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Xu Y, Yang Y, Wang Z, Sjöström M, Jiang Y, Tang Y, Cheng S, Deng S, Wang C, Gonzalez J, Johnson NA, Li X, Li X, Metang LA, Mukherji A, Xu Q, Tirado CR, Wainwright G, Yu X, Barnes S, Hofstad M, Chen Y, Zhu H, Hanker AB, Raj GV, Zhu G, He HH, Wang Z, Arteaga CL, Liang H, Feng FY, Wang Y, Wang T, Mu P. ZNF397 Deficiency Triggers TET2-Driven Lineage Plasticity and AR-Targeted Therapy Resistance in Prostate Cancer. Cancer Discov 2024; 14:1496-1521. [PMID: 38591846 PMCID: PMC11285331 DOI: 10.1158/2159-8290.cd-23-0539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 02/26/2024] [Accepted: 04/04/2024] [Indexed: 04/10/2024]
Abstract
Cancer cells exhibit phenotypical plasticity and epigenetic reprogramming that allows them to evade lineage-dependent targeted treatments by adopting lineage plasticity. The underlying mechanisms by which cancer cells exploit the epigenetic regulatory machinery to acquire lineage plasticity and therapy resistance remain poorly understood. We identified zinc finger protein 397 (ZNF397) as a bona fide coactivator of the androgen receptor (AR), essential for the transcriptional program governing AR-driven luminal lineage. ZNF397 deficiency facilitates the transition of cancer cell from an AR-driven luminal lineage to a ten-eleven translocation 2 (TET2)-driven lineage plastic state, ultimately promoting resistance to therapies inhibiting AR signaling. Intriguingly, our findings indicate that a TET2 inhibitor can eliminate the resistance to AR-targeted therapies in ZNF397-deficient tumors. These insights uncover a novel mechanism through which prostate cancer acquires lineage plasticity via epigenetic rewiring and offer promising implications for clinical interventions designed to overcome therapy resistance dictated by lineage plasticity. Significance: This study reveals a bifurcated role of ZNF397, and a TET2-driven epigenetic mechanism regulating tumor lineage plasticity and therapy response in prostate cancer, enhances the understanding of drug resistance, and unveils a new therapeutic strategy for overcoming androgen receptor-targeted therapy resistance.
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Affiliation(s)
- Yaru Xu
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, Texas.
| | - Yuqiu Yang
- Quantitative Biomedical Research Center, Peter O’Donnell Jr. School of Public Health, UT Southwestern Medical Center, Dallas, Texas.
| | - Zhaoning Wang
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, Texas.
- Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, California.
| | - Martin Sjöström
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, California.
| | - Yuyin Jiang
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, Texas.
| | - Yitao Tang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | - Siyuan Cheng
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Shreveport, Shreveport, Louisiana.
| | - Su Deng
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, Texas.
| | - Choushi Wang
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, Texas.
| | - Julisa Gonzalez
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, Texas.
| | - Nickolas A. Johnson
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, Texas.
| | - Xiang Li
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, Texas.
| | - Xiaoling Li
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, Texas.
| | - Lauren A. Metang
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, Texas.
| | - Atreyi Mukherji
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, Texas.
| | - Quanhui Xu
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, Texas.
| | - Carla R. Tirado
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, Texas.
| | - Garrett Wainwright
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, Texas.
| | - Xinzhe Yu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas.
| | - Spencer Barnes
- Bioinformatics Core Facility of the Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, Texas.
| | - Mia Hofstad
- Department of Urology, UT Southwestern Medical Center, Dallas, Texas.
| | - Yu Chen
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, NYC, New York, New York.
| | - Hong Zhu
- Division of Biostatistics, Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, Virginia.
| | - Ariella B. Hanker
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, Texas.
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, Texas.
| | - Ganesh V. Raj
- Department of Urology, UT Southwestern Medical Center, Dallas, Texas.
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, Texas.
| | - Guanghui Zhu
- Department of Medical Biophysics, University of Toronto, Toronto, Canada.
- Princess Margaret Cancer Center, University Health Network, Toronto, Canada.
| | - Housheng H. He
- Department of Medical Biophysics, University of Toronto, Toronto, Canada.
- Princess Margaret Cancer Center, University Health Network, Toronto, Canada.
| | - Zhao Wang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas.
| | - Carlos L. Arteaga
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, Texas.
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, Texas.
| | - Han Liang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | - Felix Y. Feng
- Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, California.
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California.
| | - Yunguan Wang
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229.
| | - Tao Wang
- Quantitative Biomedical Research Center, Peter O’Donnell Jr. School of Public Health, UT Southwestern Medical Center, Dallas, Texas.
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, Texas.
| | - Ping Mu
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, Texas.
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, Texas.
- Hamon Center for Regenerative Science and Medicine, UT Southwestern Medical Center, Dallas, Texas.
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Xu Y, Wang Z, Sjöström M, Deng S, Wang C, Johnson NA, Gonzalez J, Li X, Metang LA, Tirado CR, Mukherji A, Wainwright G, Yu X, Yang Y, Barnes S, Hofstad M, Zhu H, Hanker A, He HH, Chen Y, Wang Z, Raj G, Arteaga C, Feng F, Wang Y, Wang T, Mu P. ZNF397 Loss Triggers TET2-driven Epigenetic Rewiring, Lineage Plasticity, and AR-targeted Therapy Resistance in AR-dependent Cancers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.24.563645. [PMID: 37961351 PMCID: PMC10634771 DOI: 10.1101/2023.10.24.563645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Cancer cells exhibit phenotypical plasticity and epigenetic reprogramming, which allows them to evade lineage-dependent targeted treatments by adopting lineage plasticity. The underlying mechanisms by which cancer cells exploit the epigenetic regulatory machinery to acquire lineage plasticity and therapy resistance remain poorly understood. We identified Zinc Finger Protein 397 (ZNF397) as a bona fide co-activator of the androgen receptor (AR), essential for the transcriptional program governing AR-driven luminal lineage. ZNF397 deficiency facilitates the transition of cancer cell from an AR-driven luminal lineage to a Ten-Eleven Translocation 2 (TET2)-driven lineage plastic state, ultimately promoting resistance to therapies inhibiting AR signaling. Intriguingly, our findings indicate that TET2 inhibitor can eliminate the AR targeted therapies resistance in ZNF397-deficient tumors. These insights uncover a novel mechanism through which prostate and breast cancers acquire lineage plasticity via epigenetic rewiring and offer promising implications for clinical interventions designed to overcome therapy resistance dictated by lineage plasticity. Statement of Significance This study reveals a novel epigenetic mechanism regulating tumor lineage plasticity and therapy response, enhances understanding of drug resistance and unveils a new therapeutic strategy for prostate cancer and other malignancies. Our findings also illuminate TET2's oncogenic role and mechanistically connect TET2-driven epigenetic rewiring to lineage plasticity and therapy resistance.
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Greenwell AM, Baughan S, Altinok D, Marupudi NI, Kupsky W, Kumar-Sinha C, Gorsi HS. Lorlatinib for the Treatment of ALK Fusion–Positive Infant-Type Hemispheric Glioma: A Case Report. JCO Precis Oncol 2022; 6:e2200255. [DOI: 10.1200/po.22.00255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Affiliation(s)
| | - Scott Baughan
- Wayne State University School of Medicine, Detroit, MI
| | - Deniz Altinok
- Department of Radiology, Children's Hospital of Michigan, Wayne State University School of Medicine, Detroit, MI
| | - Neena I. Marupudi
- Department of Pediatric Neurosurgery, Children's Hospital of Michigan, Wayne State University School of Medicine, Detroit, MI
| | - William Kupsky
- Department of Pathology, Children's Hospital of Michigan, Wayne State University School of Medicine, Detroit, MI
| | - Chandan Kumar-Sinha
- Department of Pathology, Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI
| | - Hamza S. Gorsi
- Department of Hematology/Oncology, Children's Hospital of Michigan, Central Michigan University School of Medicine, Mount Pleasant, MI
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Yoshizaki H, Okuda S. Elucidation of the evolutionary expansion of phosphorylation signaling networks using comparative phosphomotif analysis. BMC Genomics 2014; 15:546. [PMID: 24981518 PMCID: PMC4117960 DOI: 10.1186/1471-2164-15-546] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 06/26/2014] [Indexed: 11/10/2022] Open
Abstract
Background Protein phosphorylation is catalyzed by kinases and is involved in the regulation of a wide range of processes. The phosphosites in protein sequence motifs determine the types of kinases involved. The development of phosphoproteomics has allowed the identification of huge numbers of phosphosites, some of which are not involved in physiological functions. Results We developed a method for extracting phosphosites with important roles in cellular functions and determined 178 phosphomotifs based on the analysis of 34,366 phosphosites. We compared the conservation of serine/threonine/tyrosine residues observed in humans and seven other species. Consequently, we identified 16 phosphomotifs, where the level of conservation increased among species. The highly conserved phosphomotifs in humans and the worm were kinase regulatory sites. The motifs present in the fly were novel phosphomotifs, including zinc finger motifs involved in the regulation of gene expression. Subsequently, we found that this zinc finger motif contributed to subcellular protein localization. The motifs identified in fish allowed us to detect the expansion of phosphorylation signals related to alternative splicing. We also showed that the motifs present in specific species functioned in an additional network that interacted directly with the core signaling network conserved from yeast to humans. Conclusions Our method may facilitate the efficient extraction of novel phosphomotifs with physiological functions, thereby contributing greatly to the analysis of complex phosphorylation signaling cascades. Our study suggests that the phosphorylation networks acquired during evolution have added signaling network modules to the core signaling networks. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-546) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hisayoshi Yoshizaki
- Department of Pathology I, Kanazawa Medical University, 1-1 Daigaku, Uchinada, Ishikawa 920-0293, Japan.
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Faner R, Gonzalez N, Cruz T, Kalko SG, Agustí A. Systemic inflammatory response to smoking in chronic obstructive pulmonary disease: evidence of a gender effect. PLoS One 2014; 9:e97491. [PMID: 24830457 PMCID: PMC4022517 DOI: 10.1371/journal.pone.0097491] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 04/18/2014] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Tobacco smoking is the main risk factor of chronic obstructive pulmonary disease (COPD) but not all smokers develop the disease. An abnormal pulmonary and systemic inflammatory response to smoking is thought to play a major pathogenic role in COPD, but this has never been tested directly. METHODS We studied the systemic biomarker and leukocyte transcriptomic response (Affymetrix microarrays) to smoking exposure in 10 smokers with COPD and 10 smokers with normal spirometry. We also studied 10 healthy never smokers (not exposed to smoking) as controls. Because some aspects of COPD may differ in males and females, and the inflammatory response to other stressors (infection) might be different in man and women, we stratified participant recruitment by sex. Differentially expressed genes were validated by q-PCR. Ontology enrichment was evaluated and interaction networks inferred. RESULTS Principal component analysis identified sex differences in the leukocyte transcriptomic response to acute smoking. In both genders, we identified genes that were differentially expressed in response to smoking exclusively in COPD patients (COPD related signature) or smokers with normal spirometry (Smoking related signature), their ontologies and interaction networks. CONCLUSIONS The use of an experimental intervention (smoking exposure) to investigate the transcriptomic response of peripheral leukocytes in COPD is a step beyond the standard case-control transcriptomic profiling carried out so far, and has facilitated the identification of novel COPD and Smoking expression related signatures which differ in males and females.
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Affiliation(s)
- Rosa Faner
- Fundació Privada Clínic per a la Recerca Biomèdica, Barcelona, Spain
- Institut d'investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- CIBER Enfermedades Respiratorias (CIBERES), Barcelona, Spain
| | - Nuria Gonzalez
- Fundació Privada Clínic per a la Recerca Biomèdica, Barcelona, Spain
| | - Tamara Cruz
- Fundació Privada Clínic per a la Recerca Biomèdica, Barcelona, Spain
- Institut d'investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | | | - Alvar Agustí
- Fundació Privada Clínic per a la Recerca Biomèdica, Barcelona, Spain
- Institut d'investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- CIBER Enfermedades Respiratorias (CIBERES), Barcelona, Spain
- Thorax Institute, Hospital Clinic, University of Barcelona, Barcelona, Spain
- Fundació de Investigació Sanitaria Illes Balears (FISIB), Mallorca, Spain
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TLS/FUS (translocated in liposarcoma/fused in sarcoma) regulates target gene transcription via single-stranded DNA response elements. Proc Natl Acad Sci U S A 2012; 109:6030-5. [PMID: 22460799 DOI: 10.1073/pnas.1203028109] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
TLS/FUS (TLS) is a multifunctional protein implicated in a wide range of cellular processes, including transcription and mRNA processing, as well as in both cancer and neurological disease. However, little is currently known about TLS target genes and how they are recognized. Here, we used ChIP and promoter microarrays to identify genes potentially regulated by TLS. Among these genes, we detected a number that correlate with previously known functions of TLS, and confirmed TLS occupancy at several of them by ChIP. We also detected changes in mRNA levels of these target genes in cells where TLS levels were altered, indicative of both activation and repression. Next, we used data from the microarray and computational methods to determine whether specific sequences were enriched in DNA fragments bound by TLS. This analysis suggested the existence of TLS response elements, and we show that purified TLS indeed binds these sequences with specificity in vitro. Remarkably, however, TLS binds only single-strand versions of the sequences. Taken together, our results indicate that TLS regulates expression of specific target genes, likely via recognition of specific single-stranded DNA sequences located within their promoter regions.
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