Chinnaiyan, Arul M.

Open Protocols

Protocol Name Investigatory Role Biomarkers Data Collections
Characterization of SPINK1 in Prostate Cancer (A sub-study of a single biomarker) Leading 1 0
Development and Validation of Tissue Microarray Technology to Evaluate Molecular Alterations in Cancer. IRBMED# 2000-0108 Leading 0 0
Development of a novel, urine-based molecular assay for prediction of progression, recurrence, and need for definitive therapy on active surveillance for prostate cancer Leading 0 0
Development of Breast Cancer Biomarkers Using DNA and Protein Microarray Technologies Leading 0 0
Discovery of Novel Gene Elements Associated with Prostate Cancer Progression Leading 8 0
EDRN Pre-Validation of Metabolic Biomarkers of Prostate Cancer: Follow up EDRN Challenge Coordinating 0 0
EDRN Pre-Validation of Multiplex Biomarker in Urine Coordinating 2 0
Evaluation of tissue biomarker of Urologic cancer, including prostate, bladder and kidneys using surplus human tissues Leading 0 0
Identification of Novel Cancer Biomarkers in Serum and Urine Specimens Leading 3 0
Molecular Profiling of Cancer: Identification and Characterization of Candidate Biomarkers and Regulatory Genes. IRBMED # 2001-0155 Leading 0 0
Pre-Validation of Metabolomic Biomarkers of Prostate Cancer Leading 0 0
Pre-validation of TMPRSS2:ERG+PCA3 risk models for men on active surveillance Leading 3 0
Prostate Biopsy Clinical Database/Tissue Bank IRBMED# 2004-0442 Involved 0 0
Tumor Profiling through High-throughput Sequencing Leading 0 0

Closed Protocols

Protocol Name Investigatory Role Biomarkers Data Collections
EDRN-WHI Pre-Clinical Colon Ca Specimens Involved 0 1
PCA3 Reference Set Application: Arul Chinnaiyan (2020) Leading 0 0


Publication NamePubMed IDJournal
A first-generation multiplex biomarker analysis of urine for the early detection of prostate cancer. 18245462 Cancer Res
A polycomb repression signature in metastatic prostate cancer predicts cancer outcome. 18006806 Cancer Res
Analysis of the androgen receptor-regulated lncRNA landscape identifies a role for ARLNC1 in prostate cancer progression. 29808028 Nat Genet
Antibody-based detection of ERG rearrangement-positive prostate cancer. 20651988 Neoplasia
Antibody-based detection of ERG rearrangements in prostate core biopsies, including diagnostically challenging cases: ERG staining in prostate core biopsies. 22849743 Arch Pathol Lab Med
Assessment of long-term outcomes associated with urinary prostate cancer antigen 3 and TMPRSS2:ERG gene fusion at repeat biopsy. 26280815 Cancer
Association of ERG/PTEN status with biochemical recurrence after radical prostatectomy for clinically localized prostate cancer. 30291535 Med Oncol
Autoantibody profiles reveal ubiquilin 1 as a humoral immune response target in lung adenocarcinoma. 17409457 Cancer Res
Autoantibody signatures in prostate cancer. 16177248 N Engl J Med
Beyond PSA: the next generation of prostate cancer biomarkers. 22461644 Sci Transl Med
Cancer immunomics: using autoantibody signatures in the early detection of prostate cancer. 16678056 Urol Oncol
Characterization of KRAS rearrangements in metastatic prostate cancer. 22140652 Cancer Discov
Characterization of the EZH2-MMSET histone methyltransferase regulatory axis in cancer. 23159737 Mol Cell
Characterization of TMPRSS2-ETS gene aberrations in androgen-independent metastatic prostate cancer. 18483239 Cancer Res
Characterization of TMPRSS2:ETV5 and SLC45A3:ETV5 gene fusions in prostate cancer. 18172298 Cancer Res
Classification and selection of biomarkers in genomic data using LASSO. 16046820 J Biomed Biotechnol
Combining urinary detection of TMPRSS2:ERG and PCA3 with serum PSA to predict diagnosis of prostate cancer. 21600800 Urol Oncol
Comprehensive assessment of TMPRSS2 and ETS family gene aberrations in clinically localized prostate cancer. 17334343 Mod Pathol
Concurrent AURKA and MYCN gene amplifications are harbingers of lethal treatment-related neuroendocrine prostate cancer. 23358695 Neoplasia
Concurrent nuclear ERG and MYC protein overexpression defines a subset of locally advanced prostate cancer: Potential opportunities for synergistic targeted therapeutics. 27159573 Prostate
Coordinated regulation of polycomb group complexes through microRNAs in cancer. 21840484 Cancer Cell
Correlation of urine TMPRSS2:ERG and PCA3 to ERG+ and total prostate cancer burden. 23086769 Am J Clin Pathol
Deep sequencing reveals distinct patterns of DNA methylation in prostate cancer. 21724842 Genome Res
Detection of somatic copy number alterations in cancer using targeted exome capture sequencing. 22131877 Neoplasia
Development and Validation of an 18-Gene Urine Test for High-Grade Prostate Cancer. 38635241
Development of Peptidomimetic Inhibitors of the ERG Gene Fusion Product in Prostate Cancer. 28344039 Cancer Cell
Distinct classes of chromosomal rearrangements create oncogenic ETS gene fusions in prostate cancer. 17671502 Nature
Distinct structural classes of activating FOXA1 alterations in advanced prostate cancer. 31243372 Nature
Epigenetic repression of miR-31 disrupts androgen receptor homeostasis and contributes to prostate cancer progression. 23233736 Cancer Res
Epigenomic alterations in localized and advanced prostate cancer. 23555183 Neoplasia
Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer. 22610119 Nat Genet
Expressed pseudogenes in the transcriptional landscape of human cancers. 22726445 Cell
From sequence to molecular pathology, and a mechanism driving the neuroendocrine phenotype in prostate cancer. 22553170 J Pathol
Functionally recurrent rearrangements of the MAST kinase and Notch gene families in breast cancer. 22101766 Nat Med
Gene fusions associated with recurrent amplicons represent a class of passenger aberrations in breast cancer. 22952423 Neoplasia
Genomic Hallmarks and Structural Variation in Metastatic Prostate Cancer. 30033370 Cell
Humoral immune response to alpha-methylacyl-CoA racemase and prostate cancer. 15173267 J Natl Cancer Inst
Humoral response profiling reveals pathways to prostate cancer progression. 18077443 Mol Cell Proteomics
Identification and Validation of PCAT14 as Prognostic Biomarker in Prostate Cancer. 27566105 Neoplasia
Identification of functionally active, low frequency copy number variants at 15q21.3 and 12q21.31 associated with prostate cancer risk. 22496589 Proc Natl Acad Sci U S A
Identification of recurrent NAB2-STAT6 gene fusions in solitary fibrous tumor by integrative sequencing. 23313952 Nat Genet
Inactivation of CDK12 Delineates a Distinct Immunogenic Class of Advanced Prostate Cancer. 29906450 Cell
Inflammation-Induced Oxidative Stress Mediates Gene Fusion Formation in Prostate Cancer. 27926866 Cell Rep
Integrating biomedical knowledge to model pathways of prostate cancer progression. 17495538 Cell Cycle
Integrative analysis of genomic aberrations associated with prostate cancer progression. 17804737 Cancer Res
Integrative clinical genomics of metastatic cancer. 28783718 Nature
Integrative genomic and proteomic analysis of prostate cancer reveals signatures of metastatic progression. 16286247 Cancer Cell
Integrative genomics analysis reveals silencing of beta-adrenergic signaling by polycomb in prostate cancer. 17996646 Cancer Cell
Integrative molecular concept modeling of prostate cancer progression. 17173048 Nat Genet
Mechanistic rationale for inhibition of poly(ADP-ribose) polymerase in ETS gene fusion-positive prostate cancer. 21575865 Cancer Cell
MiPanda: A Resource for Analyzing and Visualizing Next-Generation Sequencing Transcriptomics Data. 30268942 Neoplasia
Molecular characterization of TMPRSS2-ERG gene fusion in the NCI-H660 prostate cancer cell line: a new perspective for an old model. 17401460 Neoplasia
Molecular markers of prostate cancer. 17138135 Urol Oncol
MyProstateScore in men considering repeat biopsy: validation of a simple testing approach. 36585434 Prostate Cancer Prostatic Dis
New strategies in prostate cancer: translating genomics into the clinic. 23248095 Clin Cancer Res
Next generation sequencing of prostate cancer from a patient identifies a deficiency of methylthioadenosine phosphorylase, an exploitable tumor target. 22252602 Mol Cancer Ther
Noninvasive detection of TMPRSS2:ERG fusion transcripts in the urine of men with prostate cancer. 17059688 Neoplasia
Novel dual-color immunohistochemical methods for detecting ERG-PTEN and ERG-SPINK1 status in prostate carcinoma. 23348902 Mod Pathol
Oncogenic Role of THOR, a Conserved Cancer/Testis Long Non-coding RNA. 29245011 Cell
Oncomine 3.0: genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles. 17356713 Neoplasia
Pathway-directed weighted testing procedures for the integrative analysis of gene expression and metabolomic data. 22497771 Genomics
Personalized oncology through integrative high-throughput sequencing: a pilot study. 22133722 Sci Transl Med
Precision oncology in the age of integrative genomics. 29319699 Nat Biotechnol
Rearrangements of the RAF kinase pathway in prostate cancer, gastric cancer and melanoma. 20526349 Nat Med
Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. 16254181 Science
Role of the TMPRSS2-ERG gene fusion in prostate cancer. 18283340 Neoplasia
Role of transcriptional corepressor CtBP1 in prostate cancer progression. 23097625 Neoplasia
SLC45A3-ELK4 chimera in prostate cancer: spotlight on cis-splicing. 22787087 Cancer Discov
Somatic Bi-allelic Loss of TSC Genes in Eosinophilic Solid and Cystic Renal Cell Carcinoma. 29941307 Eur Urol
SPOP Mutation Drives Prostate Tumorigenesis In Vivo through Coordinate Regulation of PI3K/mTOR and AR Signaling. 28292441 Cancer Cell
Systematic, evidence-based discovery of biomarkers at the NCI. 22868876 Clin Exp Metastasis
TACO produces robust multisample transcriptome assemblies from RNA-seq. 27869815 Nat Methods
The emergence of lncRNAs in cancer biology. 22096659 Cancer Discov
The enzymatic activity of apoptosis-inducing factor supports energy metabolism benefiting the growth and invasiveness of advanced prostate cancer cells. 23118229 J Biol Chem
The Landscape of Circular RNA in Cancer. 30735636 Cell
The mutational landscape of lethal castration-resistant prostate cancer. 22722839 Nature
The neuronal repellent SLIT2 is a target for repression by EZH2 in prostate cancer. 20622896 Oncogene
Therapeutic targeting of SPINK1-positive prostate cancer. 21368222 Sci Transl Med
TMPRSS2-ERG-mediated feed-forward regulation of wild-type ERG in human prostate cancers. 21676887 Cancer Res
TMPRSS2:ERG fusion-associated deletions provide insight into the heterogeneity of prostate cancer. 16951139 Cancer Res
TMPRSS2:ERG gene fusion associated with lethal prostate cancer in a watchful waiting cohort. 17237811 Oncogene
TMPRSS2:ETV4 gene fusions define a third molecular subtype of prostate cancer. 16585160 Cancer Res
Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression. 21804560 Nat Biotechnol
Transcriptomic heterogeneity in multifocal prostate cancer. 30385730 JCI Insight
Urine TMPRSS2:ERG fusion transcript stratifies prostate cancer risk in men with elevated serum PSA. 21813756 Sci Transl Med
Whole transcriptome amplification for gene expression profiling and development of molecular archives. 16611408 Neoplasia


Cancer Genomics, Biomarkers, Proteomics, Bioinformatics
The Chinnaiyan laboratory has focused on functional genomic, proteomic, metabolomic, and bioinformatics approaches to study cancer for the purposes of understanding tumor biology as well as to discover clinical biomarkers. He and his collaborators have characterized a number of biomarkers of prostate cancer including AMACR, EZH2, hepsin, the sarcosine metabolite, and TMPRSS2-ETS gene fusions. AMACR is being used clinically across the country in the assessment of cancer in prostate needle biopsies. The Chinnaiyan laboratory is a fertile training ground for the next generation of translational researchers having already impacted the careers of over 20 graduate students and 40 research fellows.

The landmark study thus far from Dr. Chinnaiyan’s laboratory is the discovery of TMPRSS2-ETS gene fusions in a majority of prostate cancers. This discovery was made using a bioinformatics approach on tumor gene expression data. TMPRSS2-ETS gene fusions are specific markers of prostate cancer as well as presumably function as rational targets for this disease. Gene fusions and translocations such as BCR-ABL in CML were thought to primarily be the basis of hematologic malignancies and sarcomas. The finding of recurrent gene fusions in prostate cancer potentially redefines the molecular basis of this disease as well as other common epithelial cancers. The team involved with these studies was awarded the 2007 AACR Team Science Award. The Chinnaiyan lab is focused on translating the prostate cancer gene fusion discovery into better diagnostics and therapies for prostate cancer.

To update protocols, publications, biomarkers, or science data, please contact the Data Management and Coordinating Center.

Photograph of Chinnaiyan, Arul M.
University of Michigan
M.D., Ph.D.
Person ID
To update contact information, please visit the Data Management and Coordinating Center .