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Chi LH, Redfern AD, Lim Kam Sian TCC, Street IP, Burrows AD, Roslan S, Daly RJ, Anderson RL. BMP4-Induced Suppression of Breast Cancer Metastasis Is Associated with Inhibition of Cholesterol Biosynthesis. Int J Mol Sci 2024; 25:9160. [PMID: 39273106 DOI: 10.3390/ijms25179160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Revised: 08/12/2024] [Accepted: 08/19/2024] [Indexed: 09/15/2024] Open
Abstract
We reported previously that in preclinical models, BMP4 is a potent inhibitor of breast cancer metastasis and that high BMP4 protein levels predict favourable patient outcomes. Here, we analysed a breast cancer xenograft with or without enforced expression of BMP4 to gain insight into the mechanisms by which BMP4 suppresses metastasis. Transcriptomic analysis of cancer cells recovered from primary tumours and phosphoproteomic analyses of cancer cells exposed to recombinant BMP4 revealed that BMP4 inhibits cholesterol biosynthesis, with many genes in this biosynthetic pathway being downregulated by BMP4. The treatment of mice bearing low-BMP4 xenografts with a cholesterol-lowering statin partially mimicked the anti-metastatic activity of BMP4. Analysis of a cohort of primary breast cancers revealed a reduced relapse rate for patients on statin therapy if their tumours exhibited low BMP4 levels. These findings indicate that BMP4 may represent a predictive biomarker for the benefit of additional statin therapy in breast cancer patients.
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Affiliation(s)
- Lap Hing Chi
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia
- School of Cancer Medicine, La Trobe University, Bundoora, VIC 3083, Australia
| | - Andrew D Redfern
- Medical School, University of Western Australia, Perth, WA 6009, Australia
| | - Terry C C Lim Kam Sian
- Cancer Program, Monash Biomedicine Discovery Institute, Clayton, VIC 3168, Australia
- Department of Biochemistry & Molecular Biology, Monash University, Clayton, VIC 3168, Australia
| | - Ian P Street
- Children's Cancer Institute, University of New South Wales, Sydney, NSW 2052, Australia
| | - Allan D Burrows
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia
- School of Cancer Medicine, La Trobe University, Bundoora, VIC 3083, Australia
| | - Suraya Roslan
- Department of Surgery, St. Vincent's Hospital, Fitzroy, VIC 3065, Australia
| | - Roger J Daly
- Cancer Program, Monash Biomedicine Discovery Institute, Clayton, VIC 3168, Australia
- Department of Biochemistry & Molecular Biology, Monash University, Clayton, VIC 3168, Australia
| | - Robin L Anderson
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia
- School of Cancer Medicine, La Trobe University, Bundoora, VIC 3083, Australia
- Department of Clinical Pathology, The University of Melbourne, Parkville, VIC 3052, Australia
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2
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Trejo-Villegas OA, Heijink IH, Ávila-Moreno F. Preclinical evidence in the assembly of mammalian SWI/SNF complexes: Epigenetic insights and clinical perspectives in human lung disease therapy. Mol Ther 2024; 32:2470-2488. [PMID: 38910326 DOI: 10.1016/j.ymthe.2024.06.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 04/18/2024] [Accepted: 06/20/2024] [Indexed: 06/25/2024] Open
Abstract
The SWI/SNF complex, also known as the BRG1/BRM-associated factor (BAF) complex, represents a critical regulator of chromatin remodeling mechanisms in mammals. It is alternatively referred to as mSWI/SNF and has been suggested to be imbalanced in human disease compared with human health. Three types of BAF assemblies associated with it have been described, including (1) canonical BAF (cBAF), (2) polybromo-associated BAF (PBAF), and (3) non-canonical BAF (ncBAF) complexes. Each of these BAF assemblies plays a role, either functional or dysfunctional, in governing gene expression patterns, cellular processes, epigenetic mechanisms, and biological processes. Recent evidence increasingly links the dysregulation of mSWI/SNF complexes to various human non-malignant lung chronic disorders and lung malignant diseases. This review aims to provide a comprehensive general state-of-the-art and a profound examination of the current understanding of mSWI/SNF assembly processes, as well as the structural and functional organization of mSWI/SNF complexes and their subunits. In addition, it explores their intricate functional connections with potentially dysregulated transcription factors, placing particular emphasis on molecular and cellular pathogenic processes in lung diseases. These processes are reflected in human epigenome aberrations that impact clinical and therapeutic levels, suggesting novel perspectives on the diagnosis and molecular therapies for human respiratory diseases.
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Affiliation(s)
- Octavio A Trejo-Villegas
- Lung Diseases and Functional Epigenomics Laboratory (LUDIFE), Biomedicine Research Unit (UBIMED), Facultad de Estudios Superiores-Iztacala (FES-Iztacala), Universidad Nacional Autónoma de México (UNAM), Avenida de los Barrios #1, Colonia Los Reyes Iztacala, Tlalnepantla de Baz, 54090, Estado de México, México
| | - Irene H Heijink
- Departments of Pathology & Medical Biology and Pulmonology, GRIAC Research Institute, University Medical Center Groningen, University of Groningen, 9713 Groningen, the Netherlands
| | - Federico Ávila-Moreno
- Lung Diseases and Functional Epigenomics Laboratory (LUDIFE), Biomedicine Research Unit (UBIMED), Facultad de Estudios Superiores-Iztacala (FES-Iztacala), Universidad Nacional Autónoma de México (UNAM), Avenida de los Barrios #1, Colonia Los Reyes Iztacala, Tlalnepantla de Baz, 54090, Estado de México, México; Research Unit, Instituto Nacional de Enfermedades Respiratorias (INER), Ismael Cosío Villegas, 14080, Ciudad de México, México; Research Tower, Subdirección de Investigación Básica, Instituto Nacional de Cancerología (INCan), 14080, Ciudad de México, México.
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3
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Yang J, Kinyamu HK, Ward JM, Scappini E, Muse G, Archer TK. Unlocking cellular plasticity: enhancing human iPSC reprogramming through bromodomain inhibition and extracellular matrix gene expression regulation. Stem Cells 2024; 42:706-719. [PMID: 38825983 PMCID: PMC11291304 DOI: 10.1093/stmcls/sxae039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 05/15/2024] [Indexed: 06/04/2024]
Abstract
The transformation from a fibroblast mesenchymal cell state to an epithelial-like state is critical for induced pluripotent stem cell (iPSC) reprogramming. In this report, we describe studies with PFI-3, a small-molecule inhibitor that specifically targets the bromodomains of SMARCA2/4 and PBRM1 subunits of SWI/SNF complex, as an enhancer of iPSC reprogramming efficiency. Our findings reveal that PFI-3 induces cellular plasticity in multiple human dermal fibroblasts, leading to a mesenchymal-epithelial transition during iPSC formation. This transition is characterized by the upregulation of E-cadherin expression, a key protein involved in epithelial cell adhesion. Additionally, we identified COL11A1 as a reprogramming barrier and demonstrated COL11A1 knockdown increased reprogramming efficiency. Notably, we found that PFI-3 significantly reduced the expression of numerous extracellular matrix (ECM) genes, particularly those involved in collagen assembly. Our research provides key insights into the early stages of iPSC reprogramming, highlighting the crucial role of ECM changes and cellular plasticity in this process.
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Affiliation(s)
- Jun Yang
- Chromatin and Gene Expression Section, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, United States
| | - H Karimi Kinyamu
- Chromatin and Gene Expression Section, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, United States
| | - James M Ward
- Integrative Bioinformatics, Biostatistics, National Institute of Environmental Health Sciences, Research Triangle Park, NC, United States
| | - Erica Scappini
- The Fluorescence Microscopy and Imaging Center, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, United States
| | - Ginger Muse
- Chromatin and Gene Expression Section, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, United States
| | - Trevor K Archer
- Chromatin and Gene Expression Section, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, United States
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4
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Rivera O, Sharma M, Dagar S, Shahani N, Ramĺrez-Jarquĺn UN, Crynen G, Karunadharma P, McManus F, Bonneil E, Pierre T, Subramaniam S. Rhes, a striatal enriched protein, regulates post-translational small-ubiquitin-like-modifier (SUMO) modification of nuclear proteins and alters gene expression. Cell Mol Life Sci 2024; 81:169. [PMID: 38589732 PMCID: PMC11001699 DOI: 10.1007/s00018-024-05181-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 01/26/2024] [Accepted: 02/20/2024] [Indexed: 04/10/2024]
Abstract
Rhes (Ras homolog enriched in the striatum), a multifunctional protein that regulates striatal functions associated with motor behaviors and neurological diseases, can shuttle from cell to cell via the formation of tunneling-like nanotubes (TNTs). However, the mechanisms by which Rhes mediates diverse functions remain unclear. Rhes is a small GTPase family member which contains a unique C-terminal Small Ubiquitin-like Modifier (SUMO) E3-like domain that promotes SUMO post-translational modification of proteins (SUMOylation) by promoting "cross-SUMOylation" of the SUMO enzyme SUMO E1 (Aos1/Uba2) and SUMO E2 ligase (Ubc-9). Nevertheless, the identity of the SUMO substrates of Rhes remains largely unknown. Here, by combining high throughput interactome and SUMO proteomics, we report that Rhes regulates the SUMOylation of nuclear proteins that are involved in the regulation of gene expression. Rhes increased the SUMOylation of histone deacetylase 1 (HDAC1) and histone 2B, while decreasing SUMOylation of heterogeneous nuclear ribonucleoprotein M (HNRNPM), protein polybromo-1 (PBRM1) and E3 SUMO-protein ligase (PIASy). We also found that Rhes itself is SUMOylated at 6 different lysine residues (K32, K110, K114, K120, K124, and K245). Furthermore, Rhes regulated the expression of genes involved in cellular morphogenesis and differentiation in the striatum, in a SUMO-dependent manner. Our findings thus provide evidence for a previously undescribed role for Rhes in regulating the SUMOylation of nuclear targets and in orchestrating striatal gene expression via SUMOylation.
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Affiliation(s)
- Oscar Rivera
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL, 33458, USA
| | - Manish Sharma
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL, 33458, USA
| | - Sunayana Dagar
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL, 33458, USA
| | - Neelam Shahani
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL, 33458, USA
| | - Uri Nimrod Ramĺrez-Jarquĺn
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL, 33458, USA
- National Institute of Cardiology Ignacio Chávez, Department of Pharmacology, Mexico, USA
| | - Gogce Crynen
- Bioinformatics and Statistics Core, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL, 33458, USA
| | - Pabalu Karunadharma
- Genomic Core, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL, 33458, USA
| | - Francis McManus
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec, Canada
| | - Eric Bonneil
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec, Canada
| | - Thibault Pierre
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec, Canada
- Department of Chemistry, Université de Montréal, Montréal, Québec, Canada
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, Canada
| | - Srinivasa Subramaniam
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL, 33458, USA.
- The Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, La Jolla, CA, 92037, USA.
- Norman Fixel Institute for Neurological Diseases, 3009 SW Williston Rd, Gainesville, FL, 32608, USA.
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5
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Bursch KL, Goetz CJ, Jiao G, Nuñez R, Olp MD, Dhiman A, Khurana M, Zimmermann MT, Urrutia RA, Dykhuizen EC, Smith BC. Cancer-associated polybromo-1 bromodomain 4 missense variants variably impact bromodomain ligand binding and cell growth suppression. J Biol Chem 2024; 300:107146. [PMID: 38460939 PMCID: PMC11002309 DOI: 10.1016/j.jbc.2024.107146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 02/12/2024] [Accepted: 02/29/2024] [Indexed: 03/11/2024] Open
Abstract
The polybromo, brahma-related gene 1-associated factors (PBAF) chromatin remodeling complex subunit polybromo-1 (PBRM1) contains six bromodomains that recognize and bind acetylated lysine residues on histone tails and other nuclear proteins. PBRM1 bromodomains thus provide a link between epigenetic posttranslational modifications and PBAF modulation of chromatin accessibility and transcription. As a putative tumor suppressor in several cancers, PBRM1 protein expression is often abrogated by truncations and deletions. However, ∼33% of PBRM1 mutations in cancer are missense and cluster within its bromodomains. Such mutations may generate full-length PBRM1 variant proteins with undetermined structural and functional characteristics. Here, we employed computational, biophysical, and cellular assays to interrogate the effects of PBRM1 bromodomain missense variants on bromodomain stability and function. Since mutations in the fourth bromodomain of PBRM1 (PBRM1-BD4) comprise nearly 20% of all cancer-associated PBRM1 missense mutations, we focused our analysis on PBRM1-BD4 missense protein variants. Selecting 16 potentially deleterious PBRM1-BD4 missense protein variants for further study based on high residue mutational frequency and/or conservation, we show that cancer-associated PBRM1-BD4 missense variants exhibit varied bromodomain stability and ability to bind acetylated histones. Our results demonstrate the effectiveness of identifying the unique impacts of individual PBRM1-BD4 missense variants on protein structure and function, based on affected residue location within the bromodomain. This knowledge provides a foundation for drawing correlations between specific cancer-associated PBRM1 missense variants and distinct alterations in PBRM1 function, informing future cancer personalized medicine approaches.
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Affiliation(s)
- Karina L Bursch
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA; Structural Genomics Unit, Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Christopher J Goetz
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Guanming Jiao
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana, USA
| | - Raymundo Nuñez
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Michael D Olp
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Alisha Dhiman
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana, USA
| | - Mallika Khurana
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Michael T Zimmermann
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA; Structural Genomics Unit, Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin, USA; Clinical and Translational Sciences Institute, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Raul A Urrutia
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA; Structural Genomics Unit, Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin, USA; Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Emily C Dykhuizen
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana, USA
| | - Brian C Smith
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA; Structural Genomics Unit, Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin, USA; Program in Chemical Biology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.
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6
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Sun M, Sun J, Sun W, Li X, Wang Z, Sun L, Wang Y. Unveiling the anticancer effects of SGLT-2i: mechanisms and therapeutic potential. Front Pharmacol 2024; 15:1369352. [PMID: 38595915 PMCID: PMC11002155 DOI: 10.3389/fphar.2024.1369352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 03/14/2024] [Indexed: 04/11/2024] Open
Abstract
Cancer and diabetes are significant diseases that pose a threat to human health. Their interconnection is complex, particularly when they coexist, often necessitating multiple therapeutic approaches to attain remission. Sodium-glucose cotransporter protein two inhibitors (SGLT-2i) emerged as a treatment for hyperglycemia, but subsequently exhibited noteworthy extra-glycemic properties, such as being registered for the treatment of heart failure and chronic kidney disease, especially with co-existing albuminuria, prompting its assessment as a potential treatment for various non-metabolic diseases. Considering its overall tolerability and established use in diabetes management, SGLT-2i may be a promising candidate for cancer therapy and as a supplementary component to conventional treatments. This narrative review aimed to examine the potential roles and mechanisms of SGLT-2i in the management of diverse types of cancer. Future investigations should focus on elucidating the antitumor efficacy of individual SGLT-2i in different cancer types and exploring the underlying mechanisms. Additionally, clinical trials to evaluate the safety and feasibility of incorporating SGLT-2i into the treatment regimen of specific cancer patients and determining appropriate dosage combinations with established antitumor agents would be of significant interest.
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Affiliation(s)
- Min Sun
- Department of Geriatrics, First Hospital, Jilin University, Changchun, China
| | - Jilei Sun
- Changchun Traditional Chinese Medicine Hospital, Changchun, China
| | - Wei Sun
- First Affiliated Hospital of Jilin University, Changchun, China
| | - Xiaonan Li
- Department of Geriatrics, First Hospital, Jilin University, Changchun, China
| | - Zhe Wang
- Department of Geriatrics, First Hospital, Jilin University, Changchun, China
| | - Liwei Sun
- Research Center of Traditional Chinese Medicine, The Affiliated Hospital to Changchun University of Chinese Medicine, Changchun, China
| | - Yuehui Wang
- Department of Geriatrics, First Hospital, Jilin University, Changchun, China
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7
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Fultang N, Schwab AM, McAneny-Droz S, Grego A, Rodgers S, Torres BV, Heiser D, Scherle P, Bhagwat N. PBRM1 loss is associated with increased sensitivity to MCL1 and CDK9 inhibition in clear cell renal cancer. Front Oncol 2024; 14:1343004. [PMID: 38371625 PMCID: PMC10869502 DOI: 10.3389/fonc.2024.1343004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 01/19/2024] [Indexed: 02/20/2024] Open
Abstract
MCL1 is a member of the BCL2 family of apoptosis regulators, which play a critical role in promoting cancer survival and drug resistance. We previously described PRT1419, a potent, MCL1 inhibitor with anti-tumor efficacy in various solid and hematologic malignancies. To identify novel biomarkers that predict sensitivity to MCL1 inhibition, we conducted a gene essentiality analysis using gene dependency data generated from CRISPR/Cas9 cell viability screens. We observed that clear cell renal cancer (ccRCC) cell lines with damaging PBRM1 mutations displayed a strong dependency on MCL1. PBRM1 (BAF180), is a chromatin-targeting subunit of mammalian pBAF complexes. PBRM1 is frequently altered in various cancers particularly ccRCC with ~40% of tumors harboring damaging PBRM1 alterations. We observed potent inhibition of tumor growth and induction of apoptosis by PRT1419 in various preclinical models of PBRM1-mutant ccRCC but not PBRM1-WT. Depletion of PBRM1 in PBRM1-WT ccRCC cell lines induced sensitivity to PRT1419. Mechanistically, PBRM1 depletion coincided with increased expression of pro-apoptotic factors, priming cells for caspase-mediated apoptosis following MCL1 inhibition. Increased MCL1 activity has been described as a resistance mechanism to Sunitinib and Everolimus, two approved agents for ccRCC. PRT1419 synergized with both agents to potently inhibit tumor growth in PBRM1-loss ccRCC. PRT2527, a potent CDK9 inhibitor which depletes MCL1, was similarly efficacious in monotherapy and in combination with Sunitinib in PBRM1-loss cells. Taken together, these findings suggest PBRM1 loss is associated with MCL1i sensitivity in ccRCC and provide rationale for the evaluation of PRT1419 and PRT2527 for the treatment for PBRM1-deficient ccRCC.
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8
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Ho PJ, Kweon J, Blumensaadt LA, Neely AE, Kalika E, Leon DB, Oh S, Stringer CWP, Lloyd SM, Ren Z, Bao X. Multi-omics integration identifies cell-state-specific repression by PBRM1-PIAS1 cooperation. CELL GENOMICS 2024; 4:100471. [PMID: 38190100 PMCID: PMC10794847 DOI: 10.1016/j.xgen.2023.100471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 10/24/2023] [Accepted: 11/30/2023] [Indexed: 01/09/2024]
Abstract
PBRM1 is frequently mutated in cancers of epithelial origin. How PBRM1 regulates normal epithelial homeostasis, prior to cancer initiation, remains unclear. Here, we show that PBRM1's gene regulatory roles differ drastically between cell states, leveraging human skin epithelium (epidermis) as a research platform. In progenitors, PBRM1 predominantly functions to repress terminal differentiation to sustain progenitors' regenerative potential; in the differentiation state, however, PBRM1 switches toward an activator. Between these two cell states, PBRM1 retains its genomic binding but associates with differential interacting proteins. Our targeted screen identified the E3 SUMO ligase PIAS1 as a key interactor. PIAS1 co-localizes with PBRM1 on chromatin to directly repress differentiation genes in progenitors, and PIAS1's chromatin binding drastically diminishes in differentiation. Furthermore, SUMOylation contributes to PBRM1's repressive function in progenitor maintenance. Thus, our findings highlight PBRM1's cell-state-specific regulatory roles influenced by its protein interactome despite its stable chromatin binding.
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Affiliation(s)
- Patric J Ho
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Junghun Kweon
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Laura A Blumensaadt
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Amy E Neely
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Elizabeth Kalika
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Daniel B Leon
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Sanghyon Oh
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Cooper W P Stringer
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Sarah M Lloyd
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Ziyou Ren
- Department of Dermatology, Northwestern University, Chicago, IL 60611, USA
| | - Xiaomin Bao
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA; Department of Dermatology, Northwestern University, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA.
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9
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Yang J, Karimi Kinyamu H, Ward JM, Scappini E, Archer TK. Unlocking cellular plasticity: Enhancing human iPSC reprogramming through bromodomain inhibition and extracellular matrix gene expression regulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.13.562265. [PMID: 37873209 PMCID: PMC10592827 DOI: 10.1101/2023.10.13.562265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
The transformation of fibroblasts into epithelial cells is critical for iPSC reprogramming. In this report, we describe studies with PFI-3, a small molecule inhibitor that specifically targets the bromodomains of SMARCA2/4 and PBRM1 subunit of SWI/SNF complex, as an enhancer of iPSC reprogramming efficiency. Our findings revealed that PFI-3 induces cellular plasticity in multiple human dermal fibroblasts, leading to a mesenchymal-epithelial transition (MET) during iPSC formation. This transition was characterized by the upregulation of E-cadherin expression, a key protein involved in epithelial cell adhesion. Additionally, we identified COL11A1 as a reprogramming barrier and demonstrated COL11A1 knockdown increased reprogramming efficiency. Notably, we found that PFI-3 significantly reduced the expression of numerous extracellular matrix (ECM) genes, particularly those involved in collagen assembly. Our research provides key insights into the early stages of iPSC reprogramming, highlighting the crucial role of ECM changes and cellular plasticity in this process.
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10
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Abstract
Bromodomains are acetyl-lysine binding modules that are found in different classes of chromatin-interacting proteins. Among these are large chromatin remodeling complexes such as BAF and PBAF (variants of human SWI/SNF). Previous work has identified chemical probes targeting a subset of the bromodomains present in the BAF and PBAF complexes. Selective inhibitors of the individual bromodomains have proven challenging to discover, as the domains are highly similar. Here, elaboration of an aminopyridazine scaffold used previously to develop probes for the bromodomains of SMARCA2, SMARCA4, and the fifth bromodomain of PBRM1 yielded compounds with both potency and unusual selectivity for the second bromodomain of PBRM1. One of these, GNE-235, and its enantiomer control GNE-234 are suggested for initial cellular investigations of the function of the second bromodomain of PBRM1.
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Affiliation(s)
- Andrea G Cochran
- Department of Biological Chemistry, Genentech, Inc., South San Francisco, California 94080, United States
| | - Megan Flynn
- Department of Biological Chemistry, Genentech, Inc., South San Francisco, California 94080, United States
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11
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Li X, Li M, Zhao T, Zhang J. The discovery of promising candidate biomarkers in kidney renal clear cell carcinoma: evidence from the in-depth analysis of high-throughput data. Am J Cancer Res 2023; 13:4288-4304. [PMID: 37818073 PMCID: PMC10560940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 07/11/2023] [Indexed: 10/12/2023] Open
Abstract
Kidney renal clear cell carcinoma (KIRC) is the most prevalent subtype of renal tumor. The underlying mechanisms governing KIRC initiation and progression are less known. The present study aimed to reveal novel hub genes associated with the initiation and progression of KIRC, which may be utilized as novel molecular biomarkers and therapeutic targets for the treatment of KIRC. The GSE6344 dataset from the Gene Expression Omnibus (GEO) database was integrated to identify differentially expressed genes (DEGs) using the limma package. Then, hub genes were identified and UALCAN, GEPIA, OncoDB, DriverDBv3, GENT2, and HPA databases were employed for the expression, survival, and methylation analyses. cBioPortal tool was used to investigate the genetic alterations, while CancerSEA, TIMER, DAVID, ENCORI, DrugBank, and GSCAlite were utilized to explore a few more hub gene-associated parameters. Finally, targeted bisulfite sequencing (bisulfite-seq), and RT-qPCR techniques were used to validate the expression and methylation level of the hub genes using Human RCC cell line 786-O, A-498, and normal renal tubular epithelial cell line HK-2. In total, 7299 DEGs were found between KIRC and normal samples in the GSE6344 dataset. Using STRING and Cytohubba analysis, four hub genes including VEGFA (vascular endothelial growth factor), ALB (Albumin), ENO2 (enolase 2), and CAVI1 (Caveolin 1) were selected as the hub genes. Further, it was validated through extensive analysis of TCGA datasets that these VEGA, ENO2, and CAV1 hub genes were significantly up-regulated, while ALB was significantly down-regulated in KIRC samples compared to controls. The dysregulation of these genes was found to be associated with the overall survival (OS) of the KIRC patients. Moreover, this study also revealed some novel links between VEGA, ALB, ENO2, and CAV1 expression and genetic alterations, promoter methylation status, immune cell infiltration, miRNAs, gene enrichment terms, and various chemotherapeutic drugs. The present study revealed a panel of four hub genes, which contributed to improving our understanding of the underlying molecular mechanisms of KIRC development and can be utilized as promising novel biomarkers for KIRC diagnosis, prognosis, and treatment.
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Affiliation(s)
- Xue Li
- Central People's Hospital of Zhanjiang Zhanjiang, Guangdong, China
| | - Mingfeng Li
- Central People's Hospital of Zhanjiang Zhanjiang, Guangdong, China
| | - Tianyu Zhao
- Central People's Hospital of Zhanjiang Zhanjiang, Guangdong, China
| | - Jingyu Zhang
- Central People's Hospital of Zhanjiang Zhanjiang, Guangdong, China
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12
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Vemana HP, Dukhande VV. The effect of hormones insulin and glucagon on ubiquitin modifications elucidated by proteomics in liver cells. Life Sci 2023; 329:121935. [PMID: 37442415 PMCID: PMC10528490 DOI: 10.1016/j.lfs.2023.121935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 07/02/2023] [Accepted: 07/10/2023] [Indexed: 07/15/2023]
Abstract
AIMS Insulin action is intertwined with changing levels of glucose and counter-regulatory hormone glucagon. While insulin lowers blood sugar level, glucagon raises it by promoting the breakdown of the stored glycogen in liver and releases glucose into the bloodstream. The hormones insulin and glucagon are key in the pathogenesis of type 2 diabetes (T2D). Insulin resistance is a primary predisposing factor for diabetes. Phosphorylation of insulin signaling molecules is altered in the insulin-resistant state. However, ubiquitin (Ub) modifications in insulin-resistant state are relatively understudied. To dissect the underlying mechanisms, we performed a proteomics study on hepatoma cells to study the regulation of ubiquitination by insulin and glucagon. MATERIALS AND METHODS We performed western blotting, immunoprecipitations, and affinity pull down using tandem Ub binding entities (TUBE) reagents on hepatoma cells treated with insulin or glucagon. Next, we performed MS/MS analysis on Ub-linkage specific affinity pull down samples. Gene ontology analysis and protein-protein interaction network analysis was performed using DAVID GO and STRING db, respectively. KEY FINDINGS The ubiquitination pattern of total Ub, K48-linked Ub, and K63-linked Ub was altered with the treatment of hormones insulin and glucagon. Ubiquitination in immunoprecipitated samples showed enrichment with total Ub and K48-linked Ub but not with K63-linked Ub. Ubiquitination by treatment with hormones mainly enriched key signaling pathways MAPK, Akt, oxidative stress etc. SIGNIFICANCE: Our study identified key altered proteins and signal transduction pathways which aids in understanding the mechanisms of hormonal action on ubiquitination and identify new therapeutic targets for T2D.
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Affiliation(s)
- Hari Priya Vemana
- Department of Pharmaceutical Sciences, College of Pharmacy & Health Sciences, St. John's University, Queens, NY 11439, USA
| | - Vikas V Dukhande
- Department of Pharmaceutical Sciences, College of Pharmacy & Health Sciences, St. John's University, Queens, NY 11439, USA.
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13
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Petell CJ, Burkholder NT, Ruiz PA, Skela J, Foreman JR, Southwell LE, Temple BR, Krajewski K, Strahl BD. The bromo-adjacent homology domains of PBRM1 associate with histone tails and contribute to PBAF-mediated gene regulation. J Biol Chem 2023; 299:104996. [PMID: 37394010 PMCID: PMC10425938 DOI: 10.1016/j.jbc.2023.104996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 06/14/2023] [Accepted: 06/16/2023] [Indexed: 07/04/2023] Open
Abstract
A critical component of gene regulation is recognition of histones and their post-translational modifications by transcription-associated proteins or complexes. Although many histone-binding reader modules have been characterized, the bromo-adjacent homology (BAH) domain family of readers is still poorly characterized. A pre-eminent member of this family is PBRM1 (BAF180), a component of the PBAF chromatin-remodeling complex. PBRM1 contains two adjacent BAH domains of unknown histone-binding potential. We evaluated the tandem BAH domains for their capacity to associate with histones and to contribute to PBAF-mediated gene regulation. The BAH1 and BAH2 domains of human PBRM1 broadly interacted with histone tails, but they showed a preference for unmodified N-termini of histones H3 and H4. Molecular modeling and comparison of the BAH1 and BAH2 domains with other BAH readers pointed to a conserved binding mode via an extended open pocket and, in general, an aromatic cage for histone lysine binding. Point mutants that were predicted to disrupt the interaction between the BAH domains and histones reduced histone binding in vitro and resulted in dysregulation of genes targeted by PBAF in cellulo. Although the BAH domains in PBRM1 were important for PBAF-mediated gene regulation, we found that overall chromatin targeting of PBRM1 was not dependent on BAH-histone interaction. Our findings identify a function of the PBRM1 BAH domains in PBAF activity that is likely mediated by histone tail interaction.
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Affiliation(s)
- Christopher J Petell
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Nathaniel T Burkholder
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Paloma A Ruiz
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jessica Skela
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jake R Foreman
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Lauren E Southwell
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Brenda R Temple
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; R L Juliano Structural Bioinformatics Core Facility, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Krzysztof Krajewski
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Brian D Strahl
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
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14
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Martin SD, Bhuiyan I, Soleimani M, Wang G. Biomarkers for Immune Checkpoint Inhibitors in Renal Cell Carcinoma. J Clin Med 2023; 12:4987. [PMID: 37568390 PMCID: PMC10419620 DOI: 10.3390/jcm12154987] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 08/13/2023] Open
Abstract
Immune checkpoint inhibitor (ICI) therapy has revolutionized renal cell carcinoma treatment. Patients previously thought to be palliative now occasionally achieve complete cures from ICI. However, since immunotherapies stimulate the immune system to induce anti-tumor immunity, they often lead to adverse autoimmunity. Furthermore, some patients receive no benefit from ICI, thereby unnecessarily risking adverse events. In many tumor types, PD-L1 expression levels, immune infiltration, and tumor mutation burden predict the response to ICI and help inform clinical decision making to better target ICI to patients most likely to experience benefits. Unfortunately, renal cell carcinoma is an outlier, as these biomarkers fail to discriminate between positive and negative responses to ICI therapy. Emerging biomarkers such as gene expression profiles and the loss of pro-angiogenic proteins VHL and PBRM-1 show promise for identifying renal cell carcinoma cases likely to respond to ICI. This review provides an overview of the mechanistic underpinnings of different biomarkers and describes the theoretical rationale for their use. We discuss the effectiveness of each biomarker in renal cell carcinoma and other cancer types, and we introduce novel biomarkers that have demonstrated some promise in clinical trials.
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Affiliation(s)
- Spencer D. Martin
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC V5Z 1M9, Canada;
| | - Ishmam Bhuiyan
- Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z3, Canada;
| | - Maryam Soleimani
- Division of Medical Oncology, Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z3, Canada;
- British Columbia Cancer Vancouver Centre, Vancouver, BC V5Z 4E6, Canada
| | - Gang Wang
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC V5Z 1M9, Canada;
- British Columbia Cancer Vancouver Centre, Vancouver, BC V5Z 4E6, Canada
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15
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De Silva SM, Dhiman A, Sood S, Mercedes KF, Simmons W, Henen M, Vögeli B, Dykhuizen E, Musselman C. PBRM1 bromodomains associate with RNA to facilitate chromatin association. Nucleic Acids Res 2023; 51:3631-3649. [PMID: 36808431 PMCID: PMC10164552 DOI: 10.1093/nar/gkad072] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 01/03/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
PBRM1 is a subunit of the PBAF chromatin remodeling complex, which is mutated in 40-50% of clear cell renal cell carcinoma patients. It is thought to largely function as a chromatin binding subunit of the PBAF complex, but the molecular mechanism underlying this activity is not fully known. PBRM1 contains six tandem bromodomains which are known to cooperate in binding of nucleosomes acetylated at histone H3 lysine 14 (H3K14ac). Here, we demonstrate that the second and fourth bromodomains from PBRM1 also bind nucleic acids, selectively associating with double stranded RNA elements. Disruption of the RNA binding pocket is found to compromise PBRM1 chromatin binding and inhibit PBRM1-mediated cellular growth effects.
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Affiliation(s)
- Saumya M De Silva
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA
| | - Alisha Dhiman
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
| | - Surbhi Sood
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
| | - Kilsia F Mercedes
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - William J Simmons
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Morkos A Henen
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Beat Vögeli
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Emily C Dykhuizen
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
| | - Catherine A Musselman
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA
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16
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Badoiu SC, Greabu M, Miricescu D, Stanescu-Spinu II, Ilinca R, Balan DG, Balcangiu-Stroescu AE, Mihai DA, Vacaroiu IA, Stefani C, Jinga V. PI3K/AKT/mTOR Dysregulation and Reprogramming Metabolic Pathways in Renal Cancer: Crosstalk with the VHL/HIF Axis. Int J Mol Sci 2023; 24:8391. [PMID: 37176098 PMCID: PMC10179314 DOI: 10.3390/ijms24098391] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/26/2023] [Accepted: 05/04/2023] [Indexed: 05/15/2023] Open
Abstract
Renal cell carcinoma (RCC) represents 85-95% of kidney cancers and is the most frequent type of renal cancer in adult patients. It accounts for 3% of all cancer cases and is in 7th place among the most frequent histological types of cancer. Clear cell renal cell carcinoma (ccRCC), accounts for 75% of RCCs and has the most kidney cancer-related deaths. One-third of the patients with ccRCC develop metastases. Renal cancer presents cellular alterations in sugars, lipids, amino acids, and nucleic acid metabolism. RCC is characterized by several metabolic dysregulations including oxygen sensing (VHL/HIF pathway), glucose transporters (GLUT 1 and GLUT 4) energy sensing, and energy nutrient sensing cascade. Metabolic reprogramming represents an important characteristic of the cancer cells to survive in nutrient and oxygen-deprived environments, to proliferate and metastasize in different body sites. The phosphoinositide 3-kinase-AKT-mammalian target of the rapamycin (PI3K/AKT/mTOR) signaling pathway is usually dysregulated in various cancer types including renal cancer. This molecular pathway is frequently correlated with tumor growth and survival. The main aim of this review is to present renal cancer types, dysregulation of PI3K/AKT/mTOR signaling pathway members, crosstalk with VHL/HIF axis, and carbohydrates, lipids, and amino acid alterations.
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Affiliation(s)
- Silviu Constantin Badoiu
- Department of Anatomy and Embryology, Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 8 Eroii Sanitari Blvd, 050474 Bucharest, Romania;
| | - Maria Greabu
- Department of Biochemistry, Faculty of Dentistry, Carol Davila University of Medicine and Pharmacy, 8 Eroii Sanitari Blvd, Sector 5, 050474 Bucharest, Romania;
| | - Daniela Miricescu
- Department of Biochemistry, Faculty of Dentistry, Carol Davila University of Medicine and Pharmacy, 8 Eroii Sanitari Blvd, Sector 5, 050474 Bucharest, Romania;
| | - Iulia-Ioana Stanescu-Spinu
- Department of Biochemistry, Faculty of Dentistry, Carol Davila University of Medicine and Pharmacy, 8 Eroii Sanitari Blvd, Sector 5, 050474 Bucharest, Romania;
| | - Radu Ilinca
- Department of Medical Informatics and Biostatistics, Faculty of Dentistry, Carol Davila University of Medicine and Pharmacy, 8 Eroii Sanitari Blvd, 050474 Bucharest, Romania;
| | - Daniela Gabriela Balan
- Department of Physiology, Faculty of Dentistry, Carol Davila University of Medicine and Pharmacy, 8 Eroii Sanitari Blvd, 050474 Bucharest, Romania; (D.G.B.); (A.-E.B.-S.)
| | - Andra-Elena Balcangiu-Stroescu
- Department of Physiology, Faculty of Dentistry, Carol Davila University of Medicine and Pharmacy, 8 Eroii Sanitari Blvd, 050474 Bucharest, Romania; (D.G.B.); (A.-E.B.-S.)
| | - Doina-Andrada Mihai
- Department of Diabetes, Nutrition and Metabolic Diseases, Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 8 Eroii Sanitari Blvd, 050474 Bucharest, Romania;
| | - Ileana Adela Vacaroiu
- Department of Nephrology, Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania;
| | - Constantin Stefani
- Department of Family Medicine and Clinical Base, Dr. Carol Davila Central Military Emergency University Hospital, 134 Calea Plevnei, 010825 Bucharest, Romania;
| | - Viorel Jinga
- Department of Urology, “Prof. Dr. Theodor Burghele” Hospital, 050653 Bucharest, Romania
- “Prof. Dr. Theodor Burghele” Clinical Hospital, University of Medicine and Pharmacy Carol Davila, 050474 Bucharest, Romania
- Medical Sciences Section, Academy of Romanian Scientists, 050085 Bucharest, Romania
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17
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Comprehensive analysis of immune subtypes reveals the prognostic value of cytotoxicity and FAP + fibroblasts in stomach adenocarcinoma. Cancer Immunol Immunother 2023; 72:1763-1778. [PMID: 36650362 DOI: 10.1007/s00262-023-03368-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 01/04/2023] [Indexed: 01/18/2023]
Abstract
BACKGROUND The heterogeneity limits the effective application of immune checkpoint inhibitors for patients with stomach adenocarcinoma (STAD). Precise immunotyping can help select people who may benefit from immunotherapy and guide postoperative management by describing the characteristics of tumor microenvironment. METHODS Gene expression profiles and clinical information of patients were collected from ACRG and TCGA-STAD datasets. The immune subtypes (ISs) were identified by consensus clustering analysis. The tumor immune microenvironments (TIME) of each IS were characterized using a series of immunogenomics methods and further confirmed by multiplex immunohistochemistry (mIHC) staining in clinical samples. Two online datasets and one in-house dataset were utilized to construct and validate a prognostic immune-related gene (IRG) signature. RESULTS STAD patients were stratified into five reproducible ISs. IS1 (immune deserve subtype) had low immune infiltration and the highest degree of HER2 gene mutation. With abundant CD8+ T cells infiltration and activated cytotoxicity reaction, patients in the IS2 (immune-activated subtype) had the best overall survival (OS). IS3 and IS4 subtypes were both in the reactive stroma state and indicated the worst prognosis. However, IS3 (immune-inhibited subtype) was characterized by enrichment of FAP+ fibroblasts and upregulated TGF-β signaling pathway, while IS4 (activated stroma subtype) was characterized by enrichment of ACTA2+ fibroblasts. In addition, mIHC staining confirmed that TGF-β upregulated FAP+ fibroblasts were independent risk factor of OS. IS5 (chronic inflammation subtype) displayed moderate immune cells infiltration and had a relatively good survival. Lastly, we developed a nine-IRG signature model with a robust performance on overall survival prognostication. CONCLUSIONS The immunotyping is indicative for characterize the TIME heterogeneity and the prediction of tumor prognosis for STADs, which may provide valuable stratification for the design of future immunotherapy.
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18
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Czerwinska P, Mackiewicz AA. Bromodomain (BrD) Family Members as Regulators of Cancer Stemness-A Comprehensive Review. Int J Mol Sci 2023; 24:995. [PMID: 36674511 PMCID: PMC9861003 DOI: 10.3390/ijms24020995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/30/2022] [Accepted: 12/31/2022] [Indexed: 01/06/2023] Open
Abstract
Epigenetic mechanisms involving DNA methylation and chromatin modifications have emerged as critical facilitators of cancer heterogeneity, substantially affecting cancer development and progression, modulating cell phenotypes, and enhancing or inhibiting cancer cell malignant properties. Not surprisingly, considering the importance of epigenetic regulators in normal stem cell maintenance, many chromatin-related proteins are essential to maintaining the cancer stem cell (CSC)-like state. With increased tumor-initiating capacities and self-renewal potential, CSCs promote tumor growth, provide therapy resistance, spread tumors, and facilitate tumor relapse after treatment. In this review, we characterized the epigenetic mechanisms that regulate the acquisition and maintenance of cancer stemness concerning selected epigenetic factors belonging to the Bromodomain (BrD) family of proteins. An increasing number of BrD proteins reinforce cancer stemness, supporting the maintenance of the cancer stem cell population in vitro and in vivo via the utilization of distinct mechanisms. As bromodomain possesses high druggable potential, specific BrD proteins might become novel therapeutic targets in cancers exhibiting de-differentiated tumor characteristics.
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Affiliation(s)
- Patrycja Czerwinska
- Department of Cancer Immunology, Poznan University of Medical Sciences, 61-866 Poznan, Poland
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, 61-866 Poznan, Poland
| | - Andrzej Adam Mackiewicz
- Department of Cancer Immunology, Poznan University of Medical Sciences, 61-866 Poznan, Poland
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, 61-866 Poznan, Poland
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19
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Gan L, Li Q, Nie W, Zhang Y, Jiang H, Tan C, Zhang L, Zhang J, Li Q, Hou P, Yuan Y, Sun X, Liu D, Sheng W, Liu T, Xu M, Guo W. PROX1-mediated epigenetic silencing of SIRT3 contributes to proliferation and glucose metabolism in colorectal cancer. Int J Biol Sci 2023; 19:50-65. [PMID: 36594098 PMCID: PMC9760442 DOI: 10.7150/ijbs.73530] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 10/12/2022] [Indexed: 11/24/2022] Open
Abstract
Prospero-related homeobox 1 (PROX1) is a homeobox transcription factor known to promote malignant transformation and stemness in human colorectal cancer (CRC). However, the biological function of PROX1 in metabolic rearrangement in CRC remains unclear. Here, we aimed to uncover the relationship between the expression profile and role of PROX1 and CRC cell glucose metabolism and to elucidate the underlying molecular mechanism. PROX1 expression was significantly upregulated in human CRC tissues and positively associated with the maximum standardized uptake value (SUVmax), a measure of tissue 18-fluoro-2-deoxy-D-glucose uptake and an indicator of glycolysis and tumor cell activity, in patients with CRC. Knockdown of PROX1 suppressed CRC cell proliferation and glucose metabolism in vitro and in vivo. Mechanistically, through a physical interaction, PROX1 recruited EZH2 to the SIRT3 promoter and inhibited SIRT3 promoter activity. Moreover, PROX1 or EZH2 knockdown decreased cell glycolysis by targeting SIRT3. Clinically, high PROX1 expression combined with low SIRT3 expression predicted poor prognosis in patients with CRC. Thus, our study suggests that the PROX1-EZH2 complex positively regulates cell proliferation and glucose metabolism by engaging SIRT3 in CRC, which may serve as a promising therapeutic strategy for CRC.
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Affiliation(s)
- Lu Gan
- Department of Gastrointestinal Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.,Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Qingguo Li
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.,Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
| | - Wei Nie
- Department of Pulmonary Medicine, Shanghai Chest Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200032, China
| | - Yi Zhang
- Department of Gastroenterology & Clinical Nutrition, The 452nd Hospital of PLA, Chengdu 610000, Sichuan, China
| | - Hesheng Jiang
- Department of Surgery, United Health Services Southern California Medical Education Consortium, Temecula Valley Hospital, Temecula, CA 92592, USA
| | - Cong Tan
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.,Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China.,Institute of Pathology, Fudan University, Shanghai, 200032, China
| | - Long Zhang
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.,Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
| | - Jieyun Zhang
- Department of Gastrointestinal Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Qian Li
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Pengcong Hou
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Yitao Yuan
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Xun Sun
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Dongmei Liu
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Weiqi Sheng
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.,Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China.,Institute of Pathology, Fudan University, Shanghai, 200032, China
| | - Tianshu Liu
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Midie Xu
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.,Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China.,Institute of Pathology, Fudan University, Shanghai, 200032, China.,✉ Corresponding authors: Weijian Guo, PhD, Department of Gastrointestinal Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China. E-mail: ; Midie Xu, PhD, Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China. E-mail:
| | - Weijian Guo
- Department of Gastrointestinal Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.,✉ Corresponding authors: Weijian Guo, PhD, Department of Gastrointestinal Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China. E-mail: ; Midie Xu, PhD, Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China. E-mail:
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20
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Kim HJ, Seo BG, Seo EC, Lee KM, Hwangbo C. Checkpoint Kinase 1 (CHK1) Functions as Both a Diagnostic Marker and a Regulator of Epithelial-to-Mesenchymal Transition (EMT) in Triple-Negative Breast Cancer. Curr Issues Mol Biol 2022; 44:5848-5865. [PMID: 36547059 PMCID: PMC9777496 DOI: 10.3390/cimb44120398] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/17/2022] [Accepted: 11/19/2022] [Indexed: 11/25/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is more difficult to treat and has a higher mortality rate than other subtypes. Although hormone receptor-targeted therapy is an effective treatment to increase survival rate in breast cancer patients, it is not suitable for TNBC patients. To address the issues, differentially expressed genes (DEGs) in TNBC patients from the Gene Expression Omnibus (GEO) database were analyzed. A total of 170 genes were obtained from three Genomic Spatial Events (GSEs) using the intersection of each GSE dataset and 61 DEGs were identified after validation with the gene enrichment analysis. We combined this with the degree scores from the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and protein-protein interaction (PPI) network, of which 7 genes were correlated with survival rate. Finally, a proteomics database revealed that only the CHK1 protein level was differently expressed in basal-like compared with other subtypes. We demonstrated that CHK1 expression was higher in TNBC cell lines compared with non-TNBC cell lines, and CHK1 promotes epithelial to mesenchymal transition (EMT) as well as migration and invasion ability. Our study provides new insight into the TNBC subnetwork that may be useful in the prognosis and treatment of TNBC patients.
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Affiliation(s)
- Hyo-Jin Kim
- Division of Life Science, College of Natural Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea
- Division of Applied Life Science (BK21 Four), PMBBRC and Research Institute of Life Sciences, Geongsang National University, Jinju 52828, Republic of Korea
- Correspondence: (H.-J.K.); (C.H.)
| | - Bo-Gyeong Seo
- Division of Life Science, College of Natural Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea
- Division of Applied Life Science (BK21 Four), PMBBRC and Research Institute of Life Sciences, Geongsang National University, Jinju 52828, Republic of Korea
| | - Eun-Chan Seo
- Division of Life Science, College of Natural Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea
- Division of Applied Life Science (BK21 Four), PMBBRC and Research Institute of Life Sciences, Geongsang National University, Jinju 52828, Republic of Korea
| | - Kwang-Min Lee
- Division of Life Science, College of Natural Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea
- Division of Applied Life Science (BK21 Four), PMBBRC and Research Institute of Life Sciences, Geongsang National University, Jinju 52828, Republic of Korea
| | - Cheol Hwangbo
- Division of Life Science, College of Natural Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea
- Division of Applied Life Science (BK21 Four), PMBBRC and Research Institute of Life Sciences, Geongsang National University, Jinju 52828, Republic of Korea
- Correspondence: (H.-J.K.); (C.H.)
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21
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Brooks R, Monzy J, Aaron B, Zhang X, Kossenkov A, Hayden J, Keeney F, Speicher DW, Zhang L, Dang CV. Circadian lncRNA ADIRF-AS1 binds PBAF and regulates renal clear cell tumorigenesis. Cell Rep 2022; 41:111514. [PMID: 36261012 PMCID: PMC9652615 DOI: 10.1016/j.celrep.2022.111514] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 05/25/2022] [Accepted: 09/26/2022] [Indexed: 11/20/2022] Open
Abstract
We identify ADIRF-AS1 circadian long non-coding RNA (lncRNA). Deletion of ADIRF-AS1 in U2OS cells alters rhythmicity of clock-controlled genes and expression of extracellular matrix genes. ADIRF-AS1 interacts with all components of the PBAF (PBRM1/BRG1) complex in U2OS cells. Because PBRM1 is a tumor suppressor mutated in over 40% of clear cell renal carcinoma (ccRCC) cases, we evaluate ADIRF-AS1 in ccRCC cells. Reducing ADIRF-AS1 expression in ccRCC cells decreases expression of some PBAF-suppressed genes. Expression of these genes is partially rescued by PBRM1 loss, consistent with ADIRF-AS1 acting in part to modulate PBAF. ADIRF-AS1 expression correlates with survival in human ccRCC, particularly in PBRM1 wild-type, but not mutant, tumors. Loss of ADIRF-AS1 eliminates in vivo tumorigenesis, partially rescued by concurrent loss of PBRM1 only when co-injected with Matrigel, suggesting a PBRM1-independent function of ADIRF-AS1. Our findings suggest that ADIRF-AS1 functions partly through PBAF to regulate specific genes as a BMAL1-CLOCK-regulated, oncogenic lncRNA.
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Affiliation(s)
- Rebekah Brooks
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; The Wistar Institute, Philadelphia, PA, USA; The Ludwig Institute for Cancer Research, New York, NY, USA
| | - Judith Monzy
- The Wistar Institute, Philadelphia, PA, USA; The Ludwig Institute for Cancer Research, New York, NY, USA
| | - Bailey Aaron
- The Wistar Institute, Philadelphia, PA, USA; The Ludwig Institute for Cancer Research, New York, NY, USA
| | - Xue Zhang
- The Wistar Institute, Philadelphia, PA, USA; The Ludwig Institute for Cancer Research, New York, NY, USA
| | | | - James Hayden
- The Ludwig Institute for Cancer Research, New York, NY, USA
| | | | | | - Lin Zhang
- Center for Research on Reproduction & Women's Health, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Obstetrics and Gynecology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Chi V Dang
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; The Wistar Institute, Philadelphia, PA, USA; The Ludwig Institute for Cancer Research, New York, NY, USA.
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22
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Zhou Z, Hu F, Huang D, Chi Q, Tang NLS. Nonsense-Mediated Decay Targeted RNA (ntRNA): Proposal of a ntRNA–miRNA–lncRNA Triple Regulatory Network Usable as Biomarker of Prognostic Risk in Patients with Kidney Cancer. Genes (Basel) 2022; 13:genes13091656. [PMID: 36140823 PMCID: PMC9498815 DOI: 10.3390/genes13091656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/05/2022] [Accepted: 09/08/2022] [Indexed: 11/16/2022] Open
Abstract
The most prevalent subtype of renal cell carcinoma (RCC), kidney renal clear cell carcinoma (KIRC) may be associated with a poor prognosis in a high number of cases, with a stage-specific prognostic stratification currently in use. No reliable biomarkers have been utilized so far in clinical practice despite the efforts in biomarker research in the last years. Nonsense-mediated mRNA decay (NMD) is a critical safeguard against erroneous transcripts, particularly mRNA transcripts containing premature termination codons (called nonsense-mediated decay targeted RNA, ntRNA). In this study, we first characterized 296 differentially expressed ntRNAs that were independent of the corresponding gene, 261 differentially expressed miRNAs, and 4653 differentially expressed lncRNAs. Then, we constructed a hub ntRNA–miRNA–lncRNA triple regulatory network associated with the prognosis of KIRC. Moreover, the results of immune infiltration analysis indicated that this network may influence the changes of the tumor immune microenvironment. A prognostic model derived from the genes and immune cells associated with the network was developed to distinguish between high- and low-risk patients, which was a better prognostic than other models, constructed using different biomarkers. Additionally, correlation of methylation and ntRNAs in the network suggested that some ntRNAs were regulated by methylation, which is helpful to further study the causes of abnormal expression of ntRNAs. In conclusion, this study highlighted the possible clinical implications of ntRNA functions in KIRC, proposing potential significant biomarkers that could be utilized to define the prognosis and design personalized treatment plans in kidney cancer management in the next future.
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Affiliation(s)
- Zhiyue Zhou
- Department of Statistics, School of Science, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, China
| | - Fuyan Hu
- Department of Statistics, School of Science, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, China
- Correspondence: (F.H.); (N.L.S.T.)
| | - Dan Huang
- Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
| | - Qingjia Chi
- Department of Engineering Structure and Mechanics, School of Science, Wuhan University of Technology, Wuhan 430070, China
| | - Nelson L. S. Tang
- Department of Chemical Pathology and Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
- Functional Genomics and Biostatistical Computing Laboratory, CUHK Shenzhen Research Institute, Shenzhen 518000, China
- Hong Kong Branch of CAS Center for Excellence in Animal Evolution and Genetics, School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
- Correspondence: (F.H.); (N.L.S.T.)
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23
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McKernan CM, Khatri A, Hannigan M, Child J, Chen Q, Mayro B, Snyder D, Nicchitta CV, Pendergast AM. ABL kinases regulate translation in HER2+ cells through Y-box-binding protein 1 to facilitate colonization of the brain. Cell Rep 2022; 40:111268. [PMID: 36044842 PMCID: PMC9472557 DOI: 10.1016/j.celrep.2022.111268] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 06/20/2022] [Accepted: 08/04/2022] [Indexed: 11/27/2022] Open
Abstract
Patients with human epidermal growth factor receptor 2-positive (HER2+/ERBB2) breast cancer often present with brain metastasis. HER2-targeted therapies have not been successful to treat brain metastases in part due to poor blood-brain barrier (BBB) penetrance and emergence of resistance. Here, we report that Abelson (ABL) kinase allosteric inhibitors improve overall survival and impair HER2+ brain metastatic outgrowth in vivo. Mechanistically, ABL kinases phosphorylate the RNA-binding protein Y-box-binding protein 1 (YB-1). ABL kinase inhibition disrupts binding of YB-1 to the ERBB2 mRNA and impairs translation, leading to a profound decrease in HER2 protein levels. ABL-dependent tyrosine phosphorylation of YB-1 promotes HER2 translation. Notably, loss of YB-1 inhibits brain metastatic outgrowth and impairs expression of a subset of ABL-dependent brain metastatic targets. These data support a role for ABL kinases in the translational regulation of brain metastatic targets through YB-1 and offer a therapeutic target for HER2+ brain metastasis patients.
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Affiliation(s)
- Courtney M McKernan
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Aaditya Khatri
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Molly Hannigan
- Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Jessica Child
- Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Qiang Chen
- Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Benjamin Mayro
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - David Snyder
- Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
| | | | - Ann Marie Pendergast
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, USA.
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24
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The SWI/SNF chromatin remodeling factor DPF3 regulates metastasis of ccRCC by modulating TGF-β signaling. Nat Commun 2022; 13:4680. [PMID: 35945219 PMCID: PMC9363427 DOI: 10.1038/s41467-022-32472-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 08/02/2022] [Indexed: 12/23/2022] Open
Abstract
DPF3, a component of the SWI/SNF chromatin remodeling complex, has been associated with clear cell renal cell carcinoma (ccRCC) in a genome-wide association study. However, the functional role of DPF3 in ccRCC development and progression remains unknown. In this study, we demonstrate that DPF3a, the short isoform of DPF3, promotes kidney cancer cell migration both in vitro and in vivo, consistent with the clinical observation that DPF3a is significantly upregulated in ccRCC patients with metastases. Mechanistically, DPF3a specifically interacts with SNIP1, via which it forms a complex with SMAD4 and p300 histone acetyltransferase (HAT), the major transcriptional regulators of TGF-β signaling pathway. Moreover, the binding of DPF3a releases the repressive effect of SNIP1 on p300 HAT activity, leading to the increase in local histone acetylation and the activation of cell movement related genes. Overall, our findings reveal a metastasis-promoting function of DPF3, and further establish the link between SWI/SNF components and ccRCC. The functional role of DPF3, a component of the SWI/SNF chromatin remodelling complex associated with clear cell renal cell carcinoma (ccRCC), remains unknown. Here, the authors characterise the mechanism by which DPF3 promotes metastasis via the activation of the TGF-β signalling pathway in ccRCC.
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25
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Molecular features of primary hepatic undifferentiated carcinoma. Mod Pathol 2022; 35:680-687. [PMID: 34949765 DOI: 10.1038/s41379-021-00970-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/26/2021] [Accepted: 10/26/2021] [Indexed: 11/09/2022]
Abstract
The clinicopathological and molecular characteristics of primary hepatic undifferentiated carcinoma are poorly defined. It is speculated that primary hepatic undifferentiated carcinoma develops in the setting of preceding primary hepatic carcinoma. We investigated 14 primary hepatic undifferentiated carcinomas through targeted next-generation sequencing and immunohistochemistry. A panel of genes commonly mutated in primary liver carcinomas were examined. We found a similar clinical context as primary hepatic carcinoma, including a high prevalence of chronic viral hepatitis (86%), cirrhosis (57%), and elevated alpha-fetoprotein (29%). Tumors had sheet-like and poorly cohesive growth patterns. Rhabdoid cytomorphology was observed in four samples. Notably, the most common genetic mutations in primary hepatic undifferentiated carcinoma were in the promoter of TERT (n = 8, 57%) and TP53 (n = 8, 57%), which are common in hepatocellular carcinoma. The mutation rate of TP53 was elevated compared with hepatocellular carcinoma. No other typical genetic features of intrahepatic cholangiocarcinoma were identified, such as an IDH1/IDH2 mutation, FGFR2 fusions, or aberrant BAP1 expression. Furthermore, novel switch/sucrose nonfermenting complex inactivation was found, including SMARCA4/SMARCA2 (n = 1) and PBRM1 deficiency (n = 2). The three tumors demonstrated poorly cohesive histology, including rhabdoid features. High PD-L1 expression (57%) was observed in a majority of the tumors. Primary hepatic undifferentiated carcinoma shares clinical and genetic features with hepatocellular carcinoma but harbors progressive molecular characteristics that may initiate tumor dedifferentation. High PD-L1 expression in primary hepatic undifferentiated carcinoma may be a useful biomarker for potential immunotherapeutic strategies.
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26
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Morrison AJ. Cancer cell metabolism connects epigenetic modifications to transcriptional regulation. FEBS J 2022; 289:1302-1314. [PMID: 34036737 PMCID: PMC8613311 DOI: 10.1111/febs.16032] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 04/12/2021] [Accepted: 05/21/2021] [Indexed: 12/12/2022]
Abstract
Adaptation of cellular function with the nutrient environment is essential for survival. Failure to adapt can lead to cell death and/or disease. Indeed, energy metabolism alterations are a major contributing factor for many pathologies, including cancer, cardiovascular disease, and diabetes. In particular, a primary characteristic of cancer cells is altered metabolism that promotes survival and proliferation even in the presence of limited nutrients. Interestingly, recent studies demonstrate that metabolic pathways produce intermediary metabolites that directly influence epigenetic modifications in the genome. Emerging evidence demonstrates that metabolic processes in cancer cells fuel malignant growth, in part, through epigenetic regulation of gene expression programs important for proliferation and adaptive survival. In this review, recent progress toward understanding the relationship of cancer cell metabolism, epigenetic modification, and transcriptional regulation will be discussed. Specifically, the need for adaptive cell metabolism and its modulation in cancer cells will be introduced. Current knowledge on the emerging field of metabolite production and epigenetic modification will also be reviewed. Alterations of DNA (de)methylation, histone modifications, such as (de)methylation and (de)acylation, as well as chromatin remodeling, will be discussed in the context of cancer cell metabolism. Finally, how these epigenetic alterations contribute to cancer cell phenotypes will be summarized. Collectively, these studies reveal that both metabolic and epigenetic pathways in cancer cells are closely linked, representing multiple opportunities to therapeutically target the unique features of malignant growth.
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27
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Gad S, Le Teuff G, Nguyen B, Verkarre V, Duchatelle V, Molinie V, Posseme K, Grandon B, Da Costa M, Job B, Meurice G, Droin N, Mejean A, Couve S, Renaud F, Gardie B, Teh BT, Richard S, Ferlicot S. Involvement of PBRM1 in VHL disease-associated clear cell renal cell carcinoma and its putative relationship with the HIF pathway. Oncol Lett 2021; 22:835. [PMID: 34712359 PMCID: PMC8548775 DOI: 10.3892/ol.2021.13096] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 08/03/2021] [Indexed: 11/16/2022] Open
Abstract
Von Hippel-Lindau (VHL) disease is the main cause of inherited clear-cell renal cell carcinoma (ccRCC) and is caused by germline mutations in the VHL tumor suppressor gene. Bi-allelic VHL alterations lead to inactivation of pVHL, which plays a major role by downstream activation of the hypoxia inducible factor (HIF) pathway. Somatic VHL mutations occur in 80% of sporadic ccRCC cases and the second most frequently mutated gene is polybromo 1 (PBRM1). As there is currently no data regarding PBRM1 involvement in VHL disease-associated ccRCC, the aim of the present study was to assess the PBRM1 mutational status, and PBRM1 and HIF expression in VHL disease-associated ccRCC series compared with a sporadic series. PBRM1 gene was screened by Sanger sequencing for 23 VHL-disease-associated ccRCC and 22 sporadic ccRCC cases. Immunohistochemical studies were performed to detect the expression of PBRM1, HIF1 and HIF2 for all cases. In VHL-associated tumors, 13.0% (n=3/23) had PBRM1 somatic mutations and 17.4% (n=4/23) had a loss of PBRM1 nuclear expression. In sporadic cases, 27.3% (n=6/22) showed PBRM1 somatic mutations and 45.5% (n=10/22) had a loss of PBRM1 nuclear expression. Loss of PBRM1 was associated with an advanced tumor stage. HIF1-positive tumors were observed more frequently in the VHL-associated ccRCC than in the sporadic series. Furthermore, in the VHL cohort, PBRM1 expression appeared to be associated more with HIF1 than with HIF2. Given that hereditary tumors tend to be less aggressive, these results would suggest that co-expression of PBRM1 and HIF1 may have a less oncogenic role in VHL-associated ccRCC.
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Affiliation(s)
- Sophie Gad
- Ecole Pratique des Hautes Etudes (EPHE), Paris Sciences Lettres Research University, 75014 Paris, France.,Mixed Research Unit (UMR) 9019, Gustave Roussy Institute, French National Scientific Research Center (CNRS), Paris-Saclay University, 94800 Villejuif, France
| | - Gwenaël Le Teuff
- Department of Biostatistics and Epidemiology, Gustave Roussy Institute, CNRS, Paris-Saclay University, 94800 Villejuif, France.,French National Health and Medical Research Institute (INSERM), Research Center in Epidemiology and Population Health (CESP), Paris-Saclay School of Medicine, Paris-Saclay University, 94800 Villejuif, France
| | - Baptiste Nguyen
- Ecole Pratique des Hautes Etudes (EPHE), Paris Sciences Lettres Research University, 75014 Paris, France
| | - Virginie Verkarre
- Department of Pathology, Public Hospitals of Paris (AP-HP) Centre, Georges Pompidou European Hospital, Paris University, 75015 Paris, France.,INSERM UMR 970, Paris Cardiovascular Research Center (PARCC), Georges Pompidou European Hospital, 75015 Paris, France.,Department of Urology, PREDIR French National Cancer Institute (INCa), AP-HP, Bicêtre Hospital, 94270 Le Kremlin-Bicêtre, France
| | | | - Vincent Molinie
- Department of Pathology, Saint-Joseph Hospital, 75014 Paris, France.,Department of Pathology, Aix-en-Provence Hospital Center, 13616 Aix en Provence, France
| | - Katia Posseme
- Department of Pathology, AP-HP, Bicêtre Hospital, Paris-Saclay University, 94270 Le Kremlin-Bicêtre, France
| | - Benjamin Grandon
- Ecole Pratique des Hautes Etudes (EPHE), Paris Sciences Lettres Research University, 75014 Paris, France
| | - Melanie Da Costa
- Ecole Pratique des Hautes Etudes (EPHE), Paris Sciences Lettres Research University, 75014 Paris, France
| | - Bastien Job
- Bioinformatics Core Facility, Gustave Roussy Institute, CNRS, Paris-Saclay University, 94800 Villejuif, France
| | - Guillaume Meurice
- Bioinformatics Core Facility, Gustave Roussy Institute, CNRS, Paris-Saclay University, 94800 Villejuif, France
| | - Nathalie Droin
- Genomics Core Facility, Gustave Roussy Institute, CNRS, Paris-Saclay University, 94800 Villejuif, France
| | - Arnaud Mejean
- Department of Urology, PREDIR French National Cancer Institute (INCa), AP-HP, Bicêtre Hospital, 94270 Le Kremlin-Bicêtre, France.,Department of Urology, AP-HP, Georges Pompidou European Hospital, Paris University, 75015 Paris, France
| | - Sophie Couve
- Ecole Pratique des Hautes Etudes (EPHE), Paris Sciences Lettres Research University, 75014 Paris, France.,Mixed Research Unit (UMR) 9019, Gustave Roussy Institute, French National Scientific Research Center (CNRS), Paris-Saclay University, 94800 Villejuif, France
| | - Flore Renaud
- Ecole Pratique des Hautes Etudes (EPHE), Paris Sciences Lettres Research University, 75014 Paris, France.,Mixed Research Unit (UMR) 9019, Gustave Roussy Institute, French National Scientific Research Center (CNRS), Paris-Saclay University, 94800 Villejuif, France
| | - Betty Gardie
- Ecole Pratique des Hautes Etudes (EPHE), Paris Sciences Lettres Research University, 75014 Paris, France.,L'Institut du Thorax, INSERM, CNRS, Nantes University, 44000 Nantes, France
| | - Bin Tean Teh
- Program in Cancer and Stem Cell Biology, Duke-National University of Singapore (NUS) Medical School, Singapore 169610, Republic of Singapore.,Laboratory of Cancer Epigenome, Division of Medical Science, National Cancer Centre, Singapore 169610, Republic of Singapore
| | - Stephane Richard
- Ecole Pratique des Hautes Etudes (EPHE), Paris Sciences Lettres Research University, 75014 Paris, France.,Mixed Research Unit (UMR) 9019, Gustave Roussy Institute, French National Scientific Research Center (CNRS), Paris-Saclay University, 94800 Villejuif, France.,Department of Urology, PREDIR French National Cancer Institute (INCa), AP-HP, Bicêtre Hospital, 94270 Le Kremlin-Bicêtre, France
| | - Sophie Ferlicot
- Mixed Research Unit (UMR) 9019, Gustave Roussy Institute, French National Scientific Research Center (CNRS), Paris-Saclay University, 94800 Villejuif, France.,Department of Urology, PREDIR French National Cancer Institute (INCa), AP-HP, Bicêtre Hospital, 94270 Le Kremlin-Bicêtre, France.,Department of Pathology, AP-HP, Bicêtre Hospital, Paris-Saclay University, 94270 Le Kremlin-Bicêtre, France
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28
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PBRM1 loss in kidney cancer unbalances the proximal tubule master transcription factor hub to repress proximal tubule differentiation. Cell Rep 2021; 36:109747. [PMID: 34551289 PMCID: PMC8561673 DOI: 10.1016/j.celrep.2021.109747] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 07/20/2021] [Accepted: 09/01/2021] [Indexed: 01/10/2023] Open
Abstract
PBRM1, a subunit of the PBAF coactivator complex that transcription factors use to activate target genes, is genetically inactivated in almost all clear cell renal cell cancers (RCCs). Using unbiased proteomic analyses, we find that PAX8, a master transcription factor driver of proximal tubule epithelial fates, recruits PBRM1/PBAF. Reverse analyses of the PAX8 interactome confirm recruitment specifically of PBRM1/PBAF and not functionally similar BAF. More conspicuous in the PAX8 hub in RCC cells, however, are corepressors, which functionally oppose coactivators. Accordingly, key PAX8 target genes are repressed in RCC versus normal kidneys, with the loss of histone lysine-27 acetylation, but intact lysine-4 trimethylation, activation marks. Re-introduction of PBRM1, or depletion of opposing corepressors using siRNA or drugs, redress coregulator imbalance and release RCC cells to terminal epithelial fates. These mechanisms thus explain RCC resemblance to the proximal tubule lineage but with suppression of the late-epithelial program that normally terminates lineage-precursor proliferation. Gu et al. identify that transcription factor PAX8 needs the PBRM1/PBAF coactivator to activate proximal tubule genes. PBRM1 mutation/deletion thus explains the resemblance of clear cell kidney cancer to proximal tubule tissue but with suppressed terminal epithelial markers. This oncogenic mechanism could be repaired using drugs to inhibit corepressors.
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29
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Chakraborty S, Balan M, Sabarwal A, Choueiri TK, Pal S. Metabolic reprogramming in renal cancer: Events of a metabolic disease. Biochim Biophys Acta Rev Cancer 2021; 1876:188559. [PMID: 33965513 PMCID: PMC8349779 DOI: 10.1016/j.bbcan.2021.188559] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/21/2021] [Accepted: 04/28/2021] [Indexed: 12/15/2022]
Abstract
Recent studies have established that tumors can reprogram the pathways involved in nutrient uptake and metabolism to withstand the altered biosynthetic, bioenergetics and redox requirements of cancer cells. This phenomenon is called metabolic reprogramming, which is promoted by the loss of tumor suppressor genes and activation of oncogenes. Because of alterations and perturbations in multiple metabolic pathways, renal cell carcinoma (RCC) is sometimes termed as a "metabolic disease". The majority of metabolic reprogramming in renal cancer is caused by the inactivation of von Hippel-Lindau (VHL) gene and activation of the Ras-PI3K-AKT-mTOR pathway. Hypoxia-inducible factor (HIF) and Myc are other important players in the metabolic reprogramming of RCC. All types of RCCs are associated with reprogramming of glucose and fatty acid metabolism and the tricarboxylic acid (TCA) cycle. Metabolism of glutamine, tryptophan and arginine is also reprogrammed in renal cancer to favor tumor growth and oncogenesis. Together, understanding these modifications or reprogramming of the metabolic pathways in detail offer ample opportunities for the development of new therapeutic targets and strategies, discovery of biomarkers and identification of effective tumor detection methods.
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Affiliation(s)
- Samik Chakraborty
- Division of Nephrology, Boston Children's Hospital, MA 02115, United States of America; Harvard Medical School, Boston, MA 02115, United States of America
| | - Murugabaskar Balan
- Division of Nephrology, Boston Children's Hospital, MA 02115, United States of America; Harvard Medical School, Boston, MA 02115, United States of America
| | - Akash Sabarwal
- Division of Nephrology, Boston Children's Hospital, MA 02115, United States of America; Harvard Medical School, Boston, MA 02115, United States of America
| | - Toni K Choueiri
- Dana Farber Cancer Institute, Boston, MA 02115, United States of America; Harvard Medical School, Boston, MA 02115, United States of America
| | - Soumitro Pal
- Division of Nephrology, Boston Children's Hospital, MA 02115, United States of America; Harvard Medical School, Boston, MA 02115, United States of America.
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30
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Sharma T, Robinson DCL, Witwicka H, Dilworth FJ, Imbalzano AN. The Bromodomains of the mammalian SWI/SNF (mSWI/SNF) ATPases Brahma (BRM) and Brahma Related Gene 1 (BRG1) promote chromatin interaction and are critical for skeletal muscle differentiation. Nucleic Acids Res 2021; 49:8060-8077. [PMID: 34289068 PMCID: PMC8373147 DOI: 10.1093/nar/gkab617] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 06/17/2021] [Accepted: 07/08/2021] [Indexed: 12/12/2022] Open
Abstract
Skeletal muscle regeneration is mediated by myoblasts that undergo epigenomic changes to establish the gene expression program of differentiated myofibers. mSWI/SNF chromatin remodeling enzymes coordinate with lineage-determining transcription factors to establish the epigenome of differentiated myofibers. Bromodomains bind to acetylated lysines on histone N-terminal tails and other proteins. The mutually exclusive ATPases of mSWI/SNF complexes, BRG1 and BRM, contain bromodomains with undefined functional importance in skeletal muscle differentiation. Pharmacological inhibition of mSWI/SNF bromodomain function using the small molecule PFI-3 reduced differentiation in cell culture and in vivo through decreased myogenic gene expression, while increasing cell cycle-related gene expression and the number of cells remaining in the cell cycle. Comparative gene expression analysis with data from myoblasts depleted of BRG1 or BRM showed that bromodomain function was required for a subset of BRG1- and BRM-dependent gene expression. Reduced binding of BRG1 and BRM after PFI-3 treatment showed that the bromodomain is required for stable chromatin binding at target gene promoters to alter gene expression. Our findings demonstrate that mSWI/SNF ATPase bromodomains permit stable binding of the mSWI/SNF ATPases to promoters required for cell cycle exit and establishment of muscle-specific gene expression.
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Affiliation(s)
- Tapan Sharma
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Daniel C L Robinson
- Sprott Centre for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, University of Ottawa, Ottawa, ON K1H 8L6, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Hanna Witwicka
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - F Jeffrey Dilworth
- Sprott Centre for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, University of Ottawa, Ottawa, ON K1H 8L6, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Anthony N Imbalzano
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
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31
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PBRM1 Cooperates with YTHDF2 to Control HIF-1α Protein Translation. Cells 2021; 10:cells10061425. [PMID: 34200988 PMCID: PMC8228889 DOI: 10.3390/cells10061425] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/27/2021] [Accepted: 06/04/2021] [Indexed: 11/16/2022] Open
Abstract
PBRM1, a component of the chromatin remodeller SWI/SNF, is often deleted or mutated in human cancers, most prominently in renal cancers. Core components of the SWI/SNF complex have been shown to be important for the cellular response to hypoxia. Here, we investigated how PBRM1 controls HIF-1α activity. We found that PBRM1 is required for HIF-1α transcriptional activity and protein levels. Mechanistically, PBRM1 is important for HIF-1α mRNA translation, as absence of PBRM1 results in reduced actively translating HIF-1α mRNA. Interestingly, we found that PBRM1, but not BRG1, interacts with the m6A reader protein YTHDF2. HIF-1α mRNA is m6A-modified, bound by PBRM1 and YTHDF2. PBRM1 is necessary for YTHDF2 binding to HIF-1α mRNA and reduction of YTHDF2 results in reduced HIF-1α protein expression in cells. Our results identify a SWI/SNF-independent function for PBRM1, interacting with HIF-1α mRNA and the epitranscriptome machinery. Furthermore, our results suggest that the epitranscriptome-associated proteins play a role in the control of hypoxia signalling pathways.
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32
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Chabanon RM, Morel D, Eychenne T, Colmet-Daage L, Bajrami I, Dorvault N, Garrido M, Meisenberg C, Lamb A, Ngo C, Hopkins SR, Roumeliotis TI, Jouny S, Hénon C, Kawai-Kawachi A, Astier C, Konde A, Del Nery E, Massard C, Pettitt SJ, Margueron R, Choudhary JS, Almouzni G, Soria JC, Deutsch E, Downs JA, Lord CJ, Postel-Vinay S. PBRM1 Deficiency Confers Synthetic Lethality to DNA Repair Inhibitors in Cancer. Cancer Res 2021; 81:2888-2902. [PMID: 33888468 DOI: 10.1158/0008-5472.can-21-0628] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/17/2021] [Accepted: 03/19/2021] [Indexed: 11/16/2022]
Abstract
Inactivation of Polybromo 1 (PBRM1), a specific subunit of the PBAF chromatin remodeling complex, occurs frequently in cancer, including 40% of clear cell renal cell carcinomas (ccRCC). To identify novel therapeutic approaches to targeting PBRM1-defective cancers, we used a series of orthogonal functional genomic screens that identified PARP and ATR inhibitors as being synthetic lethal with PBRM1 deficiency. The PBRM1/PARP inhibitor synthetic lethality was recapitulated using several clinical PARP inhibitors in a series of in vitro model systems and in vivo in a xenograft model of ccRCC. In the absence of exogenous DNA damage, PBRM1-defective cells exhibited elevated levels of replication stress, micronuclei, and R-loops. PARP inhibitor exposure exacerbated these phenotypes. Quantitative mass spectrometry revealed that multiple R-loop processing factors were downregulated in PBRM1-defective tumor cells. Exogenous expression of the R-loop resolution enzyme RNase H1 reversed the sensitivity of PBRM1-deficient cells to PARP inhibitors, suggesting that excessive levels of R-loops could be a cause of this synthetic lethality. PARP and ATR inhibitors also induced cyclic GMP-AMP synthase/stimulator of interferon genes (cGAS/STING) innate immune signaling in PBRM1-defective tumor cells. Overall, these findings provide the preclinical basis for using PARP inhibitors in PBRM1-defective cancers. SIGNIFICANCE: This study demonstrates that PARP and ATR inhibitors are synthetic lethal with the loss of PBRM1, a PBAF-specific subunit, thus providing the rationale for assessing these inhibitors in patients with PBRM1-defective cancer. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/81/11/2888/F1.large.jpg.
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MESH Headings
- Animals
- Apoptosis
- Ataxia Telangiectasia Mutated Proteins/antagonists & inhibitors
- Carcinoma, Non-Small-Cell Lung/drug therapy
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/metabolism
- Carcinoma, Non-Small-Cell Lung/pathology
- Carcinoma, Renal Cell/drug therapy
- Carcinoma, Renal Cell/genetics
- Carcinoma, Renal Cell/metabolism
- Carcinoma, Renal Cell/pathology
- Cell Proliferation
- DNA Repair
- DNA-Binding Proteins/deficiency
- Female
- Gene Expression Regulation, Neoplastic/drug effects
- Humans
- Kidney Neoplasms/drug therapy
- Kidney Neoplasms/genetics
- Kidney Neoplasms/metabolism
- Kidney Neoplasms/pathology
- Lung Neoplasms/drug therapy
- Lung Neoplasms/genetics
- Lung Neoplasms/metabolism
- Lung Neoplasms/pathology
- Mice
- Mice, Inbred NOD
- Mice, SCID
- Poly(ADP-ribose) Polymerase Inhibitors/pharmacology
- Synthetic Lethal Mutations
- Transcription Factors/deficiency
- Tumor Cells, Cultured
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Roman M Chabanon
- ATIP-Avenir group, Inserm Unit U981, Gustave Roussy, Villejuif, France
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Daphné Morel
- ATIP-Avenir group, Inserm Unit U981, Gustave Roussy, Villejuif, France
- Université Paris Saclay, Université Paris-Sud, Faculté de Médicine, Le Kremlin Bicêtre, France
| | - Thomas Eychenne
- ATIP-Avenir group, Inserm Unit U981, Gustave Roussy, Villejuif, France
| | - Léo Colmet-Daage
- ATIP-Avenir group, Inserm Unit U981, Gustave Roussy, Villejuif, France
| | - Ilirjana Bajrami
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Nicolas Dorvault
- ATIP-Avenir group, Inserm Unit U981, Gustave Roussy, Villejuif, France
| | - Marlène Garrido
- ATIP-Avenir group, Inserm Unit U981, Gustave Roussy, Villejuif, France
| | - Cornelia Meisenberg
- Epigenetics and Genome Stability Team, The Institute of Cancer Research, London, United Kingdom
| | | | - Carine Ngo
- ATIP-Avenir group, Inserm Unit U981, Gustave Roussy, Villejuif, France
| | - Suzanna R Hopkins
- Epigenetics and Genome Stability Team, The Institute of Cancer Research, London, United Kingdom
| | | | - Samuel Jouny
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Clémence Hénon
- ATIP-Avenir group, Inserm Unit U981, Gustave Roussy, Villejuif, France
| | | | - Clémence Astier
- ATIP-Avenir group, Inserm Unit U981, Gustave Roussy, Villejuif, France
| | - Asha Konde
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Elaine Del Nery
- Institut Curie, PSL Research University, Department of Translational Research, The Biophenics High-Content Screening Laboratory, Cell and Tissue Imaging Facility (PICT-IBiSA), Paris, France
| | | | - Stephen J Pettitt
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Raphaël Margueron
- Institut Curie, PSL Research University, INSERM Unit U934, CNRS UMR 3215, Paris, France
| | - Jyoti S Choudhary
- Functional Proteomics Team, The Institute of Cancer Research, London, United Kingdom
| | - Geneviève Almouzni
- Institut Curie, PSL Research University, CNRS, UMR 3664, Equipe Labellisée Ligue contre le Cancer, Paris, France
- Sorbonne Universités, UPMC Université Paris-VI, CNRS, UMR3664, Paris, France
| | - Jean-Charles Soria
- Université Paris Saclay, Université Paris-Sud, Faculté de Médicine, Le Kremlin Bicêtre, France
| | - Eric Deutsch
- Université Paris Saclay, Université Paris-Sud, Faculté de Médicine, Le Kremlin Bicêtre, France
- INSERM UMR1030 Molecular Radiotherapy and Therapeutic Innovations, Gustave Roussy, Villejuif, France
| | - Jessica A Downs
- Epigenetics and Genome Stability Team, The Institute of Cancer Research, London, United Kingdom
| | - Christopher J Lord
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom.
| | - Sophie Postel-Vinay
- ATIP-Avenir group, Inserm Unit U981, Gustave Roussy, Villejuif, France.
- Université Paris Saclay, Université Paris-Sud, Faculté de Médicine, Le Kremlin Bicêtre, France
- Drug Development Department, DITEP, Gustave Roussy, Villejuif, France
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33
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Das S, Surve V, Marathe S, Wad S, Karulkar A, Srinivasan S, Dwivedi A, Barthel SR, Purwar R. IL-9 Abrogates the Metastatic Potential of Breast Cancer by Controlling Extracellular Matrix Remodeling and Cellular Contractility. THE JOURNAL OF IMMUNOLOGY 2021; 206:2740-2752. [PMID: 34021045 DOI: 10.4049/jimmunol.2000383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 03/30/2021] [Indexed: 11/19/2022]
Abstract
IL-9 is produced by Th9 cells and is classically known as a growth-promoting cytokine. Although protumorigenic functions of IL-9 are described in T cell lymphoma, recently, we and others have reported anti-tumor activities of IL-9 in melanoma mediated by mast cells and CD8+ T cells. However, involvement of IL-9 in invasive breast and cervical cancer remains unexplored. In this study, we demonstrate IL-9-dependent inhibition of metastasis of both human breast (MDA-MB-231 and MCF-7) and cervical (HeLa) tumor cells in physiological three-dimensional invasion assays. To dissect underlying mechanisms of IL-9-mediated suppression of invasion, we analyzed IL-9-dependent pathways of cancer cell metastasis, including proteolysis, contractility, and focal adhesion dynamics. IL-9 markedly blocked tumor cell-collagen degradation, highlighting the effects of IL-9 on extracellular matrix remodeling. Moreover, IL-9 significantly reduced phosphorylation of myosin L chain and resultant actomyosin contractility and also increased focal adhesion formation. Finally, IL-9 suppressed IL-17- and IFN-γ-induced metastasis of both human breast (MDA-MB-231) and cervical (HeLa) cancer cells. In conclusion, IL-9 inhibits the metastatic potential of breast and cervical cancer cells by controlling extracellular matrix remodeling and cellular contractility.
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Affiliation(s)
- Sreya Das
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India; and
| | - Vishakha Surve
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India; and
| | - Soumitra Marathe
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India; and
| | - Siddhi Wad
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India; and
| | - Atharva Karulkar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India; and
| | - Srisathya Srinivasan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India; and
| | - Alka Dwivedi
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India; and
| | - Steven R Barthel
- Department of Dermatology, Brigham and Women's Hospital, Boston, MA
| | - Rahul Purwar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India; and
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34
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The Role of Epigenetics in the Progression of Clear Cell Renal Cell Carcinoma and the Basis for Future Epigenetic Treatments. Cancers (Basel) 2021; 13:cancers13092071. [PMID: 33922974 PMCID: PMC8123355 DOI: 10.3390/cancers13092071] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 12/13/2022] Open
Abstract
Simple Summary The accumulated evidence on the role of epigenetic markers of prognosis in clear cell renal cell carcinoma (ccRCC) is reviewed, as well as state of the art on epigenetic treatments for this malignancy. Several epigenetic markers are likely candidates for clinical use, but still have not passed the test of prospective validation. Development of epigenetic therapies, either alone or in combination with tyrosine-kinase inhibitors of immune-checkpoint inhibitors, are still in their infancy. Abstract Clear cell renal cell carcinoma (ccRCC) is curable when diagnosed at an early stage, but when disease is non-confined it is the urologic cancer with worst prognosis. Antiangiogenic treatment and immune checkpoint inhibition therapy constitute a very promising combined therapy for advanced and metastatic disease. Many exploratory studies have identified epigenetic markers based on DNA methylation, histone modification, and ncRNA expression that epigenetically regulate gene expression in ccRCC. Additionally, epigenetic modifiers genes have been proposed as promising biomarkers for ccRCC. We review and discuss the current understanding of how epigenetic changes determine the main molecular pathways of ccRCC initiation and progression, and also its clinical implications. Despite the extensive research performed, candidate epigenetic biomarkers are not used in clinical practice for several reasons. However, the accumulated body of evidence of developing epigenetically-based biomarkers will likely allow the identification of ccRCC at a higher risk of progression. That will facilitate the establishment of firmer therapeutic decisions in a changing landscape and also monitor active surveillance in the aging population. What is more, a better knowledge of the activities of chromatin modifiers may serve to develop new therapeutic opportunities. Interesting clinical trials on epigenetic treatments for ccRCC associated with well established antiangiogenic treatments and immune checkpoint inhibitors are revisited.
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35
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Karki M, Jangid RK, Anish R, Seervai RNH, Bertocchio JP, Hotta T, Msaouel P, Jung SY, Grimm SL, Coarfa C, Weissman BE, Ohi R, Verhey KJ, Hodges HC, Burggren W, Dere R, Park IY, Prasad BVV, Rathmell WK, Walker CL, Tripathi DN. A cytoskeletal function for PBRM1 reading methylated microtubules. SCIENCE ADVANCES 2021; 7:eabf2866. [PMID: 33811077 PMCID: PMC11059954 DOI: 10.1126/sciadv.abf2866] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 02/12/2021] [Indexed: 06/12/2023]
Abstract
Epigenetic effectors "read" marks "written" on chromatin to regulate function and fidelity of the genome. Here, we show that this coordinated read-write activity of the epigenetic machinery extends to the cytoskeleton, with PBRM1 in the PBAF chromatin remodeling complex reading microtubule methyl marks written by the SETD2 histone methyltransferase. PBRM1 binds SETD2 methyl marks via BAH domains, recruiting PBAF components to the mitotic spindle. This read-write activity was required for normal mitosis: Loss of SETD2 methylation or pathogenic BAH domain mutations disrupt PBRM1 microtubule binding and PBAF recruitment and cause genomic instability. These data reveal PBRM1 functions beyond chromatin remodeling with domains that allow it to integrate chromatin and cytoskeletal activity via its acetyl-binding BD and methyl-binding BAH domains, respectively. Conserved coordinated activity of the epigenetic machinery on the cytoskeleton opens a previously unknown window into how chromatin remodeler defects can drive disease via both epigenetic and cytoskeletal dysfunction.
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Affiliation(s)
- Menuka Karki
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
| | - Rahul K Jangid
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ramakrishnan Anish
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Riyad N H Seervai
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jean-Philippe Bertocchio
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Genitourinary Oncology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Takashi Hotta
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Pavlos Msaouel
- Department of Genitourinary Oncology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sung Yun Jung
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sandra L Grimm
- Advanced Technology Cores, Baylor College of Medicine, Houston, TX 77030, USA
| | - Cristian Coarfa
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Bernard E Weissman
- Department of Pathology and Laboratory Medicine, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Ryoma Ohi
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Kristen J Verhey
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - H Courtney Hodges
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Warren Burggren
- Department of Biological Sciences, University of North Texas, Denton, TX 76201, USA
| | - Ruhee Dere
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - In Young Park
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - B V Venkataram Prasad
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - W Kimryn Rathmell
- Vanderbilt-Ingram Cancer Center, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Cheryl L Walker
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA.
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Durga N Tripathi
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA.
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
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36
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Chehrazi-Raffle A, Malhotra J, Salgia S, Favorito C, Hsu J, Wu H, Pal SK. Renal Cell Carcinoma With Urinary Bladder Metastasis: A Case Report With Metachronous Genomic Analyses. JCO Precis Oncol 2021; 5:PO.20.00423. [PMID: 33981942 PMCID: PMC8092369 DOI: 10.1200/po.20.00423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 02/11/2021] [Accepted: 02/25/2021] [Indexed: 11/20/2022] Open
Affiliation(s)
- Alexander Chehrazi-Raffle
- Department of Medical Oncology and Experimental Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA
| | - Jasnoor Malhotra
- Department of Medical Oncology and Experimental Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA
| | - Sabrina Salgia
- Department of Medical Oncology and Experimental Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA
| | - Crystal Favorito
- Krieger School of Arts and Sciences, Johns Hopkins University, Baltimore, MD
| | - JoAnn Hsu
- Department of Medical Oncology and Experimental Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA
| | - Huiqing Wu
- Department of Pathology, City of Hope Comprehensive Cancer Center, Duarte, CA
| | - Sumanta K Pal
- Department of Medical Oncology and Experimental Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA
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37
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Zhu LL, Wu Z, Li RK, Xing X, Jiang YS, Li J, Wang YH, Hu LP, Wang X, Qin WT, Sun YW, Zhang ZG, Yang Q, Jiang SH. Deciphering the genomic and lncRNA landscapes of aerobic glycolysis identifies potential therapeutic targets in pancreatic cancer. Int J Biol Sci 2021; 17:107-118. [PMID: 33390837 PMCID: PMC7757027 DOI: 10.7150/ijbs.49243] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 10/29/2020] [Indexed: 12/17/2022] Open
Abstract
Aerobic glycolysis, also known as the Warburg effect, is emerged as a hallmark of most cancer cells. Increased aerobic glycolysis is closely associated with tumor aggressiveness and predicts a poor prognosis. Pancreatic ductal adenocarcinoma (PDAC) is characterized by prominent genomic aberrations and increased glycolytic phenotype. However, the detailed molecular events implicated in aerobic glycolysis of PDAC are not well understood. In this study, we performed a comprehensive molecular characterization using multidimensional ''omic'' data from The Cancer Genome Atlas (TCGA). Detailed analysis of 89 informative PDAC tumors identified substantial copy number variations (MYC, GATA6, FGFR1, IDO1, and SMAD4) and mutations (KRAS, SMAD4, and RNF43) related to aerobic glycolysis. Moreover, integrated analysis of transcriptional profiles revealed many differentially expressed long non-coding RNAs involved in PDAC aerobic glycolysis. Loss-of-function studies showed that LINC01559 and UNC5B-AS1 knockdown significantly inhibited the glycolytic capacity of PDAC cells as revealed by reduced glucose uptake, lactate production, and extracellular acidification rate. Moreover, genetic silencing of LINC01559 and UNC5B-AS1 suppressed tumor growth and resulted in alterations in several signaling pathways, such as TNF signaling pathway, IL-17 signaling pathway, and transcriptional misregulation in cancer. Notably, high expression of LINC01559 and UNC5B-AS1 predicted poor patient prognosis and correlated with the maximum standard uptakevalue (SUVmax) in PDAC patients who received preoperative 18F-FDG PET/CT. Taken together, our results decipher the glycolysis-associated copy number variations, mutations, and lncRNA landscapes in PDAC. These findings improve our knowledge of the molecular mechanism of PDAC aerobic glycolysis and may have practical implications for precision cancer therapy.
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Affiliation(s)
- Li-Li Zhu
- State Key Laboratory of Oncogenes and Related Genes, Ren Ji Hospital, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, P.R. China.,State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, P.R. China
| | - Zheng Wu
- Department of Radiation Oncology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, PR China
| | - Rong-Kun Li
- Institute of Oncology, Affiliated Hospital of Jiangsu University, Zhenjiang 212001, P.R. China
| | - Xin Xing
- The Fengxian Hospital, Southern Medical University, Shanghai 201499, PR China
| | - Yong-Sheng Jiang
- Department of Biliary-Pancreatic Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200217, P.R. China
| | - Jun Li
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, P.R. China
| | - Ya-Hui Wang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, P.R. China
| | - Li-Peng Hu
- State Key Laboratory of Oncogenes and Related Genes, Ren Ji Hospital, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, P.R. China.,State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, P.R. China
| | - Xu Wang
- Institute of Oncology, Affiliated Hospital of Jiangsu University, Zhenjiang 212001, P.R. China
| | - Wei-Ting Qin
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, P.R. China
| | - Yong-Wei Sun
- Department of Biliary-Pancreatic Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200217, P.R. China
| | - Zhi-Gang Zhang
- State Key Laboratory of Oncogenes and Related Genes, Ren Ji Hospital, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, P.R. China.,State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, P.R. China
| | - Qin Yang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, P.R. China
| | - Shu-Heng Jiang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, P.R. China
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38
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Zarisfi M, Nguyen T, Nedrow JR, Le A. The Heterogeneity Metabolism of Renal Cell Carcinomas. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1311:117-126. [PMID: 34014538 DOI: 10.1007/978-3-030-65768-0_8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
According to data from the American Cancer Society, cancer is one of the deadliest health problems globally. Annually, renal cell carcinoma (RCC) causes more than 100,000 deaths worldwide [1-4], posing an urgent need to develop effective treatments to increase patient survival outcomes. New therapies are expected to address a major factor contributing to cancer's resistance to standard therapies: oncogenic heterogeneity. Gene expression can vary tremendously among different types of cancers, different patients of the same tumor type, and even within individual tumors; various metabolic phenotypes can emerge, making singletherapy approaches insufficient. Novel strategies targeting the diverse metabolism of cancers aim to overcome this obstacle. Though some have yielded positive results, it remains a challenge to uncover all of the distinct metabolic profiles of RCC. In the quest to overcome this obstacle, the metabolic oriented research focusing on these cancers has offered freshly new perspectives, which are expected to contribute heavily to the development of new treatments.
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Affiliation(s)
- Mohammadreza Zarisfi
- Department of Radiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Tu Nguyen
- University of California, Los Angeles (UCLA) David Geffen School of Medicine, Los Angeles, CA, USA
| | - Jessie R Nedrow
- Department of Radiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Anne Le
- Department of Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University Whiting School of Engineering, Baltimore, MD, USA.
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Liu T, Xia Q, Zhang H, Wang Z, Yang W, Gu X, Hou T, Chen Y, Pei X, Zhu G, He D, Li L, Xu S. CCL5-dependent mast cell infiltration into the tumor microenvironment in clear cell renal cell carcinoma patients. Aging (Albany NY) 2020; 12:21809-21836. [PMID: 33177244 PMCID: PMC7695370 DOI: 10.18632/aging.103999] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 08/14/2020] [Indexed: 12/13/2022]
Abstract
We investigated the mechanisms affecting tumor progression and survival outcomes in Polybromo-1-mutated (PBRM1MUT) clear cell renal cell carcinoma (ccRCC) patients. PBRM1MUT ccRCC tissues contained higher numbers of mast cells and lower numbers of CD8+ and CD4+ T cells than tissues from PBRM1WT ccRCC patients. Hierarchical clustering, pathway enrichment and GSEA analyses demonstrated that PBRM1 mutations promote tumor progression by activating hypoxia inducible factor (HIF)-related signaling pathways and increasing expression of vascular endothelial growth factor family genes. PBRM1MUT ccRCC tissues also show increased expression of C-C motif chemokine ligand 5 (CCL5). PBRM1-silenced ccRCC cells exhibited greater Matrigel tube formation and cell proliferation than controls. In addition, HMC-1 human mast cells exhibited CCL5-dependent in vitro migration on Transwell plates. High CCL5 expression in PBRM1MUT ccRCC patients correlated with increased expression of genes encoding IFN-γ, IFN-α, IL-6, JAK-STAT3, TNF-α, and NF-ΚB. Moreover, high CCL5 expression was associated with poorer survival outcomes in ccRCC patients. These findings demonstrate that CCL5-dependent mast cell infiltration promotes immunosuppression within the tumor microenvironment, resulting in tumor progression and adverse survival outcomes in PBRM1MUT ccRCC patients.
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Affiliation(s)
- Tianjie Liu
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, Shaanxi, P.R. China.,Oncology Research Laboratory, Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an 710061, Shaanxi, P.R. China.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, Xi'an Jiaotong University, Xi'an 710061, Shaanxi, P.R. China
| | - Qing Xia
- Department of Oncology, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai Cancer Institute, Shanghai 200127, P.R. China
| | - Haibao Zhang
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, Shaanxi, P.R. China.,Oncology Research Laboratory, Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an 710061, Shaanxi, P.R. China.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, Xi'an Jiaotong University, Xi'an 710061, Shaanxi, P.R. China
| | - Zixi Wang
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, Shaanxi, P.R. China.,Oncology Research Laboratory, Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an 710061, Shaanxi, P.R. China.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, Xi'an Jiaotong University, Xi'an 710061, Shaanxi, P.R. China
| | - Wenjie Yang
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, Shaanxi, P.R. China.,Oncology Research Laboratory, Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an 710061, Shaanxi, P.R. China.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, Xi'an Jiaotong University, Xi'an 710061, Shaanxi, P.R. China
| | - Xiaoyun Gu
- Shaanxi Health Information Center, Health Commission of Shaanxi Province, Xi'an 710061, Shaanxi, P.R. China
| | - Tao Hou
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, Shaanxi, P.R. China.,Oncology Research Laboratory, Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an 710061, Shaanxi, P.R. China.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, Xi'an Jiaotong University, Xi'an 710061, Shaanxi, P.R. China
| | - Yule Chen
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, Shaanxi, P.R. China.,Oncology Research Laboratory, Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an 710061, Shaanxi, P.R. China.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, Xi'an Jiaotong University, Xi'an 710061, Shaanxi, P.R. China
| | - Xinqi Pei
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, Shaanxi, P.R. China.,Oncology Research Laboratory, Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an 710061, Shaanxi, P.R. China.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, Xi'an Jiaotong University, Xi'an 710061, Shaanxi, P.R. China
| | - Guodong Zhu
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, Shaanxi, P.R. China.,Oncology Research Laboratory, Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an 710061, Shaanxi, P.R. China.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, Xi'an Jiaotong University, Xi'an 710061, Shaanxi, P.R. China
| | - Dalin He
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, Shaanxi, P.R. China.,Oncology Research Laboratory, Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an 710061, Shaanxi, P.R. China.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, Xi'an Jiaotong University, Xi'an 710061, Shaanxi, P.R. China
| | - Lei Li
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, Shaanxi, P.R. China.,Oncology Research Laboratory, Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an 710061, Shaanxi, P.R. China.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, Xi'an Jiaotong University, Xi'an 710061, Shaanxi, P.R. China
| | - Shan Xu
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, Shaanxi, P.R. China.,Oncology Research Laboratory, Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an 710061, Shaanxi, P.R. China.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, Xi'an Jiaotong University, Xi'an 710061, Shaanxi, P.R. China
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Li L, Li Y, Guo Y, Li J, Jin H. Potential roles of PBRM1 on immune infiltration in cholangiocarcinoma. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2020; 13:2661-2676. [PMID: 33165423 PMCID: PMC7642697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 08/16/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Cholangiocarcinoma (CHOL) is one of the most fatal malignancies worldwide. PBRM1 is a tumor suppressor gene in diverse cancers. It regulates cell cycle, genomic stability, centromeric cohesion, and apoptosis. However, its relevance to remodel tumor cell immune response of PBRM1 in CHOL remains unclear. METHODS PBRM1 mutation and expression of CHOL patients were analyzed by the TCGA database using R packages and cBioPortal site. The correlation between PBRM1 and tumor cell immune infiltrates among CHOL patients was investigated by TIMER2.0. Correlation analysis between PBRM1 and gene markers of tumor-infiltrating immune cells in CHOL was analyzed by GEPIA. Pathway enrichment analysis and protein-protein interaction network of PBRM1 mutation and expression was investigated using STRING and Cytoscape. RESULTS Among CHOL patients, PBRM1 has a high mutation probability and significant differential expression. Mutations and differential expression of PBRM1 both have a significant effect on the infiltration of cancer associated fibroblasts (CAF) in CHOL patients. PBRM1 was highly correlated with MMP2 and FAK, which were reported as key regulators of CAF. Through protein-protein interaction network with hub gene analysis, we discovered that NCAM1 could play key roles in the potential mechanism of how PBRM1 affects immune infiltration and progress of CHOL. CONCLUSION PBRM1 may play an important role in immune cell infiltration, matrix formation, and tumor invasion of CHOL, by regulating the function and infiltrating of tumor stromal cells including cancer-associated fibroblasts through NCAM1. Therefore, PBRM1 might be a new therapeutic target in CHOL.
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Affiliation(s)
- Ling Li
- Laboratory of Cancer Biology, Key Lab of Biotherapy in Zhejiang, Sir Run Run Shaw Hospital, Medical School of Zhejiang University Hangzhou, China
| | - Yadan Li
- Laboratory of Cancer Biology, Key Lab of Biotherapy in Zhejiang, Sir Run Run Shaw Hospital, Medical School of Zhejiang University Hangzhou, China
| | - Yan Guo
- Laboratory of Cancer Biology, Key Lab of Biotherapy in Zhejiang, Sir Run Run Shaw Hospital, Medical School of Zhejiang University Hangzhou, China
| | - Jingyi Li
- Laboratory of Cancer Biology, Key Lab of Biotherapy in Zhejiang, Sir Run Run Shaw Hospital, Medical School of Zhejiang University Hangzhou, China
| | - Hongchuan Jin
- Laboratory of Cancer Biology, Key Lab of Biotherapy in Zhejiang, Sir Run Run Shaw Hospital, Medical School of Zhejiang University Hangzhou, China
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Seervai RNH, Jangid RK, Karki M, Tripathi DN, Jung SY, Kearns SE, Verhey KJ, Cianfrocco MA, Millis BA, Tyska MJ, Mason FM, Rathmell WK, Park IY, Dere R, Walker CL. The Huntingtin-interacting protein SETD2/HYPB is an actin lysine methyltransferase. SCIENCE ADVANCES 2020; 6:6/40/eabb7854. [PMID: 33008892 PMCID: PMC7852384 DOI: 10.1126/sciadv.abb7854] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 08/07/2020] [Indexed: 05/05/2023]
Abstract
The methyltransferase SET domain-containing 2 (SETD2) was originally identified as Huntingtin (HTT) yeast partner B. However, a SETD2 function associated with the HTT scaffolding protein has not been elucidated, and no linkage between HTT and methylation has yet been uncovered. Here, we show that SETD2 is an actin methyltransferase that trimethylates lysine-68 (ActK68me3) in cells via its interaction with HTT and the actin-binding adapter HIP1R. ActK68me3 localizes primarily to the insoluble F-actin cytoskeleton in cells and regulates actin polymerization/depolymerization dynamics. Disruption of the SETD2-HTT-HIP1R axis inhibits actin methylation, causes defects in actin polymerization, and impairs cell migration. Together, these data identify SETD2 as a previously unknown HTT effector regulating methylation and polymerization of actin filaments and provide new avenues for understanding how defects in SETD2 and HTT drive disease via aberrant cytoskeletal methylation.
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Affiliation(s)
- Riyad N H Seervai
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Rahul K Jangid
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
| | - Menuka Karki
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
| | - Durga Nand Tripathi
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sung Yun Jung
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sarah E Kearns
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Kristen J Verhey
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Michael A Cianfrocco
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Bryan A Millis
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
- Vanderbilt Biophotonics Center, Department of Biomedical Engineering, Vanderbilt University, Nashville, TN 37240, USA
| | - Matthew J Tyska
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Frank M Mason
- Vanderbilt-Ingram Cancer Center, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - W Kimryn Rathmell
- Vanderbilt-Ingram Cancer Center, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - In Young Park
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Ruhee Dere
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Cheryl Lyn Walker
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
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A TAZ-AXL-ABL2 Feed-Forward Signaling Axis Promotes Lung Adenocarcinoma Brain Metastasis. Cell Rep 2020; 29:3421-3434.e8. [PMID: 31825826 DOI: 10.1016/j.celrep.2019.11.018] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 10/14/2019] [Accepted: 11/05/2019] [Indexed: 02/08/2023] Open
Abstract
Brain metastases are a common consequence of advanced lung cancer, resulting in cranial neuropathies and increased mortality. Currently, there are no effective therapies to treat brain metastases due to a lack of actionable targets and a failure of systemic therapies to penetrate the blood-brain barrier (BBB). Here we identify an autocrine signaling axis required for lung adenocarcinoma brain metastasis, whereby nuclear accumulation of the TAZ transcriptional co-activator drives expression of a panel of transcripts enriched in brain metastases, including ABL2 and AXL, encoding for protein tyrosine kinases that engage in bidirectional signaling. Activation of ABL2 in turn promotes TAZ tyrosine phosphorylation and nuclear localization, establishing an autocrine AXL-ABL2-TAZ feed-forward signaling loop required for brain metastasis colonization. Notably, treatment with a BBB-penetrant ABL allosteric inhibitor or knockdown of ABL2, AXL, or TAZ markedly decreases brain metastases. These findings suggest that ABL and AXL inhibitors might be effective against brain metastases.
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43
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Zhao Q, Xue J, Hong B, Qian W, Liu T, Fan B, Cai J, Ji Y, Liu J, Yang Y, Li Q, Guo S, Zhang N. Transcriptomic characterization and innovative molecular classification of clear cell renal cell carcinoma in the Chinese population. Cancer Cell Int 2020; 20:461. [PMID: 32982583 PMCID: PMC7510315 DOI: 10.1186/s12935-020-01552-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 09/10/2020] [Indexed: 01/03/2023] Open
Abstract
Background Large-scale initiatives like The Cancer Genome Atlas (TCGA) performed genomics studies on predominantly Caucasian kidney cancer. In this study, we aimed to investigate genomics of Chinese clear cell renal cell carcinoma (ccRCC). Methods We performed whole-transcriptomic sequencing on 55 tumor tissues and 11 matched normal tissues from Chinese ccRCC patients. We systematically analyzed the data from our cohort and comprehensively compared with the TCGA ccRCC cohort. Results It found that PBRM1 mutates with a frequency of 11% in our cohort, much lower than that in TCGA Caucasians (33%). Besides, 31 gene fusions including 5 recurrent ones, that associated with apoptosis, tumor suppression and metastasis were identified. We classified our cohort into three classes by gene expression. Class 1 shows significantly elevated gene expression in the VEGF pathway, while Class 3 has comparably suppressed expression of this pathway. Class 2 is characterized by increased expression of extracellular matrix organization genes and is associated with high-grade tumors. Applying the classification to TCGA ccRCC patients revealed better distinction of tumor prognosis than reported classifications. Class 2 shows worst survival and Class 3 is a rare subtype ccRCC in the TCGA cohort. Furthermore, computational analysis on the immune microenvironment of ccRCC identified immune-active and tolerant tumors with significant increased macrophages and depleted CD4 positive T-cells, thus some patients may benefit from immunotherapies. Conclusion In summary, results presented in this study shed light into distinct genomic expression profiles in Chinese population, modified the stratification patterns by new molecular classification, and gave practical guidelines on clinical treatment of ccRCC patients.
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Affiliation(s)
- Qiang Zhao
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Urology, Peking University Cancer Hospital & Institute, 52 Fucheng Road, Haidian District, Beijing, 100142 People's Republic of China
| | - Jia Xue
- Systems Biology, Crown Bioscience Inc., No. 218 Xinghu Street, Suzhou Industrial Park, Suzhou, 215028 People's Republic of China
| | - Baoan Hong
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Urology, Peking University Cancer Hospital & Institute, 52 Fucheng Road, Haidian District, Beijing, 100142 People's Republic of China
| | - Wubin Qian
- Systems Biology, Crown Bioscience Inc., No. 218 Xinghu Street, Suzhou Industrial Park, Suzhou, 215028 People's Republic of China
| | - Tiezhu Liu
- Department of Urology, Daqing Oilfield General Hospital, Heilongjiang, 163316 People's Republic of China
| | - Bin Fan
- Crown Bioscience Inc., No.21 Huoju Street Changping District, Beijing, 102200 People's Republic of China
| | - Jie Cai
- Crown Bioscience Inc., No.21 Huoju Street Changping District, Beijing, 102200 People's Republic of China
| | - Yongpeng Ji
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Urology, Peking University Cancer Hospital & Institute, 52 Fucheng Road, Haidian District, Beijing, 100142 People's Republic of China
| | - Jia Liu
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Urology, Peking University Cancer Hospital & Institute, 52 Fucheng Road, Haidian District, Beijing, 100142 People's Republic of China
| | - Yong Yang
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Urology, Peking University Cancer Hospital & Institute, 52 Fucheng Road, Haidian District, Beijing, 100142 People's Republic of China
| | - Qixiang Li
- Crown Bioscience Inc., 3375 Scott Blvd, Suite 108, Santa Clara, CA 95054 USA.,State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, 100191 People's Republic of China
| | - Sheng Guo
- Systems Biology, Crown Bioscience Inc., No. 218 Xinghu Street, Suzhou Industrial Park, Suzhou, 215028 People's Republic of China
| | - Ning Zhang
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Urology, Peking University Cancer Hospital & Institute, 52 Fucheng Road, Haidian District, Beijing, 100142 People's Republic of China
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Mathies LD, Lindsay JH, Handal AP, Blackwell GG, Davies AG, Bettinger JC. SWI/SNF complexes act through CBP-1 histone acetyltransferase to regulate acute functional tolerance to alcohol. BMC Genomics 2020; 21:646. [PMID: 32957927 PMCID: PMC7507291 DOI: 10.1186/s12864-020-07059-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 09/10/2020] [Indexed: 01/19/2023] Open
Abstract
Background SWI/SNF chromatin remodeling genes are required for normal acute responses to alcohol in C. elegans and are associated with alcohol use disorder in two human populations. In an effort to discover the downstream genes that are mediating this effect, we identified SWI/SNF-regulated genes in C. elegans. Results To identify SWI/SNF-regulated genes in adults, we compared mRNA expression in wild type and swsn-1(os22ts) worms under conditions that produce inactive swsn-1 in mature cells. To identify SWI/SNF-regulated genes in neurons, we compared gene expression in swsn-9(ok1354) null mutant worms that harbor a neuronal rescue or a control construct. RNA sequencing was performed to an average depth of 25 million reads per sample using 50-base, paired-end reads. We found that 6813 transcripts were significantly differentially expressed between swsn-1(os22ts) mutants and wild-type worms and 2412 transcripts were significantly differentially expressed between swsn-9(ok1354) mutants and swsn-9(ok1354) mutants with neuronal rescue. We examined the intersection between these two datasets and identified 603 genes that were differentially expressed in the same direction in both comparisons; we defined these as SWI/SNF-regulated genes in neurons and in adults. Among the differentially expressed genes was cbp-1, a C. elegans homolog of the mammalian CBP/p300 family of histone acetyltransferases. CBP has been implicated in the epigenetic regulation in response to alcohol in animal models and a polymorphism in the human CBP gene, CREBBP, has been associated with alcohol-related phenotypes. We found that cbp-1 is required for the development of acute functional tolerance to alcohol in C. elegans. Conclusions We identified 603 transcripts that were regulated by two different SWI/SNF complex subunits in adults and in neurons. The SWI/SNF-regulated genes were highly enriched for genes involved in membrane rafts, suggesting an important role for this membrane microdomain in the acute alcohol response. Among the differentially expressed genes was cbp-1; CBP-1 homologs have been implicated in alcohol responses across phyla and we found that C. elegans cbp-1 was required for the acute alcohol response in worms.
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Affiliation(s)
- Laura D Mathies
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, PO Box 980613, Richmond, VA, 23298, USA.
| | - Jonathan H Lindsay
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, PO Box 980613, Richmond, VA, 23298, USA
| | - Amal P Handal
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, PO Box 980613, Richmond, VA, 23298, USA
| | - GinaMari G Blackwell
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, PO Box 980613, Richmond, VA, 23298, USA
| | - Andrew G Davies
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, PO Box 980613, Richmond, VA, 23298, USA
| | - Jill C Bettinger
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, PO Box 980613, Richmond, VA, 23298, USA
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HIF-1α and HIF-2α differently regulate tumour development and inflammation of clear cell renal cell carcinoma in mice. Nat Commun 2020; 11:4111. [PMID: 32807776 PMCID: PMC7431415 DOI: 10.1038/s41467-020-17873-3] [Citation(s) in RCA: 146] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 07/21/2020] [Indexed: 02/06/2023] Open
Abstract
Mutational inactivation of VHL is the earliest genetic event in the majority of clear cell renal cell carcinomas (ccRCC), leading to accumulation of the HIF-1α and HIF-2α transcription factors. While correlative studies of human ccRCC and functional studies using human ccRCC cell lines have implicated HIF-1α as an inhibitor and HIF-2α as a promoter of aggressive tumour behaviours, their roles in tumour onset have not been functionally addressed. Herein we show using an autochthonous ccRCC model that Hif1a is essential for tumour formation whereas Hif2a deletion has only minor effects on tumour initiation and growth. Both HIF-1α and HIF-2α are required for the clear cell phenotype. Transcriptomic and proteomic analyses reveal that HIF-1α regulates glycolysis while HIF-2α regulates genes associated with lipoprotein metabolism, ribosome biogenesis and E2F and MYC transcriptional activities. HIF-2α-deficient tumours are characterised by increased antigen presentation, interferon signalling and CD8+ T cell infiltration and activation. Single copy loss of HIF1A or high levels of HIF2A mRNA expression correlate with altered immune microenvironments in human ccRCC. These studies reveal an oncogenic role of HIF-1α in ccRCC initiation and suggest that alterations in the balance of HIF-1α and HIF-2α activities can affect different aspects of ccRCC biology and disease aggressiveness.
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Chory EJ, Kirkland JG, Chang CY, D'Andrea VD, Gourisankar S, Dykhuizen EC, Crabtree GR. Chemical Inhibitors of a Selective SWI/SNF Function Synergize with ATR Inhibition in Cancer Cell Killing. ACS Chem Biol 2020; 15:1685-1696. [PMID: 32369697 PMCID: PMC8273930 DOI: 10.1021/acschembio.0c00312] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
SWI/SNF (BAF) complexes are a diverse family of ATP-dependent chromatin remodelers produced by combinatorial assembly that are mutated in and thought to contribute to 20% of human cancers and a large number of neurologic diseases. The gene-activating functions of BAF complexes are essential for viability of many cell types, limiting the development of small molecule inhibitors. To circumvent the potential toxicity of SWI/SNF inhibition, we identified small molecules that inhibit the specific repressive function of these complexes but are relatively nontoxic and importantly synergize with ATR inhibitors in killing cancer cells. Our studies suggest an avenue for therapeutic enhancement of ATR/ATM inhibition and provide evidence for chemical synthetic lethality of BAF complexes as a therapeutic strategy in cancer.
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Affiliation(s)
- Emma J Chory
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
- Departments of Developmental Biology and Pathology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Jacob G Kirkland
- Departments of Developmental Biology and Pathology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Chiung-Ying Chang
- Departments of Developmental Biology and Pathology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Vincent D D'Andrea
- Departments of Developmental Biology and Pathology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Sai Gourisankar
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
- Departments of Developmental Biology and Pathology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Emily C Dykhuizen
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Gerald R Crabtree
- Departments of Developmental Biology and Pathology, Stanford University School of Medicine, Stanford, California 94305, United States
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, United States
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Huang K, Sun R, Chen J, Yang Q, Wang Y, Zhang Y, Xie K, Zhang T, Li R, Zhao Q, Zou L, Li J. A novel EZH2 inhibitor induces synthetic lethality and apoptosis in PBRM1-deficient cancer cells. Cell Cycle 2020; 19:758-771. [PMID: 32093567 PMCID: PMC7145336 DOI: 10.1080/15384101.2020.1729450] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 12/09/2019] [Accepted: 12/29/2019] [Indexed: 12/24/2022] Open
Abstract
The inhibition of enhancer of zeste homolog 2 (EZH2) has been suggested to be synthetic lethal with polybromo-1 (PBRM1) deficiency, rendering EZH2 to be an attractive target for the treatment of PBRM1 frequently mutated cancers. In the current study, we combined computational and biochemical approaches to establish an efficient system for the screening and validation of synthetic lethal inhibitors from a large pool of chemical compounds. Five putative EZH2 inhibitors were identified through structure-based virtual screening from 47,737 chemical compounds and analyzed with molecular dynamics. The efficacy of these compounds against EZH2 was tested using PBRM1 deficient and wide-type cell lines. The compound L501-1669 selectively inhibited the proliferation of PBRM1-deficient cells and down-regulated the tri-methylation of histone H3 at Lysine 27 (H3K27me3). Importantly, we also observed an increase in apoptotic activities in L501-1669 treated PBRM1-deficient cells. Taken together, our results demonstrate that L501-1669 is a selective EZH2 inhibitor with promising application in the targeted therapy of PBRM1-deficient cancers.
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Affiliation(s)
- Kejia Huang
- Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu, China
| | - Rong Sun
- Basic Medical Research Center, School of Medicine, Nantong University, Jiangsu, China
| | - Jiarong Chen
- Affiliated Hospital of Chengdu University, Chengdu, Sichuan, China
| | - Qianye Yang
- Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu, China
| | - Yucheng Wang
- College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, China
| | - Yang Zhang
- Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu, China
| | - Kun Xie
- College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, China
| | - Tiantian Zhang
- College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, China
| | - Rui Li
- College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, China
| | - Qi Zhao
- Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu, China
- College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, China
| | - Liang Zou
- School of Medicine, Chengdu University, Chengdu, China
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Chengdu University, Chengdu, China
| | - Jian Li
- Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu, China
- School of Medicine, Chengdu University, Chengdu, China
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48
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Morrison AJ. Chromatin-remodeling links metabolic signaling to gene expression. Mol Metab 2020; 38:100973. [PMID: 32251664 PMCID: PMC7300377 DOI: 10.1016/j.molmet.2020.100973] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 03/01/2020] [Accepted: 03/03/2020] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND ATP-dependent chromatin remodelers are evolutionarily conserved complexes that alter nucleosome positioning to influence many DNA-templated processes, such as replication, repair, and transcription. In particular, chromatin remodeling can dynamically regulate gene expression by altering accessibility of chromatin to transcription factors. SCOPE OF REVIEW This review provides an overview of the importance of chromatin remodelers in the regulation of metabolic gene expression. Particular emphasis is placed on the INO80 and SWI/SNF (BAF/PBAF) chromatin remodelers in both yeast and mammals. This review details discoveries from the initial identification of chromatin remodelers in Saccharomyces cerevisiae to recent discoveries in the metabolic requirements of developing embryonic tissues in mammals. MAJOR CONCLUSIONS INO80 and SWI/SNF (BAF/PBAF) chromatin remodelers regulate the expression of energy metabolism pathways in S. cerevisiae and mammals in response to diverse nutrient environments. In particular, the INO80 complex organizes the temporal expression of gene expression in the metabolically synchronized S. cerevisiae system. INO80-mediated chromatin remodeling is also needed to constrain cell division during metabolically favorable conditions. Conversely, the BAF/PBAF remodeler regulates tissue-specific glycolytic metabolism and is disrupted in cancers that are dependent on glycolysis for proliferation. The role of chromatin remodeling in metabolic gene expression is downstream of the metabolic signaling pathways, such as the TOR pathway, a critical regulator of metabolic homeostasis. Furthermore, the INO80 and BAF/PBAF chromatin remodelers have both been shown to regulate heart development, the tissues of which have unique requirements for energy metabolism during development. Collectively, these results demonstrate that chromatin remodelers communicate metabolic status to chromatin and are a central component of homeostasis pathways that optimize cell fitness, organismal development, and prevent disease.
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Affiliation(s)
- Ashby J Morrison
- Department of Biology, Stanford University, Stanford CA 94305, USA.
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Prognostic and Predictive Value of PBRM1 in Clear Cell Renal Cell Carcinoma. Cancers (Basel) 2019; 12:cancers12010016. [PMID: 31861590 PMCID: PMC7016957 DOI: 10.3390/cancers12010016] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 12/13/2019] [Accepted: 12/15/2019] [Indexed: 12/27/2022] Open
Abstract
Renal cell carcinoma (RCC) is the most frequent kidney solid tumor, the clear cell RCC (ccRCC) being the major histological subtype. The probability of recurrence and the clinical behavior of ccRCC will greatly depend on the different clinical and histopathological features, already incorporated to different scoring systems, and on the genomic landscape of the tumor. In this sense, ccRCC has for a long time been known to be associated to the biallelic inactivation of Von Hippel-Lindau (VHL) gene which causes aberrant hypoxia inducible factor (HIF) accumulation. Recently, next generation-sequencing technologies have provided the bases for an in-depth molecular characterization of ccRCC, identifying additional recurrently mutated genes, such as PBRM1 (≈40-50%), SETD2 (≈12%), or BAP1 (≈10%). PBRM1, the second most common mutated gene in ccRCC after VHL, is a component of the SWI/SNF chromatin remodeling complex. Different studies have investigated the biological consequences and the potential role of PBRM1 alterations in RCC prognosis and as a drug response modulator, although some results are contradictory. In the present article, we review the current evidence on PBRM1 as potential prognostic and predictive marker in both localized and metastatic RCC.
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50
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Abstract
Renal cell carcinomas (RCCs) are a diverse set of malignancies that have recently been shown to harbour mutations in a number of chromatin modifier genes - including PBRM1, SETD2, BAP1, KDM5C, KDM6A, and MLL2 - through high-throughput sequencing efforts. Current research focuses on understanding the biological activities that chromatin modifiers employ to suppress tumorigenesis and on developing clinical approaches that take advantage of this knowledge. Unsurprisingly, several common themes unify the functions of these epigenetic modifiers, particularly regulation of histone post-translational modifications and nucleosome organization. Furthermore, chromatin modifiers also govern processes crucial for DNA repair and maintenance of genomic integrity as well as the regulation of splicing and other key processes. Many chromatin modifiers have additional non-canonical roles in cytoskeletal regulation, which further contribute to genomic stability, expanding the repertoire of functions that might be essential in tumorigenesis. Our understanding of how mutations in chromatin modifiers contribute to tumorigenesis in RCC is improving but remains an area of intense investigation. Importantly, elucidating the activities of chromatin modifiers offers intriguing opportunities for the development of new therapeutic interventions in RCC.
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Affiliation(s)
- Aguirre A de Cubas
- Department of Medicine, Division of Hematology and Oncology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - W Kimryn Rathmell
- Department of Medicine, Division of Hematology and Oncology, Vanderbilt University Medical Center, Nashville, TN, USA.
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