1
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Xiao L, Parolia A, Qiao Y, Bawa P, Eyunni S, Mannan R, Carson SE, Chang Y, Wang X, Zhang Y, Vo JN, Kregel S, Simko SA, Delekta AD, Jaber M, Zheng H, Apel IJ, McMurry L, Su F, Wang R, Zelenka-Wang S, Sasmal S, Khare L, Mukherjee S, Abbineni C, Aithal K, Bhakta MS, Ghurye J, Cao X, Navone NM, Nesvizhskii AI, Mehra R, Vaishampayan U, Blanchette M, Wang Y, Samajdar S, Ramachandra M, Chinnaiyan AM. Author Correction: Targeting SWI/SNF ATPases in enhancer-addicted prostate cancer. Nature 2024:10.1038/s41586-024-07393-1. [PMID: 38649489 DOI: 10.1038/s41586-024-07393-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Affiliation(s)
- Lanbo Xiao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Abhijit Parolia
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Molecular and Cellular Pathology Program, University of Michigan, Ann Arbor, MI, USA
| | - Yuanyuan Qiao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Pushpinder Bawa
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Sanjana Eyunni
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Molecular and Cellular Pathology Program, University of Michigan, Ann Arbor, MI, USA
| | - Rahul Mannan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Sandra E Carson
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Yu Chang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Xiaoju Wang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Yuping Zhang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Josh N Vo
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Steven Kregel
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Stephanie A Simko
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Andrew D Delekta
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Mustapha Jaber
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Heng Zheng
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Ingrid J Apel
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Lisa McMurry
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Fengyun Su
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Rui Wang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Sylvia Zelenka-Wang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Sanjita Sasmal
- Aurigene Discovery Technologies, Electronic City Phase II, Bangalore, India
| | - Leena Khare
- Aurigene Discovery Technologies, Electronic City Phase II, Bangalore, India
| | - Subhendu Mukherjee
- Aurigene Discovery Technologies, Electronic City Phase II, Bangalore, India
| | | | - Kiran Aithal
- Aurigene Discovery Technologies, Electronic City Phase II, Bangalore, India
| | | | - Jay Ghurye
- Dovetail Genomics, Scotts Valley, CA, USA
| | - Xuhong Cao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
| | - Nora M Navone
- Department of Genitourinary Medical Oncology and the David H. Koch Center for Applied Research of Genitourinary Cancers, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alexey I Nesvizhskii
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Rohit Mehra
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Ulka Vaishampayan
- Department of Internal Medicine/Oncology, University of Michigan, Ann Arbor, MI, USA
| | | | - Yuzhuo Wang
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada
- Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Susanta Samajdar
- Aurigene Discovery Technologies, Electronic City Phase II, Bangalore, India
| | - Murali Ramachandra
- Aurigene Discovery Technologies, Electronic City Phase II, Bangalore, India
| | - Arul M Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA.
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA.
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA.
- Department of Urology, University of Michigan, Ann Arbor, MI, USA.
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2
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Roberts HJ, Ji S, Picca A, Sanson M, Garcia M, Snuderl M, Schüller U, Picart T, Ducray F, Green AL, Nakano Y, Sturm D, Abdullaev Z, Aldape K, Dang D, Kumar-Sinha C, Wu YM, Robinson D, Vo JN, Chinnaiyan AM, Cartaxo R, Upadhyaya SA, Mody R, Chiang J, Baker S, Solomon D, Venneti S, Pratt D, Waszak SM, Koschmann C. Clinical, genomic, and epigenomic analyses of H3K27M-mutant diffuse midline glioma long-term survivors reveal a distinct group of tumors with MAPK pathway alterations. Acta Neuropathol 2023; 146:849-852. [PMID: 37851269 PMCID: PMC10627895 DOI: 10.1007/s00401-023-02640-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/27/2023] [Accepted: 09/28/2023] [Indexed: 10/19/2023]
Affiliation(s)
- Holly J Roberts
- Department of Pediatrics, Michigan Medicine, Ann Arbor, MI, USA
| | - Sunjong Ji
- Department of Pediatrics, Michigan Medicine, Ann Arbor, MI, USA
| | - Alberto Picca
- Department of Neurology-2, Pitié-Salpêtrière University Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Marc Sanson
- Department of Neurology-2, Pitié-Salpêtrière University Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
- Onconeurotek, AP-HP, Hôpital Pitié-Salpêtrière, 75013, Paris, France
- Sorbonne Université, Inserm, CNRS, UMR S 1127, Institut du Cerveau et de la Moelle Épinière, ICM, Paris, France
| | - Mekka Garcia
- Department of Neurology, NYU Langone Health, New York, NY, USA
| | - Matija Snuderl
- Department of Pathology, NYU Langone Health, New York, NY, USA
| | - Ulrich Schüller
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Thiébaud Picart
- Department of Neurosurgical Oncology and Vascular Neurosurgery, Pierre Wertheimer Neurological and Neurosurgical Hospital, Hospices Civils de Lyon, Université Lyon 1, CRCL, UMR Inserm 1052, CNRS 5286, 69008, Lyon, France
| | - François Ducray
- Neuro-Oncology Department, Hospices Civils de Lyon, Université Lyon 1, CRCL, UMR Inserm 1052, CNRS 5286, 69000, Lyon, France
| | - Adam L Green
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Yoshiko Nakano
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, 5-1-1, Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
- Department of Pediatric Hematology/Oncology, Osaka City General Hospital, Osaka, Japan
| | - Dominik Sturm
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Pediatric Hematology, Oncology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Zied Abdullaev
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kenneth Aldape
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Derek Dang
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Chandan Kumar-Sinha
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Yi-Mi Wu
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Dan Robinson
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Josh N Vo
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Arul M Chinnaiyan
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Urology, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Rodrigo Cartaxo
- Department of Pediatrics, Michigan Medicine, Ann Arbor, MI, USA
| | | | - Rajen Mody
- Department of Pediatrics, Michigan Medicine, Ann Arbor, MI, USA
| | - Jason Chiang
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Suzanne Baker
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - David Solomon
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Sriram Venneti
- Department of Pediatrics, Michigan Medicine, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Drew Pratt
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sebastian M Waszak
- Laboratory of Computational Neuro-Oncology, School of Life Sciences, Swiss Institute for Experimental Cancer Research, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA.
- EPFL SV ISREC UPWASZAK, AAB 238 (Batiment AAB), Station 19, 1015, Lausanne, Switzerland.
| | - Carl Koschmann
- Department of Pediatrics, Michigan Medicine, Ann Arbor, MI, USA.
- University of Michigan, 3520D MSRB I, 1150 W Medical Center Dr, Ann Arbor, MI, 48109, USA.
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3
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Harms PW, Verhaegen ME, Vo JN, Tien JC, Pratt D, Su F, Dhanasekaran SM, Cao X, Mangelberger D, VanGoor J, Choi JE, Ma VT, Dlugosz AA, Chinnaiyan AM. Viral Status Predicts the Patterns of Genome Methylation and Decitabine Response in Merkel Cell Carcinoma. J Invest Dermatol 2022; 142:641-652. [PMID: 34474081 PMCID: PMC8860850 DOI: 10.1016/j.jid.2021.07.173] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 06/22/2021] [Accepted: 07/12/2021] [Indexed: 12/13/2022]
Abstract
Merkel cell carcinoma (MCC) is an aggressive cutaneous neuroendocrine carcinoma that is classified as Merkel cell polyomavirus-positive (virus positive [VP]) or Merkel cell polyomavirus-negative (virus negative [VN]). Epigenetic changes, such as DNA methylation, can alter gene expression and influence cancer progression. However, patterns of DNA methylation and the therapeutic efficacy of hypomethylating agents have not been fully explored in MCC. We characterized genome-wide DNA methylation in 16 MCC cell lines from both molecular subclasses in comparison with other cancer types and found that the overall profile of MCC is similar to that of small-cell lung carcinoma. Comparison of VP MCC with VN MCC revealed 2,260 differentially methylated positions. The hypomethylating agent decitabine upregulated the expression of antigen-presenting machinery in MCC cell lines and stimulated membrane expression of HLA-A in VP and VN MCC xenograft tumors. Decitabine also induced prominent caspase- and large T antigen‒independent cell death in VP MCC, whereas VN MCC cell lines displayed decreased proliferation without increased cell death. In mouse xenografts, decitabine significantly decreased the size of VP tumors but not that of VN tumors. Our findings indicate that viral status predicts genomic methylation patterns in MCC and that decitabine may be therapeutically effective against MCC through antiproliferative effects, cell death, and increased immune recognition.
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Affiliation(s)
- Paul W. Harms
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, 48109, USA,Rogel Cancer Center, University of Michigan, Ann Arbor, MI, 48109, USA,Department of Dermatology, University of Michigan, Ann Arbor, MI, 48109, USA
| | | | - Josh N. Vo
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jean C. Tien
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Drew Pratt
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Fengyun Su
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Saravana M. Dhanasekaran
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Xuhong Cao
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, 48109, USA,Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Doris Mangelberger
- Department of Dermatology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Julia VanGoor
- College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jae Eun Choi
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Vincent T. Ma
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Andrzej A. Dlugosz
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, 48109, USA,Department of Dermatology, University of Michigan, Ann Arbor, MI, 48109, USA,Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Arul M. Chinnaiyan
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, 48109, USA,Rogel Cancer Center, University of Michigan, Ann Arbor, MI, 48109, USA,Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, 48109, USA,Department of Urology, University of Michigan, Ann Arbor, MI, 48109, USA,Corresponding Author: Arul M. Chinnaiyan, M.D., Ph.D., Investigator, Howard Hughes Medical Institute, American Cancer Society Professor, S. P. Hicks Endowed Professor of Pathology, Rogel Cancer Center, University of Michigan Medical School, 1400 E. Medical Center Dr. 5316 CCGC, Ann Arbor, MI 48109-0602,
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4
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Xiao L, Parolia A, Qiao Y, Bawa P, Eyunni S, Mannan R, Carson SE, Chang Y, Wang X, Zhang Y, Vo JN, Kregel S, Simko SA, Delekta AD, Jaber M, Zheng H, Apel IJ, McMurry L, Su F, Wang R, Zelenka-Wang S, Sasmal S, Khare L, Mukherjee S, Abbineni C, Aithal K, Bhakta MS, Ghurye J, Cao X, Navone NM, Nesvizhskii AI, Mehra R, Vaishampayan U, Blanchette M, Wang Y, Samajdar S, Ramachandra M, Chinnaiyan AM. Targeting SWI/SNF ATPases in enhancer-addicted prostate cancer. Nature 2022; 601:434-439. [PMID: 34937944 PMCID: PMC8770127 DOI: 10.1038/s41586-021-04246-z] [Citation(s) in RCA: 102] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 11/15/2021] [Indexed: 12/13/2022]
Abstract
The switch/sucrose non-fermentable (SWI/SNF) complex has a crucial role in chromatin remodelling1 and is altered in over 20% of cancers2,3. Here we developed a proteolysis-targeting chimera (PROTAC) degrader of the SWI/SNF ATPase subunits, SMARCA2 and SMARCA4, called AU-15330. Androgen receptor (AR)+ forkhead box A1 (FOXA1)+ prostate cancer cells are exquisitely sensitive to dual SMARCA2 and SMARCA4 degradation relative to normal and other cancer cell lines. SWI/SNF ATPase degradation rapidly compacts cis-regulatory elements bound by transcription factors that drive prostate cancer cell proliferation, namely AR, FOXA1, ERG and MYC, which dislodges them from chromatin, disables their core enhancer circuitry, and abolishes the downstream oncogenic gene programs. SWI/SNF ATPase degradation also disrupts super-enhancer and promoter looping interactions that wire supra-physiologic expression of the AR, FOXA1 and MYC oncogenes themselves. AU-15330 induces potent inhibition of tumour growth in xenograft models of prostate cancer and synergizes with the AR antagonist enzalutamide, even inducing disease remission in castration-resistant prostate cancer (CRPC) models without toxicity. Thus, impeding SWI/SNF-mediated enhancer accessibility represents a promising therapeutic approach for enhancer-addicted cancers.
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Affiliation(s)
- Lanbo Xiao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Abhijit Parolia
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Molecular and Cellular Pathology Program, University of Michigan, Ann Arbor, MI, USA
| | - Yuanyuan Qiao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Pushpinder Bawa
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Sanjana Eyunni
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Molecular and Cellular Pathology Program, University of Michigan, Ann Arbor, MI, USA
| | - Rahul Mannan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Sandra E Carson
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Yu Chang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Xiaoju Wang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Yuping Zhang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Josh N Vo
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Steven Kregel
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Stephanie A Simko
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Andrew D Delekta
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Mustapha Jaber
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Heng Zheng
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Ingrid J Apel
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Lisa McMurry
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Fengyun Su
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Rui Wang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Sylvia Zelenka-Wang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Sanjita Sasmal
- Aurigene Discovery Technologies, Electronic City Phase II, Bangalore, India
| | - Leena Khare
- Aurigene Discovery Technologies, Electronic City Phase II, Bangalore, India
| | - Subhendu Mukherjee
- Aurigene Discovery Technologies, Electronic City Phase II, Bangalore, India
| | | | - Kiran Aithal
- Aurigene Discovery Technologies, Electronic City Phase II, Bangalore, India
| | | | - Jay Ghurye
- Dovetail Genomics, Scotts Valley, CA, USA
| | - Xuhong Cao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
| | - Nora M Navone
- Department of Genitourinary Medical Oncology and the David H. Koch Center for Applied Research of Genitourinary Cancers, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alexey I Nesvizhskii
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Rohit Mehra
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Ulka Vaishampayan
- Department of Internal Medicine/Oncology, University of Michigan, Ann Arbor, MI, USA
| | | | - Yuzhuo Wang
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada
- Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Susanta Samajdar
- Aurigene Discovery Technologies, Electronic City Phase II, Bangalore, India
| | - Murali Ramachandra
- Aurigene Discovery Technologies, Electronic City Phase II, Bangalore, India
| | - Arul M Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA.
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA.
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA.
- Department of Urology, University of Michigan, Ann Arbor, MI, USA.
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5
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Qiao Y, Choi JE, Tien JC, Simko SA, Rajendiran T, Vo JN, Delekta AD, Wang L, Xiao L, Hodge NB, Desai P, Mendoza S, Juckette K, Xu A, Soni T, Su F, Wang R, Cao X, Yu J, Kryczek I, Wang XM, Wang X, Siddiqui J, Wang Z, Bernard A, Fernandez-Salas E, Navone NM, Ellison SJ, Ding K, Eskelinen EL, Heath EI, Klionsky DJ, Zou W, Chinnaiyan AM. Autophagy Inhibition by Targeting PIKfyve Potentiates Response to Immune Checkpoint Blockade in Prostate Cancer. Nat Cancer 2021; 2:978-993. [PMID: 34738088 PMCID: PMC8562569 DOI: 10.1038/s43018-021-00237-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Multi-tyrosine kinase inhibitors (MTKIs) have thus far had limited success in the treatment of castration-resistant prostate cancer (CRPC). Here, we report a phase I-cleared orally bioavailable MTKI, ESK981, with a novel autophagy inhibitory property that decreased tumor growth in diverse preclinical models of CRPC. The anti-tumor activity of ESK981 was maximized in immunocompetent tumor environments where it upregulated CXCL10 expression through the interferon gamma pathway and promoted functional T cell infiltration, which resulted in enhanced therapeutic response to immune checkpoint blockade. Mechanistically, we identify the lipid kinase PIKfyve as the direct target of ESK981. PIKfyve-knockdown recapitulated ESK981's anti-tumor activity and enhanced the therapeutic benefit of immune checkpoint blockade. Our study reveals that targeting PIKfyve via ESK981 turns tumors from cold into hot through inhibition of autophagy, which may prime the tumor immune microenvironment in advanced prostate cancer patients and be an effective treatment strategy alone or in combination with immunotherapies.
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Affiliation(s)
- Yuanyuan Qiao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA.,Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA.,Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Jae Eun Choi
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA.,School of Medicine, University of California, San Diego, California 92093, USA
| | - Jean C. Tien
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA.,Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Stephanie A. Simko
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Thekkelnaycke Rajendiran
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA.,Michigan Regional Comprehensive Metabolomics Resource Core, Ann Arbor, Michigan 48109, USA
| | - Josh N. Vo
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Andrew D. Delekta
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Lisha Wang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Lanbo Xiao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Nathan B. Hodge
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Parth Desai
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Sergio Mendoza
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Kristin Juckette
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Alice Xu
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Tanu Soni
- Michigan Regional Comprehensive Metabolomics Resource Core, Ann Arbor, Michigan 48109, USA
| | - Fengyun Su
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Rui Wang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Xuhong Cao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA.,Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Jiali Yu
- Department of Surgery, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Ilona Kryczek
- Department of Surgery, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Xiao-Ming Wang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA.,Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Xiaoju Wang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Javed Siddiqui
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Zhen Wang
- School of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Amélie Bernard
- CNRS, Laboratoire de Biogenèse Membranaire, UMR5200; Université de Bordeaux, Laboratoire de Biogenèse Membranaire, UMR5200, 33000 Bordeaux, France.,Life Sciences Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Ester Fernandez-Salas
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Nora M. Navone
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Stephanie J. Ellison
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Ke Ding
- School of Pharmacy, Jinan University, Guangzhou 510632, China
| | | | - Elisabeth I. Heath
- Karmanos Cancer Institute, Department of Oncology, Wayne State University School of Medicine, Detroit, Michigan 48201, USA
| | - Daniel J. Klionsky
- Life Sciences Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Weiping Zou
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA.,Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, USA.,Department of Surgery, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Arul M. Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA.,Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA.,Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, USA.,Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan 48109, USA.,Department of Urology, University of Michigan, Ann Arbor, Michigan 48109, USA.,Correspondence to: Arul M. Chinnaiyan, Michigan Center for Translational Pathology, Rogel Cancer Center, 1500 East Medical Center Drive, Ann Arbor, Michigan 48109, USA. Phone: 734-615-4062; Fax: 734-615-4498;
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6
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Harms KL, Zhao L, Johnson B, Wang X, Carskadon S, Palanisamy N, Rhodes DR, Mannan R, Vo JN, Choi JE, Chan MP, Fullen DR, Patel RM, Siddiqui J, Ma VT, Hrycaj S, McLean SA, Hughes TM, Bichakjian CK, Tomlins SA, Harms PW. Virus-positive Merkel Cell Carcinoma Is an Independent Prognostic Group with Distinct Predictive Biomarkers. Clin Cancer Res 2021; 27:2494-2504. [PMID: 33547200 DOI: 10.1158/1078-0432.ccr-20-0864] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 12/31/2020] [Accepted: 02/02/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE Merkel cell carcinoma (MCC) is an aggressive cutaneous neuroendocrine carcinoma that can be divided into two classes: virus-positive (VP) MCC, associated with oncogenic Merkel cell polyomavirus (MCPyV); and virus-negative (VN) MCC, associated with photodamage. EXPERIMENTAL DESIGN We classified 346 MCC tumors from 300 patients for MCPyV using a combination of IHC, ISH, and qPCR assays. In a subset of tumors, we profiled mutation status and expression of cancer-relevant genes. MCPyV and molecular profiling results were correlated with disease-specific outcomes. Potential prognostic biomarkers were further validated by IHC. RESULTS A total of 177 tumors were classified as VP-MCC, 151 tumors were VN-MCC, and 17 tumors were indeterminate. MCPyV positivity in primary tumors was associated with longer disease-specific and recurrence-free survival in univariate analysis, and in multivariate analysis incorporating age, sex, immune status, and stage at presentation. Prioritized oncogene or tumor suppressor mutations were frequent in VN-MCC but rare in VP-MCC. TP53 mutation developed with recurrence in one VP-MCC case. Importantly, for the first time we find that VP-MCC and VN-MCC display distinct sets of prognostic molecular biomarkers. For VP-MCC, shorter survival was associated with decreased expression of immune markers including granzyme and IDO1. For VN-MCC, shorter survival correlated with high expression of several genes including UBE2C. CONCLUSIONS MCPyV status is an independent prognostic factor for MCC. Features of the tumor genome, transcriptome, and microenvironment may modify prognosis in a manner specific to viral status. MCPyV status has clinicopathologic significance and allows for identification of additional prognostic subgroups.
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Affiliation(s)
- Kelly L Harms
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan.,Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
| | - Lili Zhao
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan
| | | | - Xiaoming Wang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan.,Department of Pathology, University of Michigan, Ann Arbor, Michigan
| | - Shannon Carskadon
- Department of Urology, Vattikuti Urology Institute, Henry Ford Health System, Detroit, Michigan
| | - Nallasivam Palanisamy
- Department of Urology, Vattikuti Urology Institute, Henry Ford Health System, Detroit, Michigan
| | | | - Rahul Mannan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan.,Department of Pathology, University of Michigan, Ann Arbor, Michigan
| | - Josh N Vo
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan.,Department of Pathology, University of Michigan, Ann Arbor, Michigan
| | - Jae Eun Choi
- Department of Pathology, University of Michigan, Ann Arbor, Michigan
| | - May P Chan
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan.,Department of Pathology, University of Michigan, Ann Arbor, Michigan
| | - Douglas R Fullen
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan.,Department of Pathology, University of Michigan, Ann Arbor, Michigan
| | - Rajiv M Patel
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan.,Department of Pathology, University of Michigan, Ann Arbor, Michigan
| | - Javed Siddiqui
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan.,Department of Pathology, University of Michigan, Ann Arbor, Michigan
| | - Vincent T Ma
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan.,Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, Michigan
| | - Steven Hrycaj
- Department of Pathology, University of Michigan, Ann Arbor, Michigan
| | - Scott A McLean
- Department of Otolaryngology-Head and Neck Surgery, University of Michigan, Ann Arbor, Michigan
| | - Tasha M Hughes
- Department of Surgery, University of Michigan, Ann Arbor, Michigan
| | - Christopher K Bichakjian
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan.,Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
| | - Scott A Tomlins
- Strata Oncology, Ann Arbor, Michigan.,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan.,Department of Pathology, University of Michigan, Ann Arbor, Michigan
| | - Paul W Harms
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan. .,Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan.,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan.,Department of Pathology, University of Michigan, Ann Arbor, Michigan
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7
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Kumar-Sinha C, Anderson B, Heider A, Vo JN, Robinson DR, Wu YM, Chinnaiyan AM, Mody R. Clinical Sequencing of High-Grade Undifferentiated Sarcomas: A Case Series and Report of an Aggressive Primary Cardiac Tumor With Multiple Oncogenic Drivers. JCO Precis Oncol 2020; 4:PO.19.00322. [PMID: 33015523 PMCID: PMC7529506 DOI: 10.1200/po.19.00322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/13/2020] [Indexed: 11/20/2022] Open
Affiliation(s)
- Chandan Kumar-Sinha
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI
- Department of Pathology, University of Michigan, Ann Arbor, MI
| | - Bailey Anderson
- Department of Pediatrics, University of Michigan, Ann Arbor, MI
| | - Amer Heider
- Department of Pathology, University of Michigan, Ann Arbor, MI
| | - Josh N. Vo
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI
| | - Dan R. Robinson
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI
- Department of Pathology, University of Michigan, Ann Arbor, MI
| | - Yi-Mi Wu
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI
- Department of Pathology, University of Michigan, Ann Arbor, MI
| | - Arul M. Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI
- Department of Pathology, University of Michigan, Ann Arbor, MI
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI
| | - Rajen Mody
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI
- Department of Pediatrics, University of Michigan, Ann Arbor, MI
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI
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8
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Kregel S, Malik R, Asangani IA, Wilder-Romans K, Rajendiran T, Xiao L, Vo JN, Soni T, Cieslik M, Fernadez-Salas E, Zhou B, Cao X, Speers C, Wang S, Chinnaiyan AM. Functional and Mechanistic Interrogation of BET Bromodomain Degraders for the Treatment of Metastatic Castration-resistant Prostate Cancer. Clin Cancer Res 2019; 25:4038-4048. [PMID: 30918020 DOI: 10.1158/1078-0432.ccr-18-3776] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 01/14/2019] [Accepted: 03/18/2019] [Indexed: 12/26/2022]
Abstract
PURPOSE The bromodomain and extraterminal (BET)-containing proteins (BRD2/3/4) are essential epigenetic coregulators for prostate cancer growth. BRD inhibitors have shown promise for treatment of metastatic castration-resistant prostate cancer (mCRPC), and have been shown to function even in the context of resistance to next-generation AR-targeted therapies such as enzalutamide and abiraterone. Their clinical translation, however, has been limited by off-target effects, toxicity, and rapid resistance. EXPERIMENTAL DESIGN We have developed a series of molecules that target BET bromodomain proteins through their proteasomal degradation, improving efficacy and specificity of standard inhibitors. We tested their efficacy by utilizing prostate cancer cell lines and patient-derived xenografts, as well as several techniques including RNA-sequencing, mass spectroscopic proteomics, and lipidomics. RESULTS BET degraders function in vitro and in vivo to suppress prostate cancer growth. These drugs preferentially affect AR-positive prostate cancer cells (22Rv1, LNCaP, VCaP) over AR-negative cells (PC3 and DU145), and proteomic and genomic mechanistic studies confirm disruption of oncogenic AR and MYC signaling at lower concentrations than BET inhibitors. We also identified increases in polyunsaturated fatty acids (PUFA) and thioredoxin-interacting protein (TXNIP) as potential pharmacodynamics biomarkers for targeting BET proteins. CONCLUSIONS Compounds inducing the pharmacologic degradation of BET proteins effectively target the major oncogenic drivers of prostate cancer, and ultimately present a potential advance in the treatment of mCRPC. In particular, our compound dBET-3, is most suited for further clinical development.
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Affiliation(s)
- Steven Kregel
- Michigan Center for Translational Pathology, University of Michigan.,Department of Pathology, University of Michigan, Ann Arbor, Michigan
| | - Rohit Malik
- Michigan Center for Translational Pathology, University of Michigan.,Department of Pathology, University of Michigan, Ann Arbor, Michigan
| | - Irfan A Asangani
- Michigan Center for Translational Pathology, University of Michigan.,Department of Pathology, University of Michigan, Ann Arbor, Michigan
| | - Kari Wilder-Romans
- Department of Radiation Oncology, University of Michigan, Ann Arbor, Michigan
| | - Thekkelnaycke Rajendiran
- Michigan Center for Translational Pathology, University of Michigan.,Department of Pathology, University of Michigan, Ann Arbor, Michigan
| | - Lanbo Xiao
- Michigan Center for Translational Pathology, University of Michigan.,Department of Pathology, University of Michigan, Ann Arbor, Michigan
| | - Josh N Vo
- Michigan Center for Translational Pathology, University of Michigan
| | - Tanu Soni
- Division of Bioinformatics, Michigan Regional Comprehensive Metabolomics Resource Core, University of Michigan, Ann Arbor, Michigan
| | - Marcin Cieslik
- Michigan Center for Translational Pathology, University of Michigan.,Department of Pathology, University of Michigan, Ann Arbor, Michigan
| | - Ester Fernadez-Salas
- Michigan Center for Translational Pathology, University of Michigan.,Howard Hughes Medical Institute, University of Michigan Medical School, Ann Arbor, Michigan.,Departments of Internal Medicine, Pharmacology, and Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan
| | - Bing Zhou
- Michigan Center for Translational Pathology, University of Michigan.,Departments of Internal Medicine, Pharmacology, and Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan.,Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, Michigan
| | - Xuhong Cao
- Michigan Center for Translational Pathology, University of Michigan.,Howard Hughes Medical Institute, University of Michigan Medical School, Ann Arbor, Michigan
| | - Corey Speers
- Michigan Center for Translational Pathology, University of Michigan.,Department of Radiation Oncology, University of Michigan, Ann Arbor, Michigan.,Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, Michigan
| | - Shaomeng Wang
- Michigan Center for Translational Pathology, University of Michigan.,Departments of Internal Medicine, Pharmacology, and Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan.,Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, Michigan
| | - Arul M Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan. .,Department of Pathology, University of Michigan, Ann Arbor, Michigan.,Department of Radiation Oncology, University of Michigan, Ann Arbor, Michigan.,Department of Urology, University of Michigan, Ann Arbor, Michigan.,Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, Michigan
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9
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Vo JN, Cieslik M, Zhang Y, Shukla S, Xiao L, Zhang Y, Wu YM, Dhanasekaran SM, Engelke CG, Cao X, Robinson DR, Nesvizhskii AI, Chinnaiyan AM. The Landscape of Circular RNA in Cancer. Cell 2019; 176:869-881.e13. [PMID: 30735636 PMCID: PMC6601354 DOI: 10.1016/j.cell.2018.12.021] [Citation(s) in RCA: 998] [Impact Index Per Article: 199.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 10/05/2018] [Accepted: 12/12/2018] [Indexed: 12/17/2022]
Abstract
Circular RNAs (circRNAs) are an intriguing class of RNA due to their covalently closed structure, high stability, and implicated roles in gene regulation. Here, we used an exome capture RNA sequencing protocol to detect and characterize circRNAs across >2,000 cancer samples. When compared against Ribo-Zero and RNase R, capture sequencing significantly enhanced the enrichment of circRNAs and preserved accurate circular-to-linear ratios. Using capture sequencing, we built the most comprehensive catalog of circRNA species to date: MiOncoCirc, the first database to be composed primarily of circRNAs directly detected in tumor tissues. Using MiOncoCirc, we identified candidate circRNAs to serve as biomarkers for prostate cancer and were able to detect circRNAs in urine. We further detected a novel class of circular transcripts, termed read-through circRNAs, that involved exons originating from different genes. MiOncoCirc will serve as a valuable resource for the development of circRNAs as diagnostic or therapeutic targets across cancer types.
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Affiliation(s)
- Josh N Vo
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Marcin Cieslik
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yajia Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sudhanshu Shukla
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Biosciences and Bioengineering, Indian Institute of Technology Dharwad, Dharwad, 580011, India
| | - Lanbo Xiao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yuping Zhang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yi-Mi Wu
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Saravana M Dhanasekaran
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Carl G Engelke
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Xuhong Cao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Dan R Robinson
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Alexey I Nesvizhskii
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Arul M Chinnaiyan
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Department of Urology, University of Michigan, Ann Arbor, MI 48109, USA.
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10
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Parolia A, Xiao L, Vo JN, Cieslik M, Cao X, Chinnaiyan AM. Abstract 975: Functional CRISPR screen towards identifying novel epigenetic co-factors of oncogenic AR-activity. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Prostate cancer (PCa) is the second leading cause of cancer-related mortality in North American men. In recent years, there has been mounting evidence establishing the centrality of epigenetic mechanisms in PCa initiation and progression. Accordingly, various epigenetic genes have been described to collaborate with the androgen receptor (AR) in enabling its oncogenic transcriptional program and aberrantly restoring its activity in metastatic castration resistant PCa. Concordantly, our laboratory has recently described two epigenetic genes, BRD4 and MLL2, as key co-activators of AR-signaling. Furthermore, we have demonstrated that inhibition of these genes synergistically work with AR antagonists to attenuate PCa progression in preclinical models. Thus, in a setting where all metastatic patients eventually progress to evolve resistance to anti-AR therapies, there exists a dire clinical need to identify novel therapeutic targets. To this end, using CRISPR-Cas9 technology, we have engineered a unique AR-reporter LNCaP model that harbors the mCherry gene directly downstream of the endogenous KLK3/PSA promoter (a canonical AR-target). Notably, validation experiments confirm that the mCherry reporter gene, akin to KLK3, is dynamically regulated by AR activity in response to treatment with dihydrotestosterone (DHT; a physiological AR agonist) or enzalutamide (an AR inhibitor). Furthermore, we have designed a focused, high-depth library of small-guide RNAs (sgRNAs) to target over 200 distinct epigenetic genes, both at transcriptional start sites and functionally-essential enzymatic domains. Overall, this library comprises of roughly 1400 distinct guide-RNAs that include 50 non-targeting negative controls. Using these molecular tools, we plan to perform a marker-based, functional screen that involves the sorting of sgRNA-infected AR-reporter cells into mCherryHIGH and mCherryLOW populations. Notably, we have successfully validated the stated screening design: Starting from a mixed pool of AR-targeting siRNAs or R1881 (a synthetic AR-agonist) treated reporter cells, we sorted them into LOW15% or HIGH15% fractions based on the intensity of mCherry fluorescence. As expected, transcriptomic analyses of these fractions confirmed that AR-signaling was indeed significantly inhibited and enhanced in the LOW15% and HIGH15% fractions, respectively, relative to the unsorted cells. Thus, for our CRISPR screen, we theorize that the genomic interrogation of sgRNAs enriched in the mCherryLOW population will reveal novel epigenetic genes that function as essential co-factors of oncogenic AR-activity. These epigenetic factors can be co-targeted to extort durable therapeutic responses in patients treated with the current line of anti-AR therapies, thus directly addressing an urgent clinical need.
Citation Format: Abhijit Parolia, Lanbo Xiao, Josh N. Vo, Marcin Cieslik, Xuhong Cao, Arul M. Chinnaiyan. Functional CRISPR screen towards identifying novel epigenetic co-factors of oncogenic AR-activity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 975.
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11
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Vo JN, Zhang Y, Shukla S, Xiao L, Robinson D, Wu YM, Gao S, Engelke C, Cao X, Nesvizhskii A, Chinnaiyan A. Abstract 3288: The landscape of circular RNA in cancer. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-3288] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Circular RNAs (circRNAs) are an intriguing class of RNA due to their covalently closed structure, relatively high stability, and implicated roles in gene regulation. Here we used exome capture RNA-Seq, a non-poly(A) high-throughput RNA-sequencing protocol, to detect and characterize circRNAs across >800 cancer samples. When compared against the two gold-standard methods (Ribo-Zero and RNase-R), capture sequencing significantly enhanced the enrichment of circRNAs and preserved accurate circular-to-linear ratios. We compiled the detected circRNAs from capture sequencing into the public OncoCirc database, the most comprehensive catalogue of circRNA species to-date. With this database, we identified the best circRNAs to serve as biomarkers for prostate cancer and were able to detect a novel class of circRNAs involved two genes. OncoCirc will serve as a valuable resource for the development of circRNA for diagnostic or therapeutic purposes for other cancers, as well as the study of circularization as an intriguing RNA splicing process.
Citation Format: Josh N. Vo, Yajia Zhang, Sudhanshu Shukla, Lanbo Xiao, Dan Robinson, Yi-Mi Wu, Sisi Gao, Carl Engelke, Xuhong Cao, Alexey Nesvizhskii, Arul Chinnaiyan. The landscape of circular RNA in cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3288.
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Affiliation(s)
- Josh N. Vo
- University of Michigan-Ann Arbor, Ann Arbor, MI
| | - Yajia Zhang
- University of Michigan-Ann Arbor, Ann Arbor, MI
| | | | - Lanbo Xiao
- University of Michigan-Ann Arbor, Ann Arbor, MI
| | | | - Yi-Mi Wu
- University of Michigan-Ann Arbor, Ann Arbor, MI
| | - Sisi Gao
- University of Michigan-Ann Arbor, Ann Arbor, MI
| | | | - Xuhong Cao
- University of Michigan-Ann Arbor, Ann Arbor, MI
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