Positions

Overview

  • My research focus is on understanding the molecular basis of cancer using integrative genomic, epigenetic and proteomic approach. Our groups translational cancer research involves transferring the basic research discoveries to develop disease detection markers of developing therapy for the identified targets. I have worked extensively in the area of solid tumor genomics, biomarker discovery, biology, and therapeutic targeting.
    Our group’s research helps better understand the molecular alterations during the initiation and progression of multiple human malignancies. We perform integrative analysis to identify the best targets and work towards developing agents/drugs for specific causative targets. It is expected that the insights gained from our research will aid in the development of new strategies for the cancer therapy. I would like to develop multiple collaborations in order to hasten the pace of cancer research and discovery by team science approach. In order to enhance the speed of the cancer research/target discovery, we built a discovery platform called UALCAN (http://ualcan.path.uab.edu) for cancer genomic and proteomic data analysis, making cancer research a worldwide team effort. Some of the candidate therapeutic targets that I have identified include Histone Methyltransferase EZH2, AMACR, TPD52, MTA1, ERG gene fusion, SPINK1, CtBP1, RAF kinase gene fusions, GOLM1, GLYATL1 and JAGGED1 in prostate cancer, GATA3, AGTR1, EZH2, CCN6 (WISP3) in breast cancer and MTHFD1L, PAICS and PAK4 in bladder cancer among others. I have patents for targeting histone methyltransferase EZH2 and MMSET.
    My research has resulted in prolific output of publications and currently I have published 118 articles and many of them in high impact factor (IF), prestigious journals including Science, Nature, New England Journal of Medicine, Nature Medicine, Cancer Cell, PNAS, Cancer Research, Oncogene among others. I am a highly cited researcher and our work has been cited by leading cancer researchers and biologists worldwide and have received over 30,150 citations with an h-Index of 62. I was part of the team that won the Inaugural American Association for Cancer Research (AACR) Team Science Award for this discovery in 2007.
    I am actively involved in teaching and Co-Director of the Cancer Biology Theme of UAB-Graduate Biomedical Sciences (GBS). I also direct the GBS-728, Cancer Genomics, Epigenetics and Therapy, as the director of this course. This course is designed to educate the students on the basic and novel concepts to understand cancer. I also organize the Translational Research Group Meeting, a tri-Departmental interactive seminar series.
  • Selected Publications

    Academic Article

    Year Title Altmetric
    2020 PRDM16 suppresses HIF-targeted gene expression in kidney cancer. 2020
    2020 Dysregulation of de novo nucleotide biosynthetic pathway enzymes in cancer and targeting opportunities 2020
    2020 14-3-3 proteins protect AMPK-phosphorylated ten-eleven translocation-2 (TET2) from PP2A-mediated dephosphorylation 2020
    2020 Therapeutically actionable PAK4 is amplified, overexpressed, and involved in bladder cancer progression 2020
    2019 Pan-cancer molecular subtypes revealed by mass-spectrometry-based proteomic characterization of more than 500 human cancers 2019
    2019 Expression and Role of Methylenetetrahydrofolate Dehydrogenase 1 Like (MTHFD1L) in Bladder Cancer 2019
    2019 MTHFD1L, A Folate Cycle Enzyme, Is Involved in Progression of Colorectal Cancer 2019
    2019 Pseudogene Associated Recurrent Gene Fusion in Prostate Cancer 2019
    2019 Characterization of glycine-N-acyltransferase like 1 (GLYATL1) in prostate cancer 2019
    2019 Large-scale profiling of serum metabolites in African American and European American patients with bladder cancer reveals metabolic pathways associated with patient survival 2019
    2019 Inhibition of Hedgehog signaling reprograms the dysfunctional immune microenvironment in breast cancer 2019
    2019 Genome-wide DNA methylation encodes cardiac transcriptional reprogramming in human ischemic heart failure 2019
    2019 Molecular correlates of metastasis by systematic pan-cancer analysis across the cancer genome atlas 2019
    2019 The combined survival effect of codon 72 polymorphisms and p53 somatic mutations in breast cancer depends on race and molecular subtype 2019
    2019 Characterization of glycine-N-acyltransferase like 1 (GLYATL1) in prostate cancer 2019
    2019 Ferritin light chain confers protection against sepsis-induced inflammation and organ injury 2019
    2019 Integrative epigenetic and gene expression analysis of renal tumor progression to metastasis 2019
    2018 Wnt receptor Frizzled 8 is a target of ERG in prostate cancer 2018
    2018 A Role for De Novo Purine Metabolic Enzyme PAICS in Bladder Cancer Progression 2018
    2018 Gene Expression Profiling of Advanced Penile Squamous Cell Carcinoma Receiving Cisplatin-based Chemotherapy Improves Prognostication and Identifies Potential Therapeutic Targets 2018
    2018 miR-34a regulates expression of the stathmin-1 oncoprotein and prostate cancer progression 2018
    2018 214 High fat diet accelerates UVB-induced development of basal cell and squamous cell carcinoma in Ptch+/-/SKH-1 mice 2018
    2018 Histone methyltransferase ezh2: A therapeutic target for ovarian cancer 2018
    2018 Chemotherapy induces secretion of exosomes loaded with heparanase that degrades extracellular matrix and impacts tumor and host cell behavior 2018
    2017 Prostate Cancer: An Update on Molecular Pathology with Clinical Implications 2017
    2017 Prostate cancer imaging and biomarkers guiding safe selection of active surveillance 2017
    2017 UALCAN: A Portal for Facilitating Tumor Subgroup Gene Expression and Survival Analyses 2017
    2017 Development of Peptidomimetic Inhibitors of the ERG Gene Fusion Product in Prostate Cancer 2017
    2017 Erratum: Development of Peptidomimetic Inhibitors of the ERG Gene Fusion Product in Prostate Cancer (Cancer Cell (2017) 31(4) (532–548.e7)(S1535610817300600)(10.1016/j.ccell.2017.02.017)) 2017
    2017 Amplified centrosomes and mitotic index display poor concordance between patient tumors and cultured cancer cells 2017
    2017 Loss of RUNX3 expression is an independent adverse prognostic factor in diffuse large B-cell lymphoma 2017
    2017 Expression and Role of PAICS, a De Novo Purine Biosynthetic Gene in Prostate Cancer 2017
    2016 MicroRNA-101 regulated transcriptional modulator SUB1 plays a role in prostate cancer 2016
    2016 Genomic and Epigenomic Alterations in Cancer 2016
    2016 Divergent clonal evolution of castration-resistant neuroendocrine prostate cancer 2016
    2016 Erratum: TRIP13 promotes error-prone nonhomologous end joining and induces chemoresistance in head and neck cancer (Nature Communications (2014) 5 (4527) DOI: 10.1038/ncomms5527) 2016
    2016 Association between Hepatitis C Virus Infection, p53 Phenotypes, and Gene Variants of Adenomatous Polyposis Coli in Hepatocellular Carcinomas. 2016
    2016 Cancer mediates effector T cell dysfunction by targeting microRNAs and EZH2 via glycolysis restriction 2016
    2015 Amplified centrosomes may underlie aggressive disease course in pancreatic ductal adenocarcinoma 2015
    2015 Cancer: The kinase activity of the Ser/Thr kinase BUB1 promotes TGF-β signaling 2015
    2015 Role and regulation of coordinately expressed de novo purine biosynthetic enzymes PPAT and PAICS in lung cancer 2015
    2014 TRIP13 promotes error-prone nonhomologous end joining and induces chemoresistance in head and neck cancer 2014
    2014 The miR-124-prolyl hydroxylase P4HA1-MMP1 axis plays a critical role in prostate cancer progression 2014
    2013 Targeting the link between late pregnancy and breast cancer 2013
    2013 Prostate cancer genomics: Progress and promise 2013
    2013 Erratum: Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression (Nature (2009) 457 (910-914) DOI: 10.1038/nature07762) 2013
    2013 Erratum to Mechanistic rationale for inhibition of poly(ADP-Ribose) polymerase in ETS gene fusion-positive prostate cancer [Cancer Cell, 19 (2011) 664-678] 2013
    2013 Characterization of the EZH2-MMSET Histone Methyltransferase Regulatory Axis in Cancer 2013
    2012 The enzymatic activity of apoptosis-inducing factor supports energy metabolism benefiting the growth and invasiveness of advanced prostate cancer cells. 2012
    2012 Role of dutasteride in pre-clinical ETS fusion-positive prostate cancer models 2012
    2012 Inhibition of histone methylation arrests ongoing graft-versus-host disease in mice by selectively inducing apoptosis of alloreactive effector T cells 2012
    2012 Role of transcriptional corepressor CtBP1 in prostate cancer progression 2012
    2011 The tumor suppressor gene rap1GAP is silenced by miR-101-mediated EZH2 overexpression in invasive squamous cell carcinoma 2011
    2011 Coordinated Regulation of Polycomb Group Complexes through microRNAs in Cancer 2011
    2011 TMPRSS2-ERG-mediated feed-forward regulation of wild-type ERG in human prostate cancers 2011
    2011 Targeting of microRNA-142-3p in dendritic cells regulates endotoxin-induced mortality 2011
    2011 Characterization of KRAS rearrangements in metastatic prostate cancer 2011
    2011 Mechanistic Rationale for Inhibition of Poly(ADP-Ribose) Polymerase in ETS Gene Fusion-Positive Prostate Cancer 2011
    2011 Therapeutic targeting of SPINK1-positive prostate cancer 2011
    2010 The neuronal repellent SLIT2 is a target for repression by EZH2 in prostate cancer 2010
    2010 Letter to the editor 2010
    2010 Rearrangements of the RAF kinase pathway in prostate cancer, gastric cancer and melanoma 2010
    2010 An Integrated Network of Androgen Receptor, Polycomb, and TMPRSS2-ERG Gene Fusions in Prostate Cancer Progression 2010
    2010 Antibody-based detection of ERG rearrangement-positive prostate cancer 2010
    2010 Chlorpromazine induced cataract in a young patient with schizophrenia. 2010
    2009 Induced chromosomal proximity and gene fusions in prostate cancer 2009
    2009 An integrative approach to reveal driver gene fusions from paired-end sequencing data in cancer 2009
    2009 Proteomic interrogation of androgen action in prostate cancer cells reveals roles of aminoacyl tRNA synthetases 2009
    2009 AGTR1 overexpression defines a subset of breast cancer and confers sensitivity to losartan, an AGTR1 antagonist 2009
    2009 Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression 2009
    2009 Tomlins et al. reply 2009
    2009 RHAMM (CD168) is overexpressed at the protein level and may constitute an immunogenic antigen in advanced prostate cancer disease 2009
    2008 Genomic loss of microRNA-101 leads to overexpression of histone methyltransferase EZH2 in cancer 2008
    2008 Repression of E-cadherin by the polycomb group protein EZH2 in cancer 2008
    2008 A fluorescence in situ hybridization screen for E26 transformation-specific aberrations: Identification of DDX5-ETV4 fusion protein in prostate cancer 2008
    2008 The Role of SPINK1 in ETS Rearrangement-Negative Prostate Cancers 2008
    2008 Characterization of TMPRSS2:ETV5 and SLC45A3:ETV5 gene fusions in prostate cancer 2008
    2008 Golgi protein GOLM1 is a tissue and urine biomarker of prostate cancer 2008
    2008 Inhibition of CCN6 (Wnt-1-induced signaling protein 3) down-regulates E-cadherin in the breast epithelium through induction of snail and ZEB1 2008
    2008 Role of the TMPRSS2-ERG gene fusion in prostate cancer 2008
    2007 Tumor cell-selective regulation of NOXA by c-MYC in response to proteasome inhibition 2007
    2007 A polycomb repression signature in metastatic prostate cancer predicts cancer outcome 2007
    2007 Integrative Genomics Analysis Reveals Silencing of β-Adrenergic Signaling by Polycomb in Prostate Cancer 2007
    2007 Distinct classes of chromosomal rearrangements create oncogenic ETS gene fusions in prostate cancer 2007
    2007 Role of epidermal growth factor receptor degradation in gemcitabine-mediated cytotoxicity 2007
    2007 Effect of epidermal growth factor receptor inhibitor class in the treatment of head and neck cancer with concurrent radiochemotherapy in vivo 2007
    2007 Autoantibody profiles reveal ubiquilin 1 as a humoral immune response target in lung adenocarcinoma 2007
    2007 Molecular concepts analysis links tumors, pathways, mechanisms, and drugs 2007
    2007 Oncomine 3.0: Genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles 2007
    2006 Ataxia telangiectasia mutated down-regulates phospho-extracellular signal-regulated kinase 1/2 via activation of MKP-1 in response to radiation 2006
    2006 Selection and cloning of poly(rC)-binding protein 2 and Raf kinase inhibitor protein RNA activators of 2′,5′-oligoadenylate synthetase from prostate cancer cells 2006
    2006 Differential proteomic alterations between localised and metastatic prostate cancer 2006
    2006 A systems approach to model metastatic progression 2006
    2006 Enhancing the antitumor activity of ErbB blockade with histone deacetylase (HDAC) inhibition 2006
    2006 Nod1 acts as an intracellular receptor to stimulate chemokine production and neutrophil recruitment in vivo 2006
    2006 ADAM15 disintegrin is associated with aggressive prostate and breast cancer disease 2006
    2006 Defining aggressive prostate cancer using a 12-gene model 2006
    2005 Identification of GATA3 as a breast cancer prognostic marker by global gene expression meta-analysis 2005
    2005 Integrative genomic and proteomic analysis of prostate cancer reveals signatures of metastatic progression 2005
    2005 Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer 2005
    2005 Autoantibody signatures in prostate cancer 2005
    2005 Probabilistic model of the human protein-protein interaction network 2005
    2005 The unfolded protein response modulates toxicity of the expanded glutamine androgen receptor 2005
    2005 α-methylacyl-CoA racemase protein expression is associated with the degree of differentiation in breast cancer using quantitative image analysis 2005
    2005 Mechanisms of enhanced radiation response following epidermal growth factor receptor signaling inhibition by erlotinib (Tarceva) 2005
    2005 The polycomb group protein EZH2 impairs DNA repair in breast epithelial cells 2005
    2004 Androgen-independent prostate cancer is a heterogeneous group of diseases: Lessons from a rapid autopsy program 2004
    2004 JAGGED1 expression is associated with prostate cancer metastasis and recurrence 2004
    2004 Natural antibodies sustain differentiation and maturation of human dendritic cells 2004
    2004 Overexpression, amplification, and androgen regulation of TPD52 in prostate cancer. Rubin, MA, Varambally S, Beroukhim R, Tomlins SA, Rhodes DR, Paris PL, Hofer, MD, Storz-Schweizer M, Kuefer R, Fletcher JA, Hsi BL, Byrne JA, Pienta KJ, Collins C, Sellers WR, Chinnaiyan AM, Department of Pathology, Brigham and Women's Hospital, Boston, MA. 2004
    2004 Overexpression, amplification, and androgen regulation of TPD52 in prostate cancer 2004
    2004 Natural human polyreactive IgM induce apoptosis of lymphoid cell lines and human peripheral blood mononuclear cells 2004
    2004 The Role of Metastasis-Associated Protein 1 in Prostate Cancer Progression 2004
    2004 C5a-Induced Gene Expression in Human Umbilical Vein Endothelial Cells 2004
    2003 EZH2 is a marker of aggressive breast cancer and promotes neoplastic transformation of breast epithelial cells 2003
    2002 Changes in differential gene expression because of warm ischemia time of radical prostatectomy specimens 2002
    2002 The polycomb group protein EZH2 is involved in progression of prostate cancer 2002
    2002 Autoantibodies to heat shock protein 90 in the human natural antibody repertoire 2002
    2002 α-methylacyl coenzyme A racemase as a tissue biomarker for prostate cancer 2002
    2002 Molecular cross-talk between the TRAIL and interferon signaling pathways 2002
    2002 α-Methylacyl-CoA racemase: Expression levels of this novel cancer biomarker depend on tumor differentiation 2002
    2001 Profiling of cancer cells using protein microarrays: Discovery of novel radiation-regulated proteins 2001
    2001 Delineation of prognostic biomarkers in prostate cancer 2001
    2001 Variable Sensitivity of Lymphoblastoid Cells to Apoptosis Induced by Viscum album Qu FrF, a Therapeutic Preparation of Mistletoe Lectin 2001
    2000 Natural Antibodies to Factor VIII 2000
    1999 Catalytic activity of antibodies against factor VIII in patients with hemophilia A 1999
    1998 Refolding of native and recombinant chicken riboflavin carrier (or binding) protein : evidence for the formation of non-native intermediates during the generation of active protein 1998
    1998 Identification and characterization of receptors for riboflavin carrier protein in the chicken oocyte 1998
    1996 Hyperexpression of Chicken Riboflavin Carrier Protein: Antibodies to the Recombinant Protein Curtail Pregnancy in Rodents 1996

    Education And Training

  • University Of Michigan Pathology, Postdoctoral Research 2003
  • Hôpital Broussais, INSERM Unit, Postdoctoral Research 2000
  • Doctor of Philosophy in Biochemistry, Indian Institute of Science 1997
  • Master of Science in Biochemistry, Manipal University 1991
  • Bachelor of Science or Mathematics in Chemistry, Mangalore University 1989
  • Full Name

  • Sooryanarayana Varambally