Bio

Academic Appointments


Administrative Appointments


  • Director of Genetics and Systems Biology, Sean N. Parker Center for Allergy Research (2015 - Present)

Professional Education


  • Ph.D., Yale University, Molecular, Cellular and Developmental Biology (2008)
  • M.S., Yale University, Molecular, Cellular and Developmental Biology (2005)
  • M.S., Fudan University, Biochemistry (2002)
  • B.S., Fudan University, Biology (1999)

Publications

Journal Articles


  • Whole-genome haplotyping using long reads and statistical methods NATURE BIOTECHNOLOGY Kuleshov, V., Xie, D., Chen, R., Pushkarev, D., Ma, Z., Blauwkamp, T., Kertesz, M., Snyder, M. 2014; 32 (3): 261-266

    Abstract

    The rapid growth of sequencing technologies has greatly contributed to our understanding of human genetics. Yet, despite this growth, mainstream technologies have not been fully able to resolve the diploid nature of the human genome. Here we describe statistically aided, long-read haplotyping (SLRH), a rapid, accurate method that uses a statistical algorithm to take advantage of the partially phased information contained in long genomic fragments analyzed by short-read sequencing. For a human sample, as little as 30 Gbp of additional sequencing data are needed to phase genotypes identified by 50× coverage whole-genome sequencing. Using SLRH, we phase 99% of single-nucleotide variants in three human genomes into long haplotype blocks 0.2-1 Mbp in length. We apply our method to determine allele-specific methylation patterns in a human genome and identify hundreds of differentially methylated regions that were previously unknown. SLRH should facilitate population-scale haplotyping of human genomes.

    View details for DOI 10.1038/nbt.2833

    View details for Web of Science ID 000332819800024

  • Whole-exome sequencing identifies tetratricopeptide repeat domain 7A (TTC7A) mutations for combined immunodeficiency with intestinal atresias. journal of allergy and clinical immunology Chen, R., Giliani, S., Lanzi, G., Mias, G. I., Lonardi, S., Dobbs, K., Manis, J., Im, H., Gallagher, J. E., Phanstiel, D. H., Euskirchen, G., Lacroute, P., Bettinger, K., Moratto, D., Weinacht, K., Montin, D., Gallo, E., Mangili, G., Porta, F., Notarangelo, L. D., Pedretti, S., Al-Herz, W., Alfahdli, W., Comeau, A. M., Traister, R. S., Pai, S., Carella, G., Facchetti, F., Nadeau, K. C., Snyder, M., Notarangelo, L. D. 2013; 132 (3): 656-664 e17

    Abstract

    Combined immunodeficiency with multiple intestinal atresias (CID-MIA) is a rare hereditary disease characterized by intestinal obstructions and profound immune defects.We sought to determine the underlying genetic causes of CID-MIA by analyzing the exomic sequences of 5 patients and their healthy direct relatives from 5 unrelated families.We performed whole-exome sequencing on 5 patients with CID-MIA and 10 healthy direct family members belonging to 5 unrelated families with CID-MIA. We also performed targeted Sanger sequencing for the candidate gene tetratricopeptide repeat domain 7A (TTC7A) on 3 additional patients with CID-MIA.Through analysis and comparison of the exomic sequence of the subjects from these 5 families, we identified biallelic damaging mutations in the TTC7A gene, for a total of 7 distinct mutations. Targeted TTC7A gene sequencing in 3 additional unrelated patients with CID-MIA revealed biallelic deleterious mutations in 2 of them, as well as an aberrant splice product in the third patient. Staining of normal thymus showed that the TTC7A protein is expressed in thymic epithelial cells, as well as in thymocytes. Moreover, severe lymphoid depletion was observed in the thymus and peripheral lymphoid tissues from 2 patients with CID-MIA.We identified deleterious mutations of the TTC7A gene in 8 unrelated patients with CID-MIA and demonstrated that the TTC7A protein is expressed in the thymus. Our results strongly suggest that TTC7A gene defects cause CID-MIA.

    View details for DOI 10.1016/j.jaci.2013.06.013

    View details for PubMedID 23830146

  • Promise of personalized omics to precision medicine WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE Chen, R., Snyder, M. 2013; 5 (1): 73-82

    Abstract

    The rapid development of high-throughput technologies and computational frameworks enables the examination of biological systems in unprecedented detail. The ability to study biological phenomena at omics levels in turn is expected to lead to significant advances in personalized and precision medicine. Patients can be treated according to their own molecular characteristics. Individual omes as well as the integrated profiles of multiple omes, such as the genome, the epigenome, the transcriptome, the proteome, the metabolome, the antibodyome, and other omics information are expected to be valuable for health monitoring, preventative measures, and precision medicine. Moreover, omics technologies have the potential to transform medicine from traditional symptom-oriented diagnosis and treatment of diseases toward disease prevention and early diagnostics. We discuss here the advances and challenges in systems biology-powered personalized medicine at its current stage, as well as a prospective view of future personalized health care at the end of this review.

    View details for DOI 10.1002/wsbm.1198

    View details for Web of Science ID 000312736200005

    View details for PubMedID 23184638

  • Specific plasma autoantibody reactivity in myelodysplastic syndromes. Scientific reports Mias, G. I., Chen, R., Zhang, Y., Sridhar, K., Sharon, D., Xiao, L., Im, H., Snyder, M. P., Greenberg, P. L. 2013; 3: 3311-?

    Abstract

    Increased autoantibody reactivity in plasma from Myelodysplastic Syndromes (MDS) patients may provide novel disease signatures, and possible early detection. In a two-stage study we investigated Immunoglobulin G reactivity in plasma from MDS, Acute Myeloid Leukemia post MDS patients, and a healthy cohort. In exploratory Stage I we utilized high-throughput protein arrays to identify 35 high-interest proteins showing increased reactivity in patient subgroups compared to healthy controls. In validation Stage II we designed new arrays focusing on 25 of the proteins identified in Stage I and expanded the initial cohort. We validated increased antibody reactivity against AKT3, FCGR3A and ARL8B in patients, which enabled sample classification into stable MDS and healthy individuals. We also detected elevated AKT3 protein levels in MDS patient plasma. The discovery of increased specific autoantibody reactivity in MDS patients, provides molecular signatures for classification, supplementing existing risk categorizations, and may enhance diagnostic and prognostic capabilities for MDS.

    View details for DOI 10.1038/srep03311

    View details for PubMedID 24264604

  • Personal Omics Profiling Reveals Dynamic Molecular and Medical Phenotypes CELL Chen, R., Mias, G. I., Li-Pook-Than, J., Jiang, L., Lam, H. Y., Chen, R., Miriami, E., Karczewski, K. J., Hariharan, M., Dewey, F. E., Cheng, Y., Clark, M. J., Im, H., Habegger, L., Balasubramanian, S., O'Huallachain, M., Dudley, J. T., Hillenmeyer, S., Haraksingh, R., Sharon, D., Euskirchen, G., Lacroute, P., Bettinger, K., Boyle, A. P., Kasowski, M., Grubert, F., Seki, S., Garcia, M., Whirl-Carrillo, M., Gallardo, M., Blasco, M. A., Greenberg, P. L., Snyder, P., Klein, T. E., Altman, R. B., Butte, A. J., Ashley, E. A., Gerstein, M., Nadeau, K. C., Tang, H., Snyder, M. 2012; 148 (6): 1293-1307

    Abstract

    Personalized medicine is expected to benefit from combining genomic information with regular monitoring of physiological states by multiple high-throughput methods. Here, we present an integrative personal omics profile (iPOP), an analysis that combines genomic, transcriptomic, proteomic, metabolomic, and autoantibody profiles from a single individual over a 14 month period. Our iPOP analysis revealed various medical risks, including type 2 diabetes. It also uncovered extensive, dynamic changes in diverse molecular components and biological pathways across healthy and diseased conditions. Extremely high-coverage genomic and transcriptomic data, which provide the basis of our iPOP, revealed extensive heteroallelic changes during healthy and diseased states and an unexpected RNA editing mechanism. This study demonstrates that longitudinal iPOP can be used to interpret healthy and diseased states by connecting genomic information with additional dynamic omics activity.

    View details for DOI 10.1016/j.cell.2012.02.009

    View details for Web of Science ID 000301889500023

    View details for PubMedID 22424236

  • Performance comparison of whole-genome sequencing platforms NATURE BIOTECHNOLOGY Lam, H. Y., Clark, M. J., Chen, R., Chen, R., Natsoulis, G., O'Huallachain, M., Dewey, F. E., Habegger, L., Ashley, E. A., Gerstein, M. B., Butte, A. J., Ji, H. P., Snyder, M. 2012; 30 (1): 78-U118

    View details for DOI 10.1038/nbt.2065

    View details for Web of Science ID 000299110600023

  • Performance comparison of exome DNA sequencing technologies NATURE BIOTECHNOLOGY Clark, M. J., Chen, R., Lam, H. Y., Karczewski, K. J., Chen, R., Euskirchen, G., Butte, A. J., Snyder, M. 2011; 29 (10): 908-U206

    Abstract

    Whole exome sequencing by high-throughput sequencing of target-enriched genomic DNA (exome-seq) has become common in basic and translational research as a means of interrogating the interpretable part of the human genome at relatively low cost. We present a comparison of three major commercial exome sequencing platforms from Agilent, Illumina and Nimblegen applied to the same human blood sample. Our results suggest that the Nimblegen platform, which is the only one to use high-density overlapping baits, covers fewer genomic regions than the other platforms but requires the least amount of sequencing to sensitively detect small variants. Agilent and Illumina are able to detect a greater total number of variants with additional sequencing. Illumina captures untranslated regions, which are not targeted by the Nimblegen and Agilent platforms. We also compare exome sequencing and whole genome sequencing (WGS) of the same sample, demonstrating that exome sequencing can detect additional small variants missed by WGS.

    View details for DOI 10.1038/nbt.1975

    View details for Web of Science ID 000296273000017

    View details for PubMedID 21947028

  • Whole-Exome Enrichment with the Illumina TruSeq Exome Enrichment Platform. Cold Spring Harbor protocols Chen, R., Im, H., Snyder, M. 2015

    Abstract

    Multiple platforms are available for whole-exome enrichment and sequencing (WES). This protocol is based on the Illumina TruSeq Exome Enrichment platform, which captures ∼62 Mb of the human exonic regions using 95-base DNA probes. In addition to covering the RefSeq and Ensembl coding sequences, the enriched sequences also include ∼28 Mb of RefSeq untranslated regions (UTR). The protocol can be performed at the benchside without the need for automation, and the resulting library can be used for targeted next-generation sequencing on an Illumina HiSeq 2000 sequencer.

    View details for DOI 10.1101/pdb.prot084863

    View details for PubMedID 25762418

  • Whole-Exome Enrichment with the Roche NimbleGen SeqCap EZ Exome Library SR Platform. Cold Spring Harbor protocols Chen, R., Im, H., Snyder, M. 2015

    Abstract

    Multiple platforms are available for whole-exome enrichment and sequencing (WES). This protocol is based on the Roche NimbleGen SeqCap EZ Exome Library SR platform, which enriches for ∼44 Mb of the human exonic regions. The SeqCap system uses 55- to 105-base DNA probes to capture known coding DNA sequences (CDS) from the NCBI Consensus CDS Database, RefSeq, and Sanger miRBase. The protocol can be performed at the benchside without the need for automation, and the resulting library can be used for targeted next-generation sequencing on an Illumina HiSeq 2000 sequencer.

    View details for DOI 10.1101/pdb.prot084855

    View details for PubMedID 25762419

  • Whole-Exome Enrichment with the Agilent SureSelect Human All Exon Platform. Cold Spring Harbor protocols Chen, R., Im, H., Snyder, M. 2015

    Abstract

    There are multiple platforms available for whole-exome enrichment and sequencing (WES). This protocol is based on the Agilent SureSelect Human All Exon platform, which targets ∼50 Mb of the human exonic regions. The SureSelect system uses ∼120-base RNA probes to capture known coding DNA sequences (CDS) from the NCBI Consensus CDS Database as well as other major RNA coding sequence databases, such as Sanger miRBase. The protocol can be performed at the benchside without the need for automation, and the resulting library can be used for targeted next-generation sequencing on an Illumina HiSeq 2000 sequencer.

    View details for DOI 10.1101/pdb.prot083659

    View details for PubMedID 25762417

  • The Integrative Human Microbiome Project: Dynamic Analysis of Microbiome-Host Omics Profiles during Periods of Human Health and Disease CELL HOST & MICROBE Proctor, L. M. 2014; 16 (3): 276-289

    Abstract

    Much has been learned about the diversity and distribution of human-associated microbial communities, but we still know little about the biology of the microbiome, how it interacts with the host, and how the host responds to its resident microbiota. The Integrative Human Microbiome Project (iHMP, http://hmp2.org), the second phase of the NIH Human Microbiome Project, will study these interactions by analyzing microbiome and host activities in longitudinal studies of disease-specific cohorts and by creating integrated data sets of microbiome and host functional properties. These data sets will serve as experimental test beds to evaluate new models, methods, and analyses on the interactions of host and microbiome. Here we describe the three models of microbiome-associated human conditions, on the dynamics of preterm birth, inflammatory bowel disease, and type 2 diabetes, and their underlying hypotheses, as well as the multi-omic data types to be collected, integrated, and distributed through public repositories as a community resource.

    View details for DOI 10.1016/j.chom.2014.08.014

    View details for Web of Science ID 000342057000006

    View details for PubMedID 25211071

  • Distinct Splice Variants and Pathway Enrichment in the Cell-Line Models of Aggressive Human Breast Cancer Subtypes JOURNAL OF PROTEOME RESEARCH Menon, R., Im, H., Zhang, E. (., Wu, S., Chen, R., Snyder, M., Hancock, W. S., Omenn, G. S. 2014; 13 (1): 212-227

    Abstract

    This study was conducted as a part of the Chromosome-Centric Human Proteome Project (C-HPP) of the Human Proteome Organization. The United States team of C-HPP is focused on characterizing the protein-coding genes in chromosome 17. Despite its small size, chromosome 17 is rich in protein-coding genes; it contains many cancer-associated genes, including BRCA1, ERBB2, (Her2/neu), and TP53. The goal of this study was to examine the splice variants expressed in three ERBB2 expressed breast cancer cell-line models of hormone-receptor-negative breast cancers by integrating RNA-Seq and proteomic mass spectrometry data. The cell lines represent distinct phenotypic variations subtype: SKBR3 (ERBB2+ (overexpression)/ER-/PR-; adenocarcinoma), SUM190 (ERBB2+ (overexpression)/ER-/PR-; inflammatory breast cancer), and SUM149 (ERBB2 (low expression) ER-/PR-; inflammatory breast cancer). We identified more than one splice variant for 1167 genes expressed in at least one of the three cancer cell lines. We found multiple variants of genes that are in the signaling pathways downstream of ERBB2 along with variants specific to one cancer cell line compared with the other two cancer cell lines and with normal mammary cells. The overall transcript profiles based on read counts indicated more similarities between SKBR3 and SUM190. The top-ranking Gene Ontology and BioCarta pathways for the cell-line specific variants pointed to distinct key mechanisms including: amino sugar metabolism, caspase activity, and endocytosis in SKBR3; different aspects of metabolism, especially of lipids in SUM190; cell-to-cell adhesion, integrin, and ERK1/ERK2 signaling; and translational control in SUM149. The analyses indicated an enrichment in the electron transport chain processes in the ERBB2 overexpressed cell line models and an association of nucleotide binding, RNA splicing, and translation processes with the IBC models, SUM190 and SUM149. Detailed experimental studies on the distinct variants identified from each of these three breast cancer cell line models that may open opportunities for drug target discovery and help unveil their specific roles in cancer progression and metastasis.

    View details for DOI 10.1021/pr400773v

    View details for Web of Science ID 000329472700022

    View details for PubMedID 24111759

  • Mutations in NGLY1 cause an inherited disorder of the endoplasmic reticulum-associated degradation pathway. Genetics in medicine : official journal of the American College of Medical Genetics Enns, G. M., Shashi, V., Bainbridge, M., Gambello, M. J., Zahir, F. R., Bast, T., Crimian, R., Schoch, K., Platt, J., Cox, R., Bernstein, J. A., Scavina, M., Walter, R. S., Bibb, A., Jones, M., Hegde, M., Graham, B. H., Need, A. C., Oviedo, A., Schaaf, C. P., Boyle, S., Butte, A. J., Chen, R., Clark, M. J., Haraksingh, R., Cowan, T. M., He, P., Langlois, S., Zoghbi, H. Y., Snyder, M., Gibbs, R. A., Freeze, H. H., Goldstein, D. B. 2014

    Abstract

    Purpose:The endoplasmic reticulum-associated degradation pathway is responsible for the translocation of misfolded proteins across the endoplasmic reticulum membrane into the cytosol for subsequent degradation by the proteasome. To define the phenotype associated with a novel inherited disorder of cytosolic endoplasmic reticulum-associated degradation pathway dysfunction, we studied a series of eight patients with deficiency of N-glycanase 1.Methods:Whole-genome, whole-exome, or standard Sanger sequencing techniques were employed. Retrospective chart reviews were performed in order to obtain clinical data.Results:All patients had global developmental delay, a movement disorder, and hypotonia. Other common findings included hypolacrima or alacrima (7/8), elevated liver transaminases (6/7), microcephaly (6/8), diminished reflexes (6/8), hepatocyte cytoplasmic storage material or vacuolization (5/6), and seizures (4/8). The nonsense mutation c.1201A>T (p.R401X) was the most common deleterious allele.Conclusion:NGLY1 deficiency is a novel autosomal recessive disorder of the endoplasmic reticulum-associated degradation pathway associated with neurological dysfunction, abnormal tear production, and liver disease. The majority of patients detected to date carry a specific nonsense mutation that appears to be associated with severe disease. The phenotypic spectrum is likely to enlarge as cases with a broader range of mutations are detected.Genet Med advance online publication 20 March 2014Genetics in Medicine (2014); doi:10.1038/gim.2014.22.

    View details for DOI 10.1038/gim.2014.22

    View details for PubMedID 24651605

  • Toward More Transparent and Reproducible Omics Studies Through a Common Metadata Checklist and Data Publications OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY Kolker, E., Ozdemir, V., Martens, L., Hancock, W., Anderson, G., Anderson, N., Aynacioglu, S., Baranova, A., Campagna, S. R., Chen, R., Choiniere, J., Dearth, S. P., Feng, W., Ferguson, L., Fox, G., Frishman, D., Grossman, R., Heath, A., Higdon, R., Hutz, M. H., Janko, I., Jiang, L., Joshi, S., Kel, A., Kemnitz, J. W., Kohane, I. S., Kolker, N., Lancet, D., Lee, E., Li, W., Lisitsa, A., Llerena, A., Macnealy-Koch, C., Marshall, J., Masuzzo, P., May, A., Mias, G., Monroe, M., Montague, E., Mooney, S., Nesvizhskii, A., Noronha, S., Omenn, G., Rajasimha, H., Ramamoorthy, P., Sheehan, J., Smarr, L., Smith, C. V., Smith, T., Snyder, M., Rapole, S., Srivastava, S., Stanberry, L., Stewart, E., Toppo, S., Uetz, P., Verheggen, K., Voy, B. H., Warnich, L., Wilhelm, S. W., Yandl, G. 2014; 18 (1): 10-14

    Abstract

    Biological processes are fundamentally driven by complex interactions between biomolecules. Integrated high-throughput omics studies enable multifaceted views of cells, organisms, or their communities. With the advent of new post-genomics technologies, omics studies are becoming increasingly prevalent; yet the full impact of these studies can only be realized through data harmonization, sharing, meta-analysis, and integrated research. These essential steps require consistent generation, capture, and distribution of metadata. To ensure transparency, facilitate data harmonization, and maximize reproducibility and usability of life sciences studies, we propose a simple common omics metadata checklist. The proposed checklist is built on the rich ontologies and standards already in use by the life sciences community. The checklist will serve as a common denominator to guide experimental design, capture important parameters, and be used as a standard format for stand-alone data publications. The omics metadata checklist and data publications will create efficient linkages between omics data and knowledge-based life sciences innovation and, importantly, allow for appropriate attribution to data generators and infrastructure science builders in the post-genomics era. We ask that the life sciences community test the proposed omics metadata checklist and data publications and provide feedback for their use and improvement.

    View details for DOI 10.1089/omi.2013.0149

    View details for Web of Science ID 000331085100002

    View details for PubMedID 24456465

  • A Chromosome-centric Human Proteome Project (C-HPP) to Characterize the Sets of Proteins Encoded in Chromosome 17 JOURNAL OF PROTEOME RESEARCH Liu, S., Im, H., Bairoch, A., Cristofanilli, M., Chen, R., Deutsch, E. W., Dalton, S., Fenyo, D., Fanayan, S., Gates, C., Gaudet, P., Hincapie, M., Hanash, S., Kim, H., Jeong, S., Lundberg, E., Mias, G., Menon, R., Mu, Z., Nice, E., Paik, Y., Uhlen, M., Wells, L., Wu, S., Yan, F., Zhang, F., Zhang, Y., Snyder, M., Omenn, G. S., Beavis, R. C., Hancock, W. S. 2013; 12 (1): 45-57

    Abstract

    We report progress assembling the parts list for chromosome 17 and illustrate the various processes that we have developed to integrate available data from diverse genomic and proteomic knowledge bases. As primary resources, we have used GPMDB, neXtProt, PeptideAtlas, Human Protein Atlas (HPA), and GeneCards. All sites share the common resource of Ensembl for the genome modeling information. We have defined the chromosome 17 parts list with the following information: 1169 protein-coding genes, the numbers of proteins confidently identified by various experimental approaches as documented in GPMDB, neXtProt, PeptideAtlas, and HPA, examples of typical data sets obtained by RNASeq and proteomic studies of epithelial derived tumor cell lines (disease proteome) and a normal proteome (peripheral mononuclear cells), reported evidence of post-translational modifications, and examples of alternative splice variants (ASVs). We have constructed a list of the 59 "missing" proteins as well as 201 proteins that have inconclusive mass spectrometric (MS) identifications. In this report we have defined a process to establish a baseline for the incorporation of new evidence on protein identification and characterization as well as related information from transcriptome analyses. This initial list of "missing" proteins that will guide the selection of appropriate samples for discovery studies as well as antibody reagents. Also we have illustrated the significant diversity of protein variants (including post-translational modifications, PTMs) using regions on chromosome 17 that contain important oncogenes. We emphasize the need for mandated deposition of proteomics data in public databases, the further development of improved PTM, ASV, and single nucleotide variant (SNV) databases, and the construction of Web sites that can integrate and regularly update such information. In addition, we describe the distribution of both clustered and scattered sets of protein families on the chromosome. Since chromosome 17 is rich in cancer-associated genes, we have focused the clustering of cancer-associated genes in such genomic regions and have used the ERBB2 amplicon as an example of the value of a proteogenomic approach in which one integrates transcriptomic with proteomic information and captures evidence of coexpression through coordinated regulation.

    View details for DOI 10.1021/pr300985j

    View details for Web of Science ID 000313156300007

  • Exome sequencing by targeted enrichment. Current protocols in molecular biology / edited by Frederick M. Ausubel ... [et al.] Clark, M. J., Chen, R., Snyder, M. 2013; Chapter 7: Unit7 12-?

    Abstract

    This unit describes methods for targeted enrichment of the exon-coding portions of the genome using Agilent SureSelect Human All Exon 50 Mb and Roche Nimblegen SeqCap EZ Exome platforms. Each platform targets and enriches a large overlapping portion of the greater human exome. The protocols here describe the biochemical procedures used to enrich exomic DNA with each platform, including recommended modifications to the manufacturers' protocols. In addition, a brief description of the sequencing protocol and estimation of the needed amount of sequencing for each platform is included. Finally, a detailed analytical pipeline for processing the subsequent data is described. These protocols focus specifically on human exome sequencing platforms, but can be applied with some modification to other organisms and targeted enrichment approaches.

    View details for DOI 10.1002/0471142727.mb0712s102

    View details for PubMedID 23547016

  • Systems biology: personalized medicine for the future? CURRENT OPINION IN PHARMACOLOGY Chen, R., Snyder, M. 2012; 12 (5): 623-628

    Abstract

    Systems biology is actively transforming the field of modern health care from symptom-based disease diagnosis and treatment to precision medicine in which patients are treated based on their individual characteristics. Development of high-throughput technologies such as high-throughout sequencing and mass spectrometry has enabled scientists and clinicians to examine genomes, transcriptomes, proteomes, metabolomes, and other omics information in unprecedented detail. The combined 'omics' information leads to a global profiling of health and disease, and provides new approaches for personalized health monitoring and preventative medicine. In this article, we review the efforts of systems biology in personalized medicine in the past 2 years, and discuss in detail achievements and concerns, as well as highlights and hurdles for future personalized health care.

    View details for DOI 10.1016/j.coph.2012.07.011

    View details for Web of Science ID 000310478800017

    View details for PubMedID 22858243

  • Patient-Specific Induced Pluripotent Stem Cells as a Model for Familial Dilated Cardiomyopathy SCIENCE TRANSLATIONAL MEDICINE Sun, N., Yazawa, M., Liu, J., Han, L., Sanchez-Freire, V., Abilez, O. J., Navarrete, E. G., Hu, S., Wang, L., Lee, A., Pavlovic, A., Lin, S., Chen, R., Hajjar, R. J., Snyder, M. P., Dolmetsch, R. E., Butte, M. J., Ashley, E. A., Longaker, M. T., Robbins, R. C., Wu, J. C. 2012; 4 (130)

    Abstract

    Characterized by ventricular dilatation, systolic dysfunction, and progressive heart failure, dilated cardiomyopathy (DCM) is the most common form of cardiomyopathy in patients. DCM is the most common diagnosis leading to heart transplantation and places a significant burden on healthcare worldwide. The advent of induced pluripotent stem cells (iPSCs) offers an exceptional opportunity for creating disease-specific cellular models, investigating underlying mechanisms, and optimizing therapy. Here, we generated cardiomyocytes from iPSCs derived from patients in a DCM family carrying a point mutation (R173W) in the gene encoding sarcomeric protein cardiac troponin T. Compared to control healthy individuals in the same family cohort, cardiomyocytes derived from iPSCs from DCM patients exhibited altered regulation of calcium ion (Ca(2+)), decreased contractility, and abnormal distribution of sarcomeric ?-actinin. When stimulated with a ?-adrenergic agonist, DCM iPSC-derived cardiomyocytes showed characteristics of cellular stress such as reduced beating rates, compromised contraction, and a greater number of cells with abnormal sarcomeric ?-actinin distribution. Treatment with ?-adrenergic blockers or overexpression of sarcoplasmic reticulum Ca(2+) adenosine triphosphatase (Serca2a) improved the function of iPSC-derived cardiomyocytes from DCM patients. Thus, iPSC-derived cardiomyocytes from DCM patients recapitulate to some extent the morphological and functional phenotypes of DCM and may serve as a useful platform for exploring disease mechanisms and for drug screening.

    View details for DOI 10.1126/scitranslmed.3003552

    View details for Web of Science ID 000303045900004

    View details for PubMedID 22517884

  • The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome NATURE BIOTECHNOLOGY Paik, Y., Jeong, S., Omenn, G. S., Uhlen, M., Hanash, S., Cho, S. Y., Lee, H., Na, K., Choi, E., Yan, F., Zhang, F., Zhang, Y., Snyder, M., Cheng, Y., Chen, R., Marko-Varga, G., Deutsch, E. W., Kim, H., Kwon, J., Aebersold, R., Bairoch, A., Taylor, A. D., Kim, K. Y., Lee, E., Hochstrasser, D., Legrain, P., Hancock, W. S. 2012; 30 (3): 221-223

    View details for Web of Science ID 000301303800011

    View details for PubMedID 22398612

  • Detecting and annotating genetic variations using the HugeSeq pipeline NATURE BIOTECHNOLOGY Lam, H. Y., Pan, C., Clark, M. J., Lacroute, P., Chen, R., Haraksingh, R., O'Huallachain, M., Gerstein, M. B., Kidd, J. M., Bustamante, C. D., Snyder, M. 2012; 30 (3): 226-229

    View details for Web of Science ID 000301303800013

    View details for PubMedID 22398614

  • Diverse protein kinase interactions identified by protein microarrays reveal novel connections between cellular processes GENES & DEVELOPMENT Fasolo, J., Sboner, A., Sun, M. G., Yu, H., Chen, R., Sharon, D., Kim, P. M., Gerstein, M., Snyder, M. 2011; 25 (7): 767-778

    Abstract

    Protein kinases are key regulators of cellular processes. In spite of considerable effort, a full understanding of the pathways they participate in remains elusive. We globally investigated the proteins that interact with the majority of yeast protein kinases using protein microarrays. Eighty-five kinases were purified and used to probe yeast proteome microarrays. One-thousand-twenty-three interactions were identified, and the vast majority were novel. Coimmunoprecipitation experiments indicate that many of these interactions occurred in vivo. Many novel links of kinases to previously distinct cellular pathways were discovered. For example, the well-studied Kss1 filamentous pathway was found to bind components of diverse cellular pathways, such as those of the stress response pathway and the Ccr4-Not transcriptional/translational regulatory complex; genetic tests revealed that these different components operate in the filamentation pathway in vivo. Overall, our results indicate that kinases operate in a highly interconnected network that coordinates many activities of the proteome. Our results further demonstrate that protein microarrays uncover a diverse set of interactions not observed previously.

    View details for DOI 10.1101/gad.1998811

    View details for Web of Science ID 000289062700010

    View details for PubMedID 21460040

  • Yeast proteomics and protein microarrays JOURNAL OF PROTEOMICS Chen, R., Snyder, M. 2010; 73 (11): 2147-2157

    Abstract

    Our understanding of biological processes as well as human diseases has improved greatly thanks to studies on model organisms such as yeast. The power of scientific approaches with yeast lies in its relatively simple genome, its facile classical and molecular genetics, as well as the evolutionary conservation of many basic biological mechanisms. However, even in this simple model organism, systems biology studies, especially proteomic studies had been an intimidating task. During the past decade, powerful high-throughput technologies in proteomic research have been developed for yeast including protein microarray technology. The protein microarray technology allows the interrogation of protein-protein, protein-DNA, protein-small molecule interaction networks as well as post-translational modification networks in a large-scale, high-throughput manner. With this technology, many groundbreaking findings have been established in studies with the budding yeast Saccharomyces cerevisiae, most of which could have been unachievable with traditional approaches. Discovery of these networks has profound impact on explicating biological processes with a proteomic point of view, which may lead to a better understanding of normal biological phenomena as well as various human diseases.

    View details for DOI 10.1016/j.jprot.2010.08.003

    View details for Web of Science ID 000283903000008

    View details for PubMedID 20728591

  • TWISTing stemness, inflammation and proliferation of epithelial ovarian cancer cells through MIR199A2/214 ONCOGENE Yin, G., Chen, R., Alvero, A. B., Fu, H., Holmberg, J., Glackin, C., Rutherford, T., Mor, G. 2010; 29 (24): 3545-3553

    Abstract

    Cancer stem cells are responsible for sustaining the tumor and giving rise to proliferating and progressively differentiating cells. However, the molecular mechanisms regulating the process of cancer stem cell (CSC) differentiation is not clearly understood. Recently, we reported the isolation of the epithelial ovarian cancer (EOC) stem cells (type I/CD44+). In this study, we show that type I/CD44+ cells are characterized by low levels of both miR-199a and miR-214, whereas mature EOC cells (type II/CD44-) have higher levels of miR-199a and miR-214. Moreover, these two micro RNAs (miRNAs) are regulated as a cluster on pri-miR-199a2 within the human Dnm3os gene (GenBank FJ623959). This study identify Twist1 as a regulator of this unique miRNA cluster responsible for the regulation of the IKKbeta/NF-kappaB and PTEN/AKT pathways and its association of ovarian CSC differentiation. Our data suggest that Twist1 may be an important regulator of 'stemness' in EOC cells. The regulation of MIR199A2/214 expression may be used as a potential therapeutic approach in EOC patients.

    View details for DOI 10.1038/onc.2010.111

    View details for Web of Science ID 000278835400009

    View details for PubMedID 20400975

  • Systems biology approaches to disease marker discovery DISEASE MARKERS Sharon, D., Chen, R., Snyder, M. 2010; 28 (4): 209-224

    Abstract

    Our understanding of human disease and potential therapeutics is improving rapidly. In order to take advantage of these developments it is important to be able to identify disease markers. Many new high-throughput genomics and proteomics technologies are being implemented to identify candidate disease markers. These technologies include protein microarrays, next-generation DNA sequencing and mass spectrometry platforms. Such methods are particularly important for elucidating the repertoire of molecular markers in the genome, transcriptome, proteome and metabolome of patients with diseases such as cancer, autoimmune diseases, and viral infections, resulting from the disruption of many biological pathways. These new technologies have identified many potential disease markers. These markers are expected to be valuable to achieve the promise of truly personalized medicine.

    View details for DOI 10.3233/DMA-2010-0707

    View details for Web of Science ID 000279321200003

    View details for PubMedID 20534906

  • NV-128, a Novel Isoflavone Derivative, Induces Caspase-independent Cell Death Through the Akt/Mammalian Target of Rapamycin Pathway CANCER Alvero, A. B., Montagna, M. K., Chen, R., Kim, K. H., Kyungjin, K., Visintin, I., Fu, H., Brown, D., Mor, G. 2009; 115 (14): 3204-3216

    Abstract

    Resistance to apoptosis is 1 of the key events that confer chemoresistance and is mediated by the overexpression of antiapoptotic proteins, which inhibit caspase activation. The objective of this study was to evaluate whether the activation of an alternative, caspase-independent cell death pathway could promote death in chemoresistant ovarian cancer cells. The authors report the characterization of NV-128 as an inducer of cell death through a caspase-independent pathway.Primary cultures of epithelial ovarian cancer (EOC) cells were treated with increasing concentration of NV-128, and the concentration that caused 50% growth inhibition (GI(50)) was determined using a proprietary assay. Apoptotic proteins were characterized by Western blot analyses, assays that measured caspase activity, immunohistochemistry, and flow cytometry. Protein-protein interactions were determined using immunoprecipitation. In vivo activity was measured in a xenograft mice model.NV-128 was able to induce significant cell death in both paclitaxel-resistant and carboplatin-resistant EOC cells with a GI(50) between 1 microg/mL and 5 microg/mL. Cell death was characterized by chromatin condensation but was caspase-independent. The activated pathway involved the down-regulation of phosphorylated AKT, phosphorylated mammalian target of rapamycin (mTOR), and phosphorylated ribosomal p70 S6 kinase, and the mitochondrial translocation of beclin-1 followed by nuclear translocation of endonuclease G.The authors characterized a novel compound, NV-128, which inhibits mTOR and promotes caspase-independent cell death. The current results indicated that inhibition of mTOR may represent a relevant pathway for the induction of cell death in cells resistant to the classic caspase-dependent apoptosis. These findings demonstrate the possibility of using therapeutic drugs, such as NV-128, which may have beneficial effects in patients with chemoresistant ovarian cancer.

    View details for DOI 10.1002/cncr.24397

    View details for Web of Science ID 000267813700008

    View details for PubMedID 19472400

  • Molecular phenotyping of human ovarian cancer stem cells unravel the mechanisms for repair and chemo-resistance CELL CYCLE Alvero, A. B., Chen, R., Fu, H., Montagna, M., Schwartz, P. E., Rutherford, T., Silasi, D., Steffensen, K. D., Waldstrom, M., Visintin, I., Mor, G. 2009; 8 (1): 158-166

    Abstract

    A major burden in the treatment of ovarian cancer is the high percentage of recurrence and chemoresistance. Cancer stem cells (CSCs) provide a reservoir of cells that can self-renew, can maintain the tumor by generating differentiated cells [non-stem cells (non-CSCs)] which make up the bulk of the tumor and may be the primary source of recurrence. We describe the characterization of human ovarian cancer stem cells (OCSCs). These cells have a distinctive genetic profile that confers them with the capacity to recapitulate the original tumor, proliferate with chemotherapy, and promote recurrence. CSC identified in EOC cells isolated form ascites and solid tumors are characterized by: CD44+, MyD88+, constitutive NFkappaB activity and cytokine and chemokine production, high capacity for repair, chemoresistance to conventional chemotherapies, resistance to TNFalpha-mediated apoptosis, capacity to form spheroids in suspension, and the ability to recapitulate in vivo the original tumor. Chemotherapy eliminates the bulk of the tumor but it leaves a core of cancer cells with high capacity for repair and renewal. The molecular properties identified in these cells may explain some of the unique characteristics of CSCs that control self-renewal and drive metastasis. The identification and cloning of human OCSCs can aid in the development of better therapeutic approaches for ovarian cancer patients.

    View details for Web of Science ID 000262137700025

    View details for PubMedID 19158483

  • Regulation of IKK beta by miR-199a affects NF-kappa B activity in ovarian cancer cells ONCOGENE Chen, R., Alvero, A. B., Silasi, D. A., Kelly, M. G., Fest, S., Visintin, I., Leiser, A., Schwartz, P. E., Rutherford, T., Mor, G. 2008; 27 (34): 4712-4723

    Abstract

    Cancer progression is an abnormal form of tissue repair characterized by chronic inflammation. IkappaB kinase-beta (IKKbeta) required for nuclear factor-kappaB (NF-kappaB) activation plays a critical role in this process. Using EOC cells isolated from malignant ovarian cancer ascites and solid tumors, we identified IKKbeta as a major factor promoting a functional TLR-MyD88-NF-kappaB pathway that confers to EOC cell the capacity to constitutively secrete proinflammatory/protumor cytokines and therefore promoting tumor progression and chemoresistance. Furthermore, we describe for the first time the identification of the microRNA hsa-miR-199a as a regulator of IKKbeta expression. Our study describes the property of ovarian cancer cells to enhance the inflammatory microenvironment as a result of the expression of an active IKKbeta pathway. Identification of these markers in patients' tumor samples may facilitate the adequate selection of treatment and open new venues for the development of effective therapy for chemoresistant ovarian cancers.

    View details for DOI 10.1038/onc.2008.112

    View details for Web of Science ID 000258236300009

    View details for PubMedID 18408758

  • Cancers take their Toll - the function and regulation of Toll-like receptors in cancer cells ONCOGENE Chen, R., Alvero, A. B., Silasi, D., Steffensen, K. D., Mor, G. 2008; 27 (2): 225-233

    Abstract

    Cancer could be deemed as an abnormal and uncontrolled tissue repair process. Therefore, it would not be surprising that factors that function in the tissue repair process, such as cytokines, chemokines, growth factors and Toll-like receptor (TLR) ligands, as well as growth signals for compensatory proliferation, would also be key factors in regulating and enhancing cancer progression. The TLR pathways, which play a critical role in tissue repair, are also key regulators in cancer progression as well as chemoresistance. TLRs serve as cell surface sensors that can initiate pathways leading to proliferation and chemoresistance; as well as mediators that are able to regulate the infiltrating immune cells to provide further support for cancer progression.

    View details for DOI 10.1038/sj.onc.1210907

    View details for Web of Science ID 000252163600009

    View details for PubMedID 18176604

  • Detection of cancer-related proteins in fresh-frozen ovarian cancer samples using laser capture microdissection. Methods in molecular biology (Clifton, N.J.) Silasi, D., Alvero, A. B., Mor, J., Chen, R., Fu, H., Montagna, M. K., Mor, G. 2008; 414: 35-45

    Abstract

    Tumors are heterogeneous structures that contain different cell populations. Laser capture microdissection (LCM) can be used to obtain pure cancer cells from fresh-frozen cancer tissue and the surrounded environment, thus providing an accurate snapshot of the tumor and its microenvironment in vivo. We describe a new approach to isolate pure cancer cell population and evaluate protein expression. The process includes immunocytochemistry, laser microdissection, and western blot analysis. Using this technique, we can detect proteins such as X-linked inhibitor of apoptosis protein (XIAP) and Fas ligand (FasL) with as little as 1000 cells.

    View details for PubMedID 18175810

  • Inflammation, cancer and chemoresistance: Taking advantage of the toll-like receptor signaling pathway AMERICAN JOURNAL OF REPRODUCTIVE IMMUNOLOGY Chen, R., Alvero, A. B., Silasi, D., Mor, G. 2007; 57 (2): 93-107

    Abstract

    The association between chronic inflammation and cancer has long been observed. Furthermore, NF-kappaB activation and the subsequent production of cytokines, chemokines, growth factors, and antiapoptotic proteins has been found to be involved in cancer progression and chemoresistance. However, the signals inducing NF-kappaB in cancer cells are still not well understood. Here, we reviewed the association between chronic inflammation and cancer, the role of NF-kappaB and its inhibitors as potential anticancer drugs, and Toll-like receptors as possible signal initiators for NF-kappaB activation and inflammation-induced carcinogenesis and chemoresistance. Furthermore, we propose that, the stimulation of Toll-like receptors by microbial components and/or endogenous ligands may represent the initial signal promoting a proinflammatory environment that will enhance tumor growth and chemoresistance.

    View details for DOI 10.1111/j.1600-0897.2006.00441.x

    View details for Web of Science ID 000243294400001

    View details for PubMedID 17217363

  • Trophoblast-macrophage interactions: a regulatory network for the protection of pregnancy AMERICAN JOURNAL OF REPRODUCTIVE IMMUNOLOGY Fest, S., Aldo, P. B., Abrahams, V. M., Visintin, I., Alvero, A., Chen, R., Chavez, S. L., Romero, R., Mor, G. 2007; 57 (1): 55-66

    Abstract

    Macrophages are one of the first immune cells observed at the implantation site. Their presence has been explained as the result of an immune response toward paternal antigens. The mechanisms regulating monocyte migration and differentiation at the implantation site are largely unknown. In the present study, we demonstrate that trophoblast cells regulate monocyte migration and differentiation. We propose that trophoblast cells 'educate' monocytes/macrophages to create an adequate environment that promote trophoblast survival.CD14(+) monocytes were isolated from peripheral blood using magnetic beads. Co-culture experiments were conducted using a two-chamber system. Monocytes were stimulated with lipopolysaccharide (LPS) and cytokine levels were determined using multiplex cytokine detecting assay.Trophoblast cells increase monocyte migration and induce a significant increase in the secretion and production of the pro-inflammatory cytokines [interleukin-6 (IL-6), IL-8, tumor necrosis factor-alpha] and chemokines (growth-related oncogen-alpha, monocyte chemoattractant protein-1, macrophage inflammatory protein-1beta, RANTES). Furthermore, the response of monocytes to LPS was different in monocytes pre-exposed to trophoblast cells.The results of this study suggest that trophoblast cells are able to recruit and successfully educate monocytes to produce and secrete a pro-inflammatory cytokine and chemokine profile supporting its growth and survival. Furthermore we demonstrate that trophoblast cells can modulate monocytes response to bacterial stimuli.

    View details for DOI 10.1111/j.1600-0897.2006.00446.x

    View details for Web of Science ID 000242888800008

    View details for PubMedID 17156192

  • MyD88 predicts chemoresistance to paclitaxel in epithelial ovarian cancer. Yale journal of biology and medicine Silasi, D., Alvero, A. B., Illuzzi, J., Kelly, M., Chen, R., Fu, H., Schwartz, P., Rutherford, T., Azodi, M., Mor, G. 2006; 79 (3-4): 153-163

    Abstract

    Early identification of chemoresistance in patients with ovarian cancer is of utmost importance in order to provide them with the most appropriate therapy. Recently, we described the expression of MyD88 in ovarian cancer cells that were resistant to the cytotoxic agent paclitaxel. In addition to chemoresistance, in MyD88 positive ovarian cancer cells, paclitaxel stimulates growth and production of proinflammatory cytokines. The objective of this study was to determine the correlation of MyD88 expression in primary and recurrent epithelial ovarian cancers with the response to carboplatin and paclitaxel combination chemotherapy.Tumors are heterogeneous structures that contain different cell populations, thus rendering the identification of specific tumor markers difficult. Using laser capture microdissection, pure cancer cells were isolated from ovarian malignant tumors that were obtained from 20 patients at the time of surgery. The microdissected cells were evaluated for the expression of MyD88, FasL, and XIAP by western blot analysis.Protein expression was observed in samples containing as low as 500 cells. The results were correlated with the clinical course of those patients. It was evident that MyD88 expression in ovarian cancer cells accurately predicts a poor response to paclitaxel chemotherapy as shown by a short progression-free interval and overall survival.We describe for the first time a molecular approach to identify paclitaxel chemoresistance. Toxicity from agents without therapeutic benefit can be avoided by identifying those patients who will not respond to a specific agent. Molecular markers will enable us to design individualized treatments and improve overall survival.

    View details for PubMedID 17940625

  • TLR-4 signaling promotes tumor growth and paclitaxel chemoresistance in ovarian cancer CANCER RESEARCH Kelly, M. G., Alvero, A. B., Chen, R., Silasi, D. A., Abrahams, V. M., Chan, S., Visintin, I., Rutherford, T., Mor, G. 2006; 66 (7): 3859-3868

    Abstract

    Evidence suggests that an inflammatory profile of cytokines and chemokines persisting at a particular site would lead to the development of a chronic disease. Recent studies implicate bacterial infection as one possible link between inflammation and carcinogenesis; however, the crucial molecular pathways involved remain unknown. We hypothesized that one possible upstream signaling pathway leading to inflammation in carcinogenesis may be mediated by Toll-like receptors (TLR). We describe for the first time an adaptive mechanism acquired by ovarian cancer cells that allows them to promote a proinflammatory environment and develop chemoresistance. We propose that the TLR-4-MyD88 signaling pathway may be a risk factor for developing cancer and may represent a novel target for the development of biomodulators. Our work explains how bacterial products, such as lipopolysaccharide, can promote, directly from the tumor, the production of proinflammatory cytokines and the enhancement of tumor survival. In addition, we provide new evidence that links TLR-4 signaling, inflammation, and chemoresistance in ovarian cancer cells.

    View details for DOI 10.1158/0008-5472.CAN-05-3948

    View details for Web of Science ID 000236657800067

    View details for PubMedID 16585214

  • Simultaneous detection of microsatellite repeats and SNPs in the macrophage migration inhibitory factor (MIF) gene by thin-film biosensor chips and application to rural field studies NUCLEIC ACIDS RESEARCH Zhong, X. B., Leng, L., Beitin, A., Chen, R., McDonald, C., Hsiao, B., Jenison, R. D., Kang, I., Park, S. H., Lee, A., Gregersen, P., Thuma, P., Bray-Ward, P., WARD, D. C., Bucala, R. 2005; 33 (13)

    Abstract

    Microsatellite repeat and single nucleotide polymorphisms (SNPs) are abundant sources of genetic variation, but existing methodologies cannot simultaneously detect these variants in a facile or inexpensive way. We describe herein a thin-film biosensor chip based on an allele-discriminating oligonucleotide array that enables genotyping for both microsatellite repeats and SNPs in a single analysis. We validated this methodology for the functionally polymorphic -794 CATT(5-8) repeat and -173 G/C SNP present in the promoter of the human gene for macrophage migration inhibitory factor (MIF). In a comparison of 30 samples collected at a rural hospital in Zambia, we observed a 100% concordance for both the CATT repeat and G/C SNP between the biosensor methodology and the conventional capillary electrophoresis. The biosensor chips are low in cost and once printed, they are robust and require no instrumentation for analysis. When combined with multiple displacement amplification, this methodology can be utilized in primitive settings for the genotyping of nanogram quantities of DNA present in blood, dried and stored on filter paper samples. We applied this methodology to a field study of MIF genotype in children with malaria, and provide first evidence for a potential association between MIF alleles and malaria infection. We also present data supporting significant population stratification of the low- versus high-expression forms of MIF that may bear on the role of this gene in infectious diseases.

    View details for DOI 10.1093/nar/gni.123

    View details for Web of Science ID 000231516900051

    View details for PubMedID 16077028

  • Characterization and transcriptional profiles of two rice MADS-box genes. Plant science : an international journal of experimental plant biology Jia, H., Chen, R., Cong, B., Cao, K., Sun, C., Luo, D. 2000; 155 (2): 115-122

    Abstract

    The plant MADS-box gene family plays a key role in plant development, especially in flower development. We designed degenerate primer according to the MADS-box conserved region and isolated two cDNA from rice, FDRMADS6 and FDRMADS7, which are homologous to AP1. RT-PCR expression analyses by using total RNA isolated from root, shoot and flower showed that the FDRMADS6 transcript was detectable only in flower while FDRMADS7 was expressed in all three tissues. In situ hybridization experiments indicated that at the early stage of rice flower development, the transcripts of FDRMADS6 and FDRMADS7 were detected in the spikelet apical meristem, which were same as AP1. At the late stage, when flower organ primordia started differentiating, the expression of FDRMADS6 appeared to be specifically localized in developing stamens and the pistil primordia, while the transcripts of FDRMADS7 were detectable abundantly throughout the organ primordia. Our results suggest the two MADS-box genes may be members of the AP1 family, but may have different functions.

    View details for PubMedID 10814814

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