., Khavari, P. BLACKWELL PUBLISHING INC. 2005: A72
  • Direct cutaneous plasmid DNA delivery via single intradermal injection of the cis-acting Sleeping Beauty transposon system Siprashvili, Z., Mikkelsen, J. G., Yant, S., Kay, M., Khavari, P. BLACKWELL PUBLISHING INC. 2005: A87
  • Disrupting TNFR1-JNK-AP1 action inhibits Ras-driven human epidermal neoplasia 66th Annual Meeting of the Society-for-Investigative-Dermatology Zhang, J. Y., Tao, S., Khavari, P. NATURE PUBLISHING GROUP. 2005: A97–A97
  • Functional characterization of class IIPI3-kinase in epidermal differentiation via targeted gene disruption and RNA interference 66th Annual Meeting of the Society-for-Investigative-Dermatology Harada, K., Cai, T., Truong, A., Khavari, P. NATURE PUBLISHING GROUP. 2005: A98–A98
  • Two distinct roles for the laminin-5 beta 3 chain in epidermal carcinogenesis and adhesion 66th Annual Meeting of the Society-for-Investigative-Dermatology Waterman, E. A., Ortiz-Urda, S., Nguyen, N. T., Veitch, D. P., Horst, B. A., Dey, C. N., Khavari, P. A., Marinkovich, M. P. NATURE PUBLISHING GROUP. 2005: A22–A22
  • Type VII collagen is required for Ras-driven human epidermal tumorigenesis SCIENCE Ortiz-Urda, S., Garcia, J., Green, C. L., Chen, L., Lin, Q., Veitch, D. P., Sakai, L. Y., LEE, H., Marinkovich, M. P., Khavari, P. A. 2005; 307 (5716): 1773-1776

    Abstract

    Type VII collagen defects cause recessive dystrophic epidermolysis bullosa (RDEB), a blistering skin disorder often accompanied by epidermal cancers. To study the role of collagen VII in these cancers, we examined Ras-driven tumorigenesis in RDEB keratinocytes. Cells devoid of collagen VII did not form tumors in mice, whereas those retaining a specific collagen VII fragment (the amino-terminal noncollagenous domain NC1) were tumorigenic. Forced NC1 expression restored tumorigenicity to collagen VII-null epidermis in a non-cell-autonomous fashion. Fibronectin-like sequences within NC1 (FNC1) promoted tumor cell invasion in a laminin 5-dependent manner and were required for tumorigenesis. Tumor-stroma interactions mediated by collagen VII thus promote neoplasia, and retention of NC1 sequences in a subset of RDEB patients may contribute to their increased susceptibility to squamous cell carcinoma.

    View details for DOI 10.1126/science.1106209

    View details for Web of Science ID 000227883900044

    View details for PubMedID 15774758

  • The Society's casework in 2004: Review of selected cases (Ancient Monuments Society) TRANSACTIONS OF THE ANCIENT MONUMENTS SOCIETY Lazarov, M., Green, C. L., Zhang, J. Y., Kubo, Y., Dajee, M., Khavari, P. A. 2005; 49: 87–128
  • Invasive human melanocytic neoplasia generated using defined genetic elements 65th Annual Meeting of the Society-for-Investigative-Dermatology Chudnovsky, Y., Adams, A. E., Lin, Q., Robbins, P. B., Khavari, P. NATURE PUBLISHING GROUP. 2004: A157–A157
  • Class II PI3-kinase mediates cell cycle inhibition and terminal differentiation in epidermis Cai, T., Harada, K., Yang, E., Khavari, P. BLACKWELL PUBLISHING INC. 2004: A77
  • Mek1, but not Mek2, alters epidermal growth and differentiation Scholl, F. A., Dumesic, P. A., Charron, J., Khavari, P. BLACKWELL PUBLISHING INC. 2004: A77
  • The ATP2C1 golgi ATPase is required for Ras-driven human epidermal neoplasia Kimmel, R., Khavari, P. BLACKWELL PUBLISHING INC. 2004: A89
  • NF-kappa B blockade and oncogenic Ras trigger invasive human epidermal neoplasia NATURE Dajee, M., Lazarov, M., Zhang, J. Y., Cai, T., Green, C. L., Russell, A. J., Marinkovich, M. P., Tao, S. Y., Lin, Q., Kubo, Y., Khavari, P. A. 2003; 421 (6923): 639-643

    Abstract

    The nuclear factor NF-kappaB and oncogenic Ras can alter proliferation in epidermis, the most common site of human cancer. These proteins are implicated in epidermal squamous cell carcinoma in mice, however, the potential effects of altering their function are uncertain. Whereas inhibition of NF-kappaB enhances apoptosis in certain tumours, blockade of NF-kappaB predisposes murine skin to squamous cell carcinoma. Because therapeutics inhibiting Ras and NF-kappaB pathways are being developed to treat human cancer, it is essential to assess the effects of altering these regulators. The medical relevance of murine studies is limited, however, by differences between mouse and human skin, and by the greater ease of transforming murine cells. Here we show that in normal human epidermal cells both NF-kappaB and oncogenic Ras trigger cell-cycle arrest. Growth arrest triggered by oncogenic Ras can be bypassed by IkappaBalpha-mediated blockade of NF-kappaB, generating malignant human epidermal tissue resembling squamous cell carcinoma. Human cell tumorigenesis is dependent on laminin 5 and alpha6beta4 integrin. Thus, IkappaBalpha circumvents restraints on growth promotion induced by oncogenic Ras and can act with Ras to induce invasive human tissue neoplasia.

    View details for DOI 10.1038/nature01283

    View details for PubMedID 12571598

  • CDK4 coexpression with Ras generates malignant human epidermal tumorigenesis NATURE MEDICINE Lazarov, M., Kubo, Y., Cai, T., Dajee, M., Tarutani, M., Lin, Q., Fang, M., Tao, S. Y., Green, C. L., Khavari, P. A. 2002; 8 (10): 1105-1114

    Abstract

    Ras acts with other proteins to induce neoplasia. By itself, however, strong Ras signaling can suppress proliferation of normal cells. In primary epidermal cells, we found that oncogenic Ras transiently decreases cyclin-dependent kinase (CDK) 4 expression in association with cell cycle arrest in G1 phase. CDK4 co-expression circumvents Ras growth suppression and induces invasive human neoplasia resembling squamous cell carcinoma. Tumorigenesis is dependent on CDK4 kinase function, with cyclin D1 required but not sufficient for this process. In facilitating escape from G1 growth restraints, Ras and CDK4 alter the composition of cyclin D and cyclin E complexes and promote resistance to growth inhibition by INK4 cyclin-dependent kinase inhibitors. These data identify a new role for oncogenic Ras in CDK4 regulation and highlight the functional importance of CDK4 suppression in preventing uncontrolled growth.

    View details for DOI 10.1038/nm779

    View details for PubMedID 12357246

  • Stable nonviral genetic correction of inherited human skin disease NATURE MEDICINE Ortiz-Urda, S., Thyagarajan, B., Keene, D. R., Lin, Q., Fang, M., Calos, M. P., Khavari, P. A. 2002; 8 (10): 1166-1170

    Abstract

    Current gene-transfer technologies display limitations in achieving effective gene delivery. Among these limitations are difficulties in stably integrating large corrective sequences into the genomes of long-lived progenitor-cell populations. Current larger-capacity viral vectors suffer from biosafety concerns, whereas plasmid-based approaches have poor efficiency of stable gene transfer. These barriers hinder genetic correction of many severe inherited human diseases, such as the blistering skin disorder recessive dystrophic epidermolysis bullosa (RDEB), caused by mutations in the large COL7A1 gene. To circumvent these barriers, we used the phi C31 bacteriophage integrase, which stably integrates large DNA sequences containing a specific 285-base-pair attB sequence into genomic 'pseudo-attP sites'. phi C31 integrase-based gene transfer stably integrated the COL7A1 cDNA into genomes of primary epidermal progenitor cells from four unrelated RDEB patients. Skin regenerated using these cells displayed stable correction of hallmark RDEB disease features, including Type VII collagen protein expression, anchoring fibril formation and dermal-epidermal cohesion. These findings establish a practical approach to nonviral genetic correction of severe human genetic disorders requiring stable genomic integration of large DNA sequences.

    View details for DOI 10.1038/nm766

    View details for PubMedID 12244305

  • Restoration of full-length type VII collagen expression in RDEB via nonviral gene integration using the phiC31 integrase Ortiz-Urda, S., Thyagarajan, B., Calos, M., Khavari, P. BLACKWELL PUBLISHING INC. 2002: 343
  • NF-kappa B blockade and oncogenic Ras induce invasive human epidermal neoplasia by circumventing cell cycle arrest Dajee, M., Lazarov, M., Khavari, P. BLACKWELL PUBLISHING INC. 2002: 220
  • Bypassing CDK4 suppression by oncogenic Ras leads to invasive human epidermal carcinoma capable of visceral dissemination Lazarov, M., Kubo, Y., Dajee, M., Cai, T., Khavari, P. BLACKWELL PUBLISHING INC. 2002: 219
  • Transposase-based stable nonviral laminin 5 gene delivery in junctional epidermolysis bullosa Ortiz-Urda, S., Yant, S., Scholl, F., Siprashvili, Z., Chen, P., Kay, M., Khavari, P. BLACKWELL PUBLISHING INC. 2002: 230
  • Laminin 5 integrin beta 4 are required for Ras-driven human epidermal tumorigenesis Dajee, A. M., Lazarov, M., Russell, A., Marinkovich, P., Reuter, J., Khavari, P. BLACKWELL PUBLISHING INC. 2002: 229
  • Regulated Ras function in transgenic skin demonstrates potent and reversible Ras effects on epidermal growth and differentiation Tarutani, M., Dajee, M., Cai, T., Khavari, P. BLACKWELL PUBLISHING INC. 2002: 254
  • Generation of transgenic skin with regulated NF-kappa B function and epidermis deficient in the Re1A/p65 indicate that NF-kappa B subunits regulate epidermal growth but not differentiation Zhang, Y., Kimmel, R., Tao, S., Khavari, P. NATURE PUBLISHING GROUP. 2002: 267–67
  • Potential redundancy of MEK kinase impacts on epidermal growth and differentiation Scholl, F., Dajee, M., Charron, J., Khavari, P. BLACKWELL PUBLISHING INC. 2002: 279
  • Upstream regulators of Ras function in epidermal cells Cai, T., Khavari, P. BLACKWELL PUBLISHING INC. 2002: 278
  • Impact of Ras effectors RalGDS, Akt and Raf on epidermal growth and differentiation Tarutani, M., Dajee, M., Lin, Q., Khavari, P. BLACKWELL PUBLISHING INC. 2002: 279
  • Regulation of CDK4 expression levels by TGF beta, TNF alpha, IL-1, NF-kappa B and Ras determines cellular proliferative responses to these regulators of epidermal growth Lazarov, M., Dajee, M., Kubo, Y., Khavari, P. BLACKWELL PUBLISHING INC. 2002: 279
  • Oncogenic Ras and telomerase induce invasive human melanocytic neoplasia Robbins, P., Sheu, S., Chudnovsky, J., Cai, T., Khavari, P. BLACKWELL PUBLISHING INC. 2002: 339
  • Regulated lentivectors for controlled and reversible cutaneous gene delivery Siprashvili, Z., Khavari, P. BLACKWELL PUBLISHING INC. 2002: 343
  • Stable nonviral genetic correction of inherited human skin disease Nature Medicine Ortiz-Urda S, Thyagarajan B, Keene DR, Lin Q, Fang M, Calos MP, Khavari PA 2002; 8: 1166-1170
  • Profiling genomic expression in disorders of epidermal proliferation identifies Egr1 as a potent regulator of epidermal growth. Fang, M., Wee, S. A., Fan, H., Morrisey, G., Tao, S., Lin, Q., Khavari, P. A. CELL PRESS. 2001: 220–20
  • Sustainable systemic erythropoietin delivery via a single injection of lentivirus into human skin Baek, S., Sheu, S., Lin, Q., Robbins, P., Khavari, P. BLACKWELL SCIENCE INC. 2001: 549
  • I kappa B kinase (IKK) complex function inhibits epidermal growth via NF-kappa B and fails to alter epidermal differentiation Goodnough, J., Robbins, P., Sheu, S., Khavari, P. BLACKWELL SCIENCE INC. 2001: 403
  • Spatially localized Ras action inhibits epidermal differentiation and promotes growth capacity via the Raf effector pathway Dajee, M., Deng, H., Tao, S., Khavari, P. NATURE PUBLISHING GROUP. 2001: 403–
  • Non-invasive topical immunization by a peptide vaccine against hepatitis B and rubella virus Tao, S., Dajee, M., Wee, S., Khavari, P. NATURE PUBLISHING GROUP. 2001: 435–35
  • Induction of invasive human epidermal neoplasia resembling squamous cell carcinoma (SCC) by defined genetic elements Ras and CDK4 Kubo, Y., Dajee, M., Lazarov, M., Tao, S., Khavari, P. NATURE PUBLISHING GROUP. 2001: 472–72
  • Impact of specific receptor tyrosine kinases on Ras in epithelial cells Cai, T., Khavari, P. BLACKWELL SCIENCE INC. 2001: 476
  • Profiling genomic expression in disorders of epidermal proliferation identifies Egr-1 as a potent regulator of epidermal growth Wee, S., Lin, Q., Tao, S., Fan, H., Khavari, P. NATURE PUBLISHING GROUP. 2001: 477–77
  • Induction of invasive human melanocytic neoplasia by defined genetic elements Khavari, P., Sheu, S., Robbins, P., Kubo, Y., Dajee, M., Goodnough, J. BLACKWELL SCIENCE INC. 2001: 483
  • Generation of inducible NF-kappa B subunits: Confirmation of a primary growth inhibitory role for NF-kappa B in epidermal cells Zhang, Y., Khavari, P. BLACKWELL SCIENCE INC. 2001: 525
  • Regulated induction of Ras and its effectors in epithelial cells Tarutani, M., Dajee, M., Khavari, P. BLACKWELL SCIENCE INC. 2001: 526
  • Differential target gene induction mediates opposing growth effects of NF-kappa B in keratinocytes and fibroblasts Hinata, K., Khavari, P. BLACKWELL SCIENCE INC. 2001: 526
  • Impact of gene vs. protein replacement on genomic expression patterns in functional epidermolysis bullosa Goodnough, J., Robbins, P., Sheu, S., Khavari, P. BLACKWELL SCIENCE INC. 2001: 541
  • Molecular transporters facilitate topical protein transduction into the skin Rothbard, J., Robbins, P., Sheu, S., Oliver, S., Goodnough, J., Wender, P., Khavari, P. BLACKWELL SCIENCE INC. 2001: 549
  • Conjugation of arginine oligomers to cyclosporin A facilitates topical delivery and inhibition of inflammation NATURE MEDICINE Rothbard, J. B., Garlington, S., Lin, Q., Kirschberg, T., Kreider, E., McGrane, P. L., Wender, P. A., Khavari, P. A. 2000; 6 (11): 1253-1257

    Abstract

    Many systemically effective drugs such as cyclosporin A are ineffective topically because of their poor penetration into skin. To surmount this problem, we conjugated a heptamer of arginine to cyclosporin A through a pH-sensitive linker to produce R7-CsA. In contrast to unmodified cyclosporin A, which fails to penetrate skin, topically applied R7-CsA was efficiently transported into cells in mouse and human skin. R7-CsA reached dermal T lymphocytes and inhibited cutaneous inflammation. These data establish a general strategy for enhancing delivery of poorly absorbed drugs across tissue barriers and provide a new topical approach to the treatment of inflammatory skin disorders.

    View details for Web of Science ID 000165114800033

    View details for PubMedID 11062537

  • Immunization via hair follicles by topical application of naked DNA to normal skin NATURE BIOTECHNOLOGY Fan, H. R., Lin, Q., Morrissey, G. R., Khavari, P. A. 1999; 17 (9): 870-872

    Abstract

    In order to test the immune response generated to small amounts of foreign protein in skin, we applied naked DNA in aqueous solution to untreated normal skin. Topical application of plasmid expression vectors for lacZ and the hepatitis B surface antigen (HBsAg) to intact skin induced antigen-specific immune responses that displayed TH2 features. For HBsAg, specific antibody and cellular responses were induced to the same order of magnitude as those produced by intramuscular injection of the commercially available recombinant HBsAg polypeptide vaccine. Finally, topical gene transfer was dependent on the presence of normal hair follicles.

    View details for Web of Science ID 000082365800027

    View details for PubMedID 10471927

  • Analysis of human basal cell carcinoma gene expression at a genomic scale via cDNA microarrays Fan, H., Barry, C. T., Baek, S. C., Lin, Q., Brown, P. O., Khavari, P. A. NATURE PUBLISHING GROUP. 1999: 528–28
  • cDNA microarray screening for genes differentially expressed in keratinocyte stem cell enriched populations Freiberg, R., Barry, C., Fang, M., Alvarez-Saavedra, E., Robbins, P., BROWN, P., Khavari, P. NATURE PUBLISHING GROUP. 1999: 560–60
  • Genomic analysis of human squamous cell carcinoma gene expression via cDNA microarrays Fan, H., Barry, C., Lin, Q., Baek, S., BROWN, P., Khavari, P. NATURE PUBLISHING GROUP. 1999: 558–58
  • Identification of new keratinocyte differentiation candidates genes by a genome-wide screening approach Freiberg, R., Barry, C., BROWN, P., Khavari, P. NATURE PUBLISHING GROUP. 1999: 624–24
  • Genome-wide characterization of NF-01 kappa B target genes in human epithelial cells via high density cDNA microarrays Hinata, K., Barry, C., BROWN, P., Khavari, P. NATURE PUBLISHING GROUP. 1999: 637–37
  • Sonic hedgehog opposes epithelial cell cycle arrest Fan, H., Wee, S. A., Khavari, P. A. BLACKWELL SCIENCE INC. 1999: 525
  • NF-kappa B function determiner localization and features of programmed cell death in epidermis Seitz, C. S., Freiberg, R. A., Khavari, P. A. BLACKWELL SCIENCE INC. 1999: 526
  • NF-kappa B-directed transcription is normally localized to non-proliferating cells within epidermis and is strongly induced by ultraviolet injury but not by wounding Gervin, A. M., Memet, S., Freiberg, R. A., Israel, A., Khavari, P. A. BLACKWELL SCIENCE INC. 1999: 530
  • Sustainable TGM1 gene delivery in human lamellar ichthyosis patient skin in vivo Lin, Q., Deng, H., Fan, H., Khavari, P. NATURE PUBLISHING GROUP. 1999: 638–38
  • Durable laminin 5 01 beta 3 gene delivery vectors for gene therapy of junctional epidermolysis bullosa Robbins, P., Alvarez-Saavedra, E., Lin, Q., Chen, X. J., Khavari, P. BLACKWELL SCIENCE INC. 1999: 639
  • Rv inhibition lends to epidermal proliferation in vivo Deng, H., Seitz, C., Khavari, P. NATURE PUBLISHING GROUP. 1999: 641–41
  • Genetic immunization by topical application of naked DNA to normal skin Fan, H., Lin, Q., Morrissey, G., Khavari, P. BLACKWELL SCIENCE INC. 1999: 638
  • Towards development of an in vitro model of human BCC formation. Oro, A. E., Fan, H., Khavari, P. A., Scott, M. P. ACADEMIC PRESS INC ELSEVIER SCIENCE. 1998: 196–96
  • Towards development of an in vitro model of human BC formation. Oro, A. E., Fan, H., Khavari, P. A., Scott, M. P. NATURE PUBLISHING GROUP. 1998: 500–500
  • NF-kappa B triggers cell cycle arrest in epidermis via specific induction of the cyclin-dependent kinase inhibitor p21(Cip1). Seitz, C. S., Deng, H., Khavari, P. A. NATURE PUBLISHING GROUP. 1998: 475–75
  • Sonic hedgehog regulates keratinocyte differentiation gene expression and cell cycle progression. Fan, H., Khavari, P. A. BLACKWELL SCIENCE INC. 1998: 486
  • Durable gene delivery to human epidermis in vivo: Relative contributions of gene regulatory elements and stem cell targeting. Khavari, P. A., Lin, Q., Deng, H. NATURE PUBLISHING GROUP. 1998: 503–
  • Sustainable cutaneous gene delivery NATURE BIOTECHNOLOGY Deng, H., Lin, Q., Khavari, P. A. 1997; 15 (13): 1388-1391

    Abstract

    Durable gene delivery to human skin is necessary for lasting correction of human genetic skin disease. Current cutaneous gene-delivery strategies, however, have achieved only transient gene expression, often only within a small percentage of tissue cells. The recent inability to sustain phenotypic correction of human genetic skin disease due to loss of therapeutic gene expression in regenerated epidermal tissue has highlighted this current limitation. In an effort to surmount this problem, we have generated gene delivery vectors that produce more durable gene delivery in human skin tissue in vivo.

    View details for Web of Science ID A1997YK36100031

    View details for PubMedID 9415892

  • Induction of basal cell carcinoma features in transgenic human skin expressing Sonic Hedgehog NATURE MEDICINE Fan, H. R., Oro, A. E., Scott, M. P., Khavari, P. A. 1997; 3 (7): 788-792

    Abstract

    Hedgehog (HH) signaling proteins mediate inductive events during animal development. Mutation of the only known HH receptor gene, Patched (PTC), has recently been implicated in inherited and sporadic forms of the most common human cancer, basal cell carcinoma (BCC). In Drosophila, HH acts by inactivating PTC function, raising the possibility that overexpression of Sonic Hedgehog (SHH) in human epidermis might have a tumorigenic effect equivalent to loss of PTC function. We used retroviral transduction of normal human keratinocytes to constitutively express SHH. SHH-expressing cells demonstrated increased expression of both the known HH target, BMP-2B, as well as bcl-2, a protein prominently expressed by keratinocytes in BCCs. These keratinocytes were then used to regenerate human skin transgenic for long terminal repeat-driven SHH (LTR-SHH) on immune-deficient mice. LTR-SHH human skin consistently displays the abnormal specific histologic features seen in BCCs, including downgrowth of epithelial buds into the dermis, basal cell palisading and separation of epidermis from the underlying dermis. In addition, LTR-SHH skin displays the gene expression abnormalities previously described for human BCCs, including decreased BP180/BPAG2 and laminin 5 adhesion proteins and expression of basal epidermal keratins. These data indicate that expression of SHH in human skin recapitulates features of human BCC in vivo, suggest that activation of this conserved signaling pathway contributes to the development of epithelial neoplasia and describe a new transgenic human tissue model of neoplasia.

    View details for Web of Science ID A1997XG76700042

    View details for PubMedID 9212109

  • Gene therapy: Progress, problems, prospects. NATURE MEDICINE Blau, H., Khavari, P. 1997; 3 (6): 612-613

    View details for Web of Science ID A1997XB97400028

    View details for PubMedID 9176485

  • Corrective gene transfer in the human skin disorder lamellar ichthyosis NATURE MEDICINE Choate, K. A., Medalie, D. A., Morgan, J. R., Khavari, P. A. 1996; 2 (11): 1263-1267

    Abstract

    Lamellar ichthyosis (LI) is a disfiguring skin disease characterized by abnormal epidermal differentiation and defective cutaneous barrier function. LI has been associated with loss of keratinocyte transglutaminase 1 (TGase1), an enzyme believed necessary for normal formation of the cornified epidermal barrier. Using LI as a prototype for therapeutic cutaneous gene delivery, we have used the human skin/immunodeficient mouse xenograft model to correct the molecular, histologic and functional abnormalities of LI patient skin in vivo. We have used TGase1-deficient primary keratinocytes from LI patients combined with high-efficiency transfer of functional TGase1 to regenerate engineered human LI epidermis on immunodeficient mice. Engineered LI epidermis displayed normal TGase1 expression in vivo, unlike unengineered LI epidermis where TGase1 was absent. Epidermal architecture was also normalized by TGase1 restoration, as was expression of the epidermal differentiation marker filaggrin. Engineered LI skin demonstrated restoration of cutaneous barrier function measures to levels seen in epidermis regenerated by keratinocytes from patients with normal skin, indicating functional correction in vivo of the proposed primary pathophysiologic defect in LI. These results confirm a major role for TGase1 in epidermal differentiation and demonstrate a potential future approach to therapeutic gene delivery in human skin.

    View details for Web of Science ID A1996VQ10100046

    View details for PubMedID 8898758

  • Fas signal transduction effects in the skin differ by cellular target and magnitude of receptor activation. Khavari, P., Freiberg, R. BLACKWELL SCIENCE INC. 1996: 634
  • SPECIFIC TRIGGERING OF TNF RECEPTOR SUPERFAMILY SIGNAL-TRANSDUCTION PATHWAYS USING CYTOPLASMIC DOMAINS OF FAS AND TNF-R1 FREIBERG, R. A., DUH, H., SPENCER, D., SCHREIBER, S. L., CRABTREE, G. R., KHAVARI, P. A. BLACKWELL SCIENCE PUBL INC CAMBRIDGE. 1995: 560
  • SPECIFIC GENE-REGULATION IN KERATINOCYTES AND FIBROBLASTS BY DOSE-DEPENDENT INTRACELLULAR MOLECULAR OLIGOMERIZATION FREIBERG, R. A., HO, S., SPENCER, D. M., WANDLESS, T., SCHREIBER, S. L., CRABTREE, G. R., KHAVARI, P. A. BLACKWELL SCIENCE PUBL INC CAMBRIDGE. 1995: 559
  • THE RETINOBLASTOMA PROTEIN AND BRG1 FORM A COMPLEX AND COOPERATE TO INDUCE CELL-CYCLE ARREST CELL Dunaief, J. L., Strober, B. E., Guha, S., Khavari, P. A., Alin, K., Luban, J., Begemann, M., Crabtree, G. R., Goff, S. P. 1994; 79 (1): 119-130

    Abstract

    The retinoblastoma tumor suppressor protein (RB) binds several cellular proteins involved in cell cycle progression. Using the yeast two-hybrid system, we found that RB bound specifically to the protein BRG1. BRG1 shares extensive sequence similarity to Drosophila brahma, an activator of homeotic gene expression, and the yeast transcriptional activator SNF2/SW12. BRG1 contains an RB-binding motif found in viral oncoproteins and bound to the A/B pocket and the hypophosphorylated form of RB. BRG1 did not bind RB in viral oncoprotein-transformed cells. Coimmunoprecipitation experiments suggested BRG1 associates with the RB family in vivo. In the human carcinoma cell line SW13, BRG1 exhibited tumor suppressor activity by inducing formation of flat, growth-arrested cells. This activity depended on the ability of BRG1 to cooperate and complex with RB, as both an RB-nonbinding mutant of BRG1 and the sequestration of RB by adenovirus E1A protein abolished flat cell formation.

    View details for Web of Science ID A1994PK58500013

    View details for PubMedID 7923370

  • NUCLEOSOME DISRUPTION AND ENHANCEMENT OF ACTIVATOR BINDING BY A HUMAN SW1/SNF COMPLEX NATURE Kwon, H., Imbalzano, A. N., Khavari, P. A., Kingston, R. E., GREEN, M. R. 1994; 370 (6489): 477-481

    Abstract

    CHROMATIN structure can affect the transcriptional activity of eukaryotic structural genes by blocking access of sequence-specific activator proteins (activators) to their promoter-binding sites. For example, the DNA-binding domain of the yeast GAL4 protein interacts very poorly with nucleosome cores compared with naked DNA2 (and see below), and binding of other activators is even more strongly inhibited. The way in which activators bind to nucleosomal DNA is therefore a critical aspect of transcriptional activation. Genetic studies have suggested that the multi-component SWI/SNF complex of Saccharomyces cerevisiae facilitates transcription by altering the structure of the chromatin. Here we identify and partially purify a human homologue of the yeast SWI/SNF complex (hSWI/SNF complex). We show that a partially purified hSWI/SNF complex mediates the ATP-dependent disruption of a nucleosome, thereby enabling the activators, GAL4-VP16 and GAL4-AH, to bind within a nucleosome core. We conclude that the hSWI/SNF complex acts directly to reorganize chromatin structure so as to facilitate binding of transcription factors.

    View details for Web of Science ID A1994PB40700061

    View details for PubMedID 8047169

  • INTERACTION BETWEEN THE RETINOBLASTOMA PROTEIN AND THE HUMAN HOMOLOG OF BRAHMA, A REGULATOR OF HOMEOTIC GENES DUNAIEF, J., KHAVARI, P., GUHA, S., ALIN, K., LUBAN, J., CRABTREE, G., GOFF, S. WILEY-LISS. 1994: 175
  • BRG1 CONTAINS A CONSERVED DOMAIN OF THE SWI2/SNF2 FAMILY NECESSARY FOR NORMAL MITOTIC GROWTH AND TRANSCRIPTION NATURE Khavari, P. A., Peterson, C. L., Tamkun, J. W., Mendel, D. B., Crabtree, G. R. 1993; 366 (6451): 170-174

    Abstract

    Sequence-specific DNA binding activators of gene transcription may be assisted by SWI2 (SNF2), which contains a DNA-dependent ATPase domain. We have isolated a human complementary DNA encoding a 205K nuclear protein, BRG1, that contains extensive homology to SWI2 and Drosophila brahma. We report here that a SWI2/BRG1 chimera with the DNA-dependent ATPase domain replaced by corresponding human sequence restored normal mitotic growth and capacity for transcriptional activation to swi2- yeast cells. Point mutation of the conserved ATP binding site lysine abolished this complementation. This mutation in SWI2 exerted a dominant negative effect on transcription in yeast. A lysine to arginine substitution at the corresponding residue of BRG1 also generated a transcriptional dominant negative in human cells. BRG1 is exclusively nuclear and present in a high M(r) complex of about 2 x 10(6). These results show that the SWI2 family DNA-dependent ATPase domain has functional conservation between yeast and humans and suggest that a SWI/SNF protein complex is required for the activation of selective mammalian genes.

    View details for PubMedID 8232556

  • IDENTIFICATION OF A 205-KD KERATINOCYTE-EXPRESSED ACTIVATOR OF GLUCOCORTICOID RECEPTOR (GR)-DRIVEN GENE-TRANSCRIPTION Khavari, P. A., Petersen, C. L. NATURE PUBLISHING GROUP. 1993: 524–24
  • CHARACTERIZATION OF A COFACTOR THAT REGULATES DIMERIZATION OF A MAMMALIAN HOMEODOMAIN PROTEIN SCIENCE Mendel, D. B., Khavari, P. A., Conley, P. B., Graves, M. K., Hansen, L. P., Admon, A., Crabtree, G. R. 1991; 254 (5039): 1762-1767

    Abstract

    Dimerization among transcription factors has become a recurrent theme in the regulation of eukaryotic gene expression. Hepatocyte nuclear factor-1 alpha (HNF-1 alpha) is a homeodomain-containing protein that functions as a dimer. A dimerization cofactor of HNF-1 alpha (DCoH) was identified that displayed a restricted tissue distribution and did not bind to DNA, but, rather, selectively stabilized HNF-1 alpha dimers. The formation of a stable tetrameric DCoH-HNF-1 alpha complex, which required the dimerization domain of HNF-1 alpha, did not change the DNA binding characteristics of HNF-1 alpha, but enhanced its transcriptional activity. However, DCoH did not confer transcriptional activation to the GAL4 DNA binding domain. These results indicate that DCoH regulates formation of transcriptionally active tetrameric complexes and may contribute to the developmental specificity of the complex.

    View details for PubMedID 1763325