Bio

Clinical Focus

  • Internal Medicine
  • Diagnostic Medicine
  • Undiagnosed Diseases
  • Mystery Illness
  • Rare Disorders
  • Complex Conditions

Academic Appointments

Administrative Appointments

  • Co-Director, Stanford Consultative Medicine Clinic (2019 - Present)
  • Chief Resident, Stanford Internal Medicine Residency Program (2018 - 2019)

Honors & Awards

  • Julian Wolfsohn Award (for clinical excellence, leadership, teaching, kindness), Stanford Internal Medicine Residency (2016)
  • Harold M. Weintraub Graduate Student Award (National), Fred Hutchinson Cancer Research Center (2012)
  • Alpha Omega Alpha (Medical Honor Society), Stanford University chapter (2019)
  • Phi Beta Kappa (Honor Society), Rice University chapter (2006)

Professional Education

  • Board Certification: American Board of Internal Medicine, Internal Medicine (2019)
  • Visiting scholar, NIH, Undiagnosed Diseases Program (2019)
  • Chief Resident, Stanford University Internal Medicine Residency (2019)
  • Residency: Stanford University Internal Medicine Residency (2018) CA
  • Medical Education: University of Washington School of Medicine (2015) WA
  • Ph.D., University of Washington, Molecular and Cellular Biology (2011)

Contact

  • Stanford Internal Medicine 211 Quarry Rd Ste 305 MC 5987 Palo Alto, CA 94304
    • Tel: (650) 498-9000
    Fax: (650) 725-7078

Links

Research & Scholarship

Current Research and Scholarly Interests

My scholarly interests are focused on defining, studying, and improving patients' diagnostic journeys. What prolongs the journey to the correct diagnosis and how can we shorten it? With this question in mind, we are exploring crowdsourcing, informatics/AI, health data visualization, and advanced laboratory testing as ways to help tackle the toughest cases in medicine-- complex, rare, and mystery conditions.

Teaching

2020-21 Courses

Publications

All Publications

  • Phases of the Diagnostic Journey: A Framework International Archives of Internal Medicine Geng, L. N., Sum-Ping, O., Geng, Y. 2019

    View details for DOI 10.23937/2643-4466/1710013

  • Genomics in medicine: a novel elective rotation for internal medicine residents. Postgraduate medical journal Geng, L. N., Kohler, J. N., Levonian, P., Bernstein, J. A., Ford, J. M., Ahuja, N., Witteles, R., Hom, J., Wheeler, M. 2019

    Abstract

    It is well recognised that medical training globally and at all levels lacks sufficient incorporation of genetics and genomics education to keep up with the rapid advances and growing application of genomics to clinical care. However, the best strategy to implement these desired changes into postgraduate medical training and engage learners is still unclear. We developed a novel elective rotation in 'Genomic Medicine and Undiagnosed Diseases' for categorical Internal Medicine Residents to address this educational gap and serve as an adaptable model for training that can be applied broadly across different specialties and at other institutions. Key curriculum goals achieved include increased understanding about genetic testing modalities and tools available for diagnosis and risk analysis, the role of genetics-trained allied health professionals, and indications and limitations of genetic and genomic testing in both rare and common conditions.

    View details for DOI 10.1136/postgradmedj-2018-136355

    View details for PubMedID 31439813

  • Loss of Paneth Cell Autophagy Causes Acute Susceptibility to Toxoplasma gondii-Mediated Inflammation. Cell host & microbe Burger, E., Araujo, A., López-Yglesias, A., Rajala, M. W., Geng, L., Levine, B., Hooper, L. V., Burstein, E., Yarovinsky, F. 2018; 23 (2): 177?90.e4

    Abstract

    The protozoan parasite Toxoplasma gondii triggers severe small intestinal immunopathology characterized by IFN-?- and intestinal microbiota-mediated inflammation, Paneth cell loss, and bacterial dysbiosis. Paneth cells are a prominent secretory epithelial cell type that resides at the base of intestinal crypts and releases antimicrobial peptides. We demonstrate that the microbiota triggers basal Paneth cell-specific autophagy via induction of IFN-?, a known trigger of autophagy, to maintain intestinal homeostasis. Deletion of the autophagy protein Atg5 specifically in Paneth cells results in exaggerated intestinal inflammation characterized by complete destruction of the intestinal crypts resembling that seen in pan-epithelial Atg5-deficient mice. Additionally, lack of functional autophagy in Paneth cells within intestinal organoids and T. gondii-infected mice causes increased sensitivity to the proinflammatory cytokine TNF along with increased intestinal permeability, leading to exaggerated microbiota- and IFN-?-dependent intestinal immunopathology. Thus, Atg5 expression in Paneth cells is essential for tissue protection against cytokine-mediated immunopathology during acute gastrointestinal infection.

    View details for DOI 10.1016/j.chom.2018.01.001

    View details for PubMedID 29358083

    View details for PubMedCentralID PMC6179445

  • COMMD1 is linked to the WASH complex and regulates endosomal trafficking of the copper transporter ATP7A. Molecular biology of the cell Phillips-Krawczak, C. A., Singla, A., Starokadomskyy, P., Deng, Z., Osborne, D. G., Li, H., Dick, C. J., Gomez, T. S., Koenecke, M., Zhang, J. S., Dai, H., Sifuentes-Dominguez, L. F., Geng, L. N., Kaufmann, S. H., Hein, M. Y., Wallis, M., McGaughran, J., Gecz, J., Sluis, B. v., Billadeau, D. D., Burstein, E. 2015; 26 (1): 91?103

    Abstract

    COMMD1 deficiency results in defective copper homeostasis, but the mechanism for this has remained elusive. Here we report that COMMD1 is directly linked to early endosomes through its interaction with a protein complex containing CCDC22, CCDC93, and C16orf62. This COMMD/CCDC22/CCDC93 (CCC) complex interacts with the multisubunit WASH complex, an evolutionarily conserved system, which is required for endosomal deposition of F-actin and cargo trafficking in conjunction with the retromer. Interactions between the WASH complex subunit FAM21, and the carboxyl-terminal ends of CCDC22 and CCDC93 are responsible for CCC complex recruitment to endosomes. We show that depletion of CCC complex components leads to lack of copper-dependent movement of the copper transporter ATP7A from endosomes, resulting in intracellular copper accumulation and modest alterations in copper homeostasis in humans with CCDC22 mutations. This work provides a mechanistic explanation for the role of COMMD1 in copper homeostasis and uncovers additional genes involved in the regulation of copper transporter recycling.

    View details for DOI 10.1091/mbc.E14-06-1073

    View details for PubMedID 25355947

    View details for PubMedCentralID PMC4279232

  • DUX4 binding to retroelements creates promoters that are active in FSHD muscle and testis. PLoS genetics Young, J. M., Whiddon, J. L., Yao, Z., Kasinathan, B., Snider, L., Geng, L. N., Balog, J., Tawil, R., van der Maarel, S. M., Tapscott, S. J. 2013; 9 (11): e1003947

    Abstract

    The human double-homeodomain retrogene DUX4 is expressed in the testis and epigenetically repressed in somatic tissues. Facioscapulohumeral muscular dystrophy (FSHD) is caused by mutations that decrease the epigenetic repression of DUX4 in somatic tissues and result in mis-expression of this transcription factor in skeletal muscle. DUX4 binds sites in the human genome that contain a double-homeobox sequence motif, including sites in unique regions of the genome as well as many sites in repetitive elements. Using ChIP-seq and RNA-seq on myoblasts transduced with DUX4 we show that DUX4 binds and activates transcription of mammalian apparent LTR-retrotransposons (MaLRs), endogenous retrovirus (ERVL and ERVK) elements, and pericentromeric satellite HSATII sequences. Some DUX4-activated MaLR and ERV elements create novel promoters for genes, long non-coding RNAs, and antisense transcripts. Many of these novel transcripts are expressed in FSHD muscle cells but not control cells, and thus might contribute to FSHD pathology. For example, HEY1, a repressor of myogenesis, is activated by DUX4 through a MaLR promoter. DUX4-bound motifs, including those in repetitive elements, show evolutionary conservation and some repeat-initiated transcripts are expressed in healthy testis, the normal expression site of DUX4, but more rarely in other somatic tissues. Testis expression patterns are known to have evolved rapidly in mammals, but the mechanisms behind this rapid change have not yet been identified: our results suggest that mobilization of MaLR and ERV elements during mammalian evolution altered germline gene expression patterns through transcriptional activation by DUX4. Our findings demonstrate a role for DUX4 and repetitive elements in mammalian germline evolution and in FSHD muscular dystrophy.

    View details for DOI 10.1371/journal.pgen.1003947

    View details for PubMedID 24278031

    View details for PubMedCentralID PMC3836709

  • Deregulation of the protocadherin gene FAT1 alters muscle shapes: implications for the pathogenesis of facioscapulohumeral dystrophy. PLoS genetics Caruso, N., Herberth, B., Bartoli, M., Puppo, F., Dumonceaux, J., Zimmermann, A., Denadai, S., Lebossé, M., Roche, S., Geng, L., Magdinier, F., Attarian, S., Bernard, R., Maina, F., Levy, N., Helmbacher, F. 2013; 9 (6): e1003550

    Abstract

    Generation of skeletal muscles with forms adapted to their function is essential for normal movement. Muscle shape is patterned by the coordinated polarity of collectively migrating myoblasts. Constitutive inactivation of the protocadherin gene Fat1 uncoupled individual myoblast polarity within chains, altering the shape of selective groups of muscles in the shoulder and face. These shape abnormalities were followed by early onset regionalised muscle defects in adult Fat1-deficient mice. Tissue-specific ablation of Fat1 driven by Pax3-cre reproduced muscle shape defects in limb but not face muscles, indicating a cell-autonomous contribution of Fat1 in migrating muscle precursors. Strikingly, the topography of muscle abnormalities caused by Fat1 loss-of-function resembles that of human patients with facioscapulohumeral dystrophy (FSHD). FAT1 lies near the critical locus involved in causing FSHD, and Fat1 mutant mice also show retinal vasculopathy, mimicking another symptom of FSHD, and showed abnormal inner ear patterning, predictive of deafness, reminiscent of another burden of FSHD. Muscle-specific reduction of FAT1 expression and promoter silencing was observed in foetal FSHD1 cases. CGH array-based studies identified deletion polymorphisms within a putative regulatory enhancer of FAT1, predictive of tissue-specific depletion of FAT1 expression, which preferentially segregate with FSHD. Our study identifies FAT1 as a critical determinant of muscle form, misregulation of which associates with FSHD.

    View details for DOI 10.1371/journal.pgen.1003550

    View details for PubMedID 23785297

    View details for PubMedCentralID PMC3681729

  • Behcet's disease with major vascular involvement. BMJ case reports Geng, L. N., Conway, D., Barnhart, S., Nowatzky, J. 2013; 2013

    Abstract

    A 40-year-old Chinese man was admitted for haemoptysis and progressive deep vein thrombosis involving the inferior vena cava (IVC) despite anticoagulation. An IVC filter had been placed earlier at an outside hospital. CT angiography revealed two pulmonary artery aneurysms. The patient was found to have a history of oral and genital ulcers, uveitis and erythema nodosum, thus meeting criteria for Behçet's disease. Other causes of the haemoptysis and thrombophilia were excluded. He underwent successful coil embolisation of the pulmonary artery aneurysms and responded well to immunosuppressive therapy with cyclophosphamide and steroids. Anticoagulation was cautiously continued to limit the long-term risk of secondary thrombosis from his IVC filter. The patient remains well 5 months after initiation of immunosuppressive therapy. Making a diagnosis of Behçet's disease in the setting of thrombosis is crucial, as treatment must include immunosuppression, and, thus, fundamentally differs from the management of most other thrombotic disorders.

    View details for DOI 10.1136/bcr-2013-200893

    View details for PubMedID 24214153

    View details for PubMedCentralID PMC3830209

  • Generation of isogenic D4Z4 contracted and noncontracted immortal muscle cell clones from a mosaic patient: a cellular model for FSHD. The American journal of pathology Krom, Y. D., Dumonceaux, J., Mamchaoui, K., den Hamer, B., Mariot, V., Negroni, E., Geng, L. N., Martin, N., Tawil, R., Tapscott, S. J., van Engelen, B. G., Mouly, V., Butler-Browne, G. S., van der Maarel, S. M. 2012; 181 (4): 1387?1401

    Abstract

    In most cases facioscapulohumeral muscular dystrophy (FSHD) is caused by contraction of the D4Z4 repeat in the 4q subtelomere. This contraction is associated with local chromatin decondensation and derepression of the DUX4 retrogene. Its complex genetic and epigenetic cause and high clinical variability in disease severity complicate investigations on the pathogenic mechanism underlying FSHD. A validated cellular model bypassing the considerable heterogeneity would facilitate mechanistic and therapeutic studies of FSHD. Taking advantage of the high incidence of somatic mosaicism for D4Z4 repeat contraction in de novo FSHD, we have established a clonal myogenic cell model from a mosaic patient. Individual clones are genetically identical except for the size of the D4Z4 repeat array, being either normal or FSHD sized. These clones retain their myogenic characteristics, and D4Z4 contracted clones differ from the noncontracted clones by the bursts of expression of DUX4 in sporadic nuclei, showing that this burst-like phenomenon is a locus-intrinsic feature. Consequently, downstream effects of DUX4 expression can be observed in D4Z4 contracted clones, like differential expression of DUX4 target genes. We also show their participation to in vivo regeneration with immunodeficient mice, further expanding the potential of these clones for mechanistic and therapeutic studies. These cell lines will facilitate pairwise comparisons to identify FSHD-specific differences and are expected to create new opportunities for high-throughput drug screens.

    View details for DOI 10.1016/j.ajpath.2012.07.007

    View details for PubMedID 22871573

    View details for PubMedCentralID PMC3463638

  • DUX4 activates germline genes, retroelements, and immune mediators: implications for facioscapulohumeral dystrophy. Developmental cell Geng, L. N., Yao, Z., Snider, L., Fong, A. P., Cech, J. N., Young, J. M., van der Maarel, S. M., Ruzzo, W. L., Gentleman, R. C., Tawil, R., Tapscott, S. J. 2012; 22 (1): 38?51

    Abstract

    Facioscapulohumeral dystrophy (FSHD) is one of the most common inherited muscular dystrophies. The causative gene remains controversial and the mechanism of pathophysiology unknown. Here we identify genes associated with germline and early stem cell development as targets of the DUX4 transcription factor, a leading candidate gene for FSHD. The genes regulated by DUX4 are reliably detected in FSHD muscle but not in controls, providing direct support for the model that misexpression of DUX4 is a causal factor for FSHD. Additionally, we show that DUX4 binds and activates LTR elements from a class of MaLR endogenous primate retrotransposons and suppresses the innate immune response to viral infection, at least in part through the activation of DEFB103, a human defensin that can inhibit muscle differentiation. These findings suggest specific mechanisms of FSHD pathology and identify candidate biomarkers for disease diagnosis and progression.

    View details for DOI 10.1016/j.devcel.2011.11.013

    View details for PubMedID 22209328

    View details for PubMedCentralID PMC3264808

  • Immunodetection of human double homeobox 4. Hybridoma (2005) Geng, L. N., Tyler, A. E., Tapscott, S. J. 2011; 30 (2): 125?30

    Abstract

    Double homeobox 4 (DUX4) is a candidate disease gene for facioscapulohumeral dystrophy (FSHD), one of the most common muscular dystrophies characterized by progressive skeletal muscle degeneration. Despite great strides in understanding precise genetics of FSHD, the molecular pathophysiology of the disease remains unclear. One of the major limitations has been the availability of appropriate molecular tools to study DUX4 protein. In the present study, we report the development of five new monoclonal antibodies targeted against the N- and C-termini of human DUX4, and characterize their reactivity using Western blot and immunofluorescence staining. Additionally, we show that expression of the canonical full coding DUX4 induces cell death in human primary muscle cells, whereas the expression of a shorter splice form of DUX4 results in no such toxicity. Immunostaining with these new antibodies reveals a differential effect of two DUX4 isoforms on human muscle cells. These antibodies will provide an excellent tool for investigating the role of DUX4 in FSHD pathogenesis.

    View details for DOI 10.1089/hyb.2010.0094

    View details for PubMedID 21529284

    View details for PubMedCentralID PMC3132944

  • Variability in the Androgen Response of Prostate Epithelium to 5 alpha-Reductase Inhibition: Implications for Prostate Cancer Chemoprevention CANCER RESEARCH Mostaghel, E. A., Geng, L., Holcomb, I., Coleman, I. M., Lucas, J., True, L. D., Nelson, P. S. 2010; 70 (4): 1286-1295

    Abstract

    Inhibitors of 5alpha-reductase (SRD5A) that lower intraprostatic levels of dihydrotestosterone (DHT) reduce the overall incidence of prostate cancer (PCa), but there is significant variation in chemopreventive activity between individual men. In seeking molecular alterations that might underlie this variation, we compared gene expression patterns in patients with localized PCa who were randomized to prostatectomy alone versus treatment with two different doses of the SRD5A inhibitor dutasteride. Prostatic levels of DHT were decreased by >90% in both dutasteride-treated patient groups versus the untreated patient group. Despite significant and uniform suppression of tissue DHT, unsupervised clustering based on prostatic gene expression did not discriminate these groups. However, subjects could be resolved into distinct cohorts characterized by high or low expression of genes regulated by the androgen receptor (AR), based solely on AR transcript expression. The higher-dose dutasteride treatment group was found to include significantly fewer cancers with TMPRSS2-ERG genetic fusions. Dutasteride treatment was associated with highly variable alterations in benign epithelial gene expression. Segregating subjects based on expression of AR and androgen-regulated genes revealed that patients are differentially sensitive to SRD5A inhibition. Our findings suggest that AR levels may predict the chemopreventive efficacy of SRD5A inhibitors.

    View details for DOI 10.1158/0008-5472.CAN-09-2509

    View details for Web of Science ID 000278485700003

    View details for PubMedID 20124490

    View details for PubMedCentralID PMC2822890

  • Facioscapulohumeral dystrophy: incomplete suppression of a retrotransposed gene. PLoS genetics Snider, L., Geng, L. N., Lemmers, R. J., Kyba, M., Ware, C. B., Nelson, A. M., Tawil, R., Filippova, G. N., van der Maarel, S. M., Tapscott, S. J., Miller, D. G. 2010; 6 (10): e1001181

    Abstract

    Each unit of the D4Z4 macrosatellite repeat contains a retrotransposed gene encoding the DUX4 double-homeobox transcription factor. Facioscapulohumeral dystrophy (FSHD) is caused by deletion of a subset of the D4Z4 units in the subtelomeric region of chromosome 4. Although it has been reported that the deletion of D4Z4 units induces the pathological expression of DUX4 mRNA, the association of DUX4 mRNA expression with FSHD has not been rigorously investigated, nor has any human tissue been identified that normally expresses DUX4 mRNA or protein. We show that FSHD muscle expresses a different splice form of DUX4 mRNA compared to control muscle. Control muscle produces low amounts of a splice form of DUX4 encoding only the amino-terminal portion of DUX4. FSHD muscle produces low amounts of a DUX4 mRNA that encodes the full-length DUX4 protein. The low abundance of full-length DUX4 mRNA in FSHD muscle cells represents a small subset of nuclei producing a relatively high abundance of DUX4 mRNA and protein. In contrast to control skeletal muscle and most other somatic tissues, full-length DUX4 transcript and protein is expressed at relatively abundant levels in human testis, most likely in the germ-line cells. Induced pluripotent (iPS) cells also express full-length DUX4 and differentiation of control iPS cells to embryoid bodies suppresses expression of full-length DUX4, whereas expression of full-length DUX4 persists in differentiated FSHD iPS cells. Together, these findings indicate that full-length DUX4 is normally expressed at specific developmental stages and is suppressed in most somatic tissues. The contraction of the D4Z4 repeat in FSHD results in a less efficient suppression of the full-length DUX4 mRNA in skeletal muscle cells. Therefore, FSHD represents the first human disease to be associated with the incomplete developmental silencing of a retrogene array normally expressed early in development.

    View details for DOI 10.1371/journal.pgen.1001181

    View details for PubMedID 21060811

    View details for PubMedCentralID PMC2965761

  • DNA methylation of developmental genes in pediatric medulloblastomas identified by denaturation analysis of methylation differences. Proceedings of the National Academy of Sciences of the United States of America Diede, S. J., Guenthoer, J., Geng, L. N., Mahoney, S. E., Marotta, M., Olson, J. M., Tanaka, H., Tapscott, S. J. 2010; 107 (1): 234?39

    Abstract

    DNA methylation might have a significant role in preventing normal differentiation in pediatric cancers. We used a genomewide method for detecting regions of CpG methylation on the basis of the increased melting temperature of methylated DNA, termed denaturation analysis of methylation differences (DAMD). Using the DAMD assay, we find common regions of cancer-specific methylation changes in primary medulloblastomas in critical developmental regulatory pathways, including Sonic hedgehog (Shh), Wingless (Wnt), retinoic acid receptor (RAR), and bone morphogenetic protein (BMP). One of the commonly methylated loci is the PTCH1-1C promoter, a negative regulator of the Shh pathway that is methylated in both primary patient samples and human medulloblastoma cell lines. Treatment with the DNA methyltransferase inhibitor 5-aza-2'-deoxycytidine (5-aza-dC) increases the expression of PTCH1 and other methylated loci. Whereas genetic mutations in PTCH1 have previously been shown to lead to medulloblastoma, our study indicates that epigenetic silencing of PTCH1, and other critical developmental loci, by DNA methylation is a fundamental process of pediatric medulloblastoma formation. This finding warrants strong consideration for DNA demethylating agents in future clinical trials for children with this disease.

    View details for DOI 10.1073/pnas.0907606106

    View details for PubMedID 19966297

    View details for PubMedCentralID PMC2806770

  • RNA transcripts, miRNA-sized fragments and proteins produced from D4Z4 units: new candidates for the pathophysiology of facioscapulohumeral dystrophy. Human molecular genetics Snider, L., Asawachaicharn, A., Tyler, A. E., Geng, L. N., Petek, L. M., Maves, L., Miller, D. G., Lemmers, R. J., Winokur, S. T., Tawil, R., van der Maarel, S. M., Filippova, G. N., Tapscott, S. J. 2009; 18 (13): 2414?30

    Abstract

    Deletion of a subset of the D4Z4 macrosatellite repeats in the subtelomeric region of chromosome 4q causes facioscapulohumeral muscular dystrophy (FSHD) when occurring on a specific haplotype of 4qter (4qA161). Several genes have been examined as candidates for causing FSHD, including the DUX4 homeobox gene in the D4Z4 repeat, but none have been definitively shown to cause the disease, nor has the full extent of transcripts from the D4Z4 region been carefully characterized. Using strand-specific RT-PCR, we have identified several sense and antisense transcripts originating from the 4q D4Z4 units in wild-type and FSHD muscle cells. Consistent with prior reports, we find that the DUX4 transcript from the last (most telomeric) D4Z4 unit is polyadenylated and has two introns in its 3-prime untranslated region. In addition, we show that this transcript generates (i) small si/miRNA-sized fragments, (ii) uncapped, polyadenylated 3-prime fragments that encode the conserved C-terminal portion of DUX4 and (iii) capped and polyadenylated mRNAs that contain the double-homeobox domain of DUX4 but splice-out the C-terminal portion. Transfection studies demonstrate that translation initiation at an internal methionine can produce the C-terminal polypeptide and developmental studies show that this peptide inhibits myogenesis at a step between MyoD transcription and the activation of MyoD target genes. Together, we have identified new sense and anti-sense RNA transcripts, novel mRNAs and mi/siRNA-sized RNA fragments generated from the D4Z4 units that are new candidates for the pathophysiology of FSHD.

    View details for DOI 10.1093/hmg/ddp180

    View details for PubMedID 19359275

    View details for PubMedCentralID PMC2694690

  • Type 1 diabetes promotes disruption of advanced atherosclerotic lesions in LDL receptor-deficient mice. Proceedings of the National Academy of Sciences of the United States of America Johansson, F., Kramer, F., Barnhart, S., Kanter, J. E., Vaisar, T., Merrill, R. D., Geng, L., Oka, K., Chan, L., Chait, A., Heinecke, J. W., Bornfeldt, K. E. 2008; 105 (6): 2082?87

    Abstract

    Cardiovascular disease, largely because of disruption of atherosclerotic lesions, accounts for the majority of deaths in people with type 1 diabetes. Recent mouse models have provided insights into the accelerated atherosclerotic lesion initiation in diabetes, but it is unknown whether diabetes directly worsens more clinically relevant advanced lesions. We therefore used an LDL receptor-deficient mouse model, in which type 1 diabetes can be induced at will, to investigate the effects of diabetes on preexisting lesions. Advanced lesions were induced by feeding mice a high-fat diet for 16 weeks before induction of diabetes. Diabetes, independently of lesion size, increased intraplaque hemorrhage and plaque disruption in the brachiocephalic artery of mice fed low-fat or high-fat diets for an additional 14 weeks. Hyperglycemia was not sufficient to induce plaque disruption. Furthermore, diabetes resulted in increased accumulation of monocytic cells positive for S100A9, a proinflammatory biomarker for cardiovascular events, and for a macrophage marker protein, without increasing lesion macrophage content. S100A9 immunoreactivity correlated with intraplaque hemorrhage. Aggressive lowering primarily of triglyceride-rich lipoproteins prevented both plaque disruption and the increased S100A9 in diabetic atherosclerotic lesions. Conversely, oleate promoted macrophage differentiation into an S100A9-positive population in vitro, thereby mimicking the effects of diabetes. Thus, diabetes increases plaque disruption, independently of effects on plaque initiation, through a mechanism that requires triglyceride-rich lipoproteins and is associated with an increased accumulation of S100A9-positive monocytic cells. These findings indicate an important link between diabetes, plaque disruption, and the innate immune system.

    View details for DOI 10.1073/pnas.0709958105

    View details for PubMedID 18252823

    View details for PubMedCentralID PMC2538884

  • Structure and enzymatic properties of a chimeric bacteriophage RB69 DNA polymerase and single-stranded DNA binding protein with increased processivity. Proteins Sun, S., Geng, L., Shamoo, Y. 2006; 65 (1): 231?38

    Abstract

    In vivo, replicative DNA polymerases are made more processive by their interactions with accessory proteins at the replication fork. Single-stranded DNA binding protein (SSB) is an essential protein that binds tightly and cooperatively to single-stranded DNA during replication to remove adventitious secondary structures and protect the exposed DNA from endogenous nucleases. Using information from high resolution structures and biochemical data, we have engineered a functional chimeric enzyme of the bacteriophage RB69 DNA polymerase and SSB with substantially increased processivity. Fusion of RB69 DNA polymerase with its cognate SSB via a short six amino acid linker increases affinity for primer-template DNA by sixfold and subsequently increases processivity by sevenfold while maintaining fidelity. The crystal structure of this fusion protein was solved by a combination of multiwavelength anomalous diffraction and molecular replacement to 3.2 A resolution and shows that RB69 SSB is positioned proximal to the N-terminal domain of RB69 DNA polymerase near the template strand channel. The structural and biochemical data suggest that SSB interactions with DNA polymerase are transient and flexible, consistent with models of a dynamic replisome during elongation.

    View details for DOI 10.1002/prot.21088

    View details for PubMedID 16881051

  • Structural and functional characterization of the first intracellular loop of human thromboxane A(2) receptor ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS Geng, L., Wu, J. X., So, S. P., Huang, G. X., Ruan, K. H. 2004; 423 (2): 253-265

    Abstract

    The conformation of a constrained peptide mimicking the putative first intracellular domain (iLP1) of thromboxane A(2) receptor (TP) was determined by (1)H 2D NMR spectroscopy. Through completed assignments of TOCSY, DQF-COSY, and NOESY spectra, a NMR structure of the peptide showed a beta-turn in residues 56-59 and a short helical structure in the residues 63-66. It suggests that residues 63-66 may be part of the second transmembrane domain (TM), and that Arg60, in an exposed position on the outer surface of the loop, may be involved in signaling through charge contact with Gq protein. The sequence alignment of Lys residue in the same position of other prostanoid receptors mediates different G protein couplings, suggesting that the chemical properties of Arg and Lys may also affect the receptor signaling activity. These hypotheses were supported by mutagenesis studies, in which the mutant of Arg60Leu completely lost activity in increasing intracellular calcium level through Gq coupling, and the mutant of Arg60Lys retained only about 35% signaling activity. The difference between the side chain functions of Lys and Arg in effecting the signaling was discussed.

    View details for DOI 10.1016/j.abb.2004.01.001

    View details for Web of Science ID 000220164100003

    View details for PubMedID 15001390

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