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Minervini G. Feature Paper in Oral Physiology and Pathology. Life (Basel) 2024; 14:895. [PMID: 39063647 PMCID: PMC11278310 DOI: 10.3390/life14070895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2024] [Accepted: 07/11/2024] [Indexed: 07/28/2024] Open
Abstract
In the realm of life sciences, the journal 'Life' has consistently served as a beacon for groundbreaking research and scientific discovery [...].
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Affiliation(s)
- Giuseppe Minervini
- Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai 602105, Tamil Nadu, India;
- Multidisciplinary Department of Medical-Surgical and Odontostomatological Specialties, University of Campania “Luigi Vanvitelli”, 80121 Naples, Italy
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2
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Alasady MJ, Koeva M, Takagishi SR, Segal D, Amici DR, Smith RS, Ansel DJ, Lindquist S, Whitesell L, Bartom ET, Taipale M, Mendillo ML. An HSF1-JMJD6-HSP feedback circuit promotes cell adaptation to proteotoxic stress. Proc Natl Acad Sci U S A 2024; 121:e2313370121. [PMID: 38985769 PMCID: PMC11260097 DOI: 10.1073/pnas.2313370121] [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: 08/10/2023] [Accepted: 05/10/2024] [Indexed: 07/12/2024] Open
Abstract
Heat Shock Factor 1 (HSF1) is best known as the master transcriptional regulator of the heat-shock response (HSR), a conserved adaptive mechanism critical for protein homeostasis (proteostasis). Combining a genome-wide RNAi library with an HSR reporter, we identified Jumonji domain-containing protein 6 (JMJD6) as an essential mediator of HSF1 activity. In follow-up studies, we found that JMJD6 is itself a noncanonical transcriptional target of HSF1 which acts as a critical regulator of proteostasis. In a positive feedback circuit, HSF1 binds and promotes JMJD6 expression, which in turn reduces heat shock protein 70 (HSP70) R469 monomethylation to disrupt HSP70-HSF1 repressive complexes resulting in enhanced HSF1 activation. Thus, JMJD6 is intricately wired into the proteostasis network where it plays a critical role in cellular adaptation to proteotoxic stress.
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Affiliation(s)
- Milad J. Alasady
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL60611
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL60611
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL60611
| | - Martina Koeva
- Whitehead Institute for Biomedical Research, Cambridge, MA02142
- Massachusetts Institute of Technology, Cambridge, MA02142
- HHMI, Cambridge, MA02139
| | - Seesha R. Takagishi
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL60611
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL60611
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL60611
| | - Dmitri Segal
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ONM5S 3E1, Canada
| | - David R. Amici
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL60611
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL60611
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL60611
| | - Roger S. Smith
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL60611
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL60611
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL60611
| | - Daniel J. Ansel
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL60611
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL60611
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL60611
| | - Susan Lindquist
- Whitehead Institute for Biomedical Research, Cambridge, MA02142
- Massachusetts Institute of Technology, Cambridge, MA02142
- HHMI, Cambridge, MA02139
| | - Luke Whitesell
- Whitehead Institute for Biomedical Research, Cambridge, MA02142
- Massachusetts Institute of Technology, Cambridge, MA02142
| | - Elizabeth T. Bartom
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL60611
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL60611
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL60611
| | - Mikko Taipale
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ONM5S 3E1, Canada
| | - Marc L. Mendillo
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL60611
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL60611
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL60611
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3
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Mayer MP. Hsf1 and Hsf2 in normal, healthy human tissues: Immunohistochemistry provokes new questions. Cell Stress Chaperones 2024; 29:437-439. [PMID: 38641046 PMCID: PMC11067330 DOI: 10.1016/j.cstres.2024.04.004] [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: 04/09/2024] [Revised: 04/09/2024] [Accepted: 04/09/2024] [Indexed: 04/21/2024] Open
Abstract
The heat shock transcription factors heat shock transcription factor 1 and Hsf2 have been studied for many years, mainly in the context of stress response and in malignant cells. Their physiological function in nonmalignant human cells under nonstress conditions is still largely unknown. To approach this important issue, Joutsen et al. present immunohistochemical staining data on Hsf1 and Hsf2 in 80 nonpathological human tissue samples. The wealth of these data elicits many interesting questions that will spur many future research projects.
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Affiliation(s)
- Matthias P Mayer
- Center for Molecular Biology Heidelberg University (ZMBH), DKFZ-ZMBH-Alliance, Heidelberg, Germany.
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4
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Amici DR, Alhayek S, Klein AT, Wang YZ, Wilen AP, Song W, Zhu P, Thakkar A, King MA, Steffeck AW, Alasady MJ, Peek C, Savas JN, Mendillo ML. Tight regulation of a nuclear HAPSTR1-HUWE1 pathway essential for mammalian life. Life Sci Alliance 2024; 7:e202302370. [PMID: 38453366 PMCID: PMC10921065 DOI: 10.26508/lsa.202302370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 02/26/2024] [Accepted: 02/27/2024] [Indexed: 03/09/2024] Open
Abstract
The recently discovered HAPSTR1 protein broadly oversees cellular stress responses. This function requires HUWE1, a ubiquitin ligase that paradoxically marks HAPSTR1 for degradation, but much about this pathway remains unclear. Here, leveraging multiplexed proteomics, we find that HAPSTR1 enables nuclear localization of HUWE1 with implications for nuclear protein quality control. We show that HAPSTR1 is tightly regulated and identify ubiquitin ligase TRIP12 and deubiquitinase USP7 as upstream regulators titrating HAPSTR1 stability. Finally, we generate conditional Hapstr1 knockout mice, finding that Hapstr1-null mice are perinatal lethal, adult mice depleted of Hapstr1 have reduced fitness, and primary cells explanted from Hapstr1-null animals falter in culture coincident with HUWE1 mislocalization and broadly remodeled signaling. Notably, although HAPSTR1 potently suppresses p53, we find that Hapstr1 is essential for life even in mice lacking p53. Altogether, we identify novel components and functional insights into the conserved HAPSTR1-HUWE1 pathway and demonstrate its requirement for mammalian life.
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Affiliation(s)
- David R Amici
- https://ror.org/000e0be47 Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- https://ror.org/000e0be47 Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- https://ror.org/000e0be47 Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- https://ror.org/000e0be47 Medical Scientist Training Program, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Sammy Alhayek
- https://ror.org/000e0be47 Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- https://ror.org/000e0be47 Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- https://ror.org/000e0be47 Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Austin T Klein
- https://ror.org/000e0be47 Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- https://ror.org/000e0be47 Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- https://ror.org/000e0be47 Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Yi-Zhi Wang
- https://ror.org/000e0be47 Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Anika P Wilen
- https://ror.org/000e0be47 Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Weimin Song
- https://ror.org/000e0be47 Comprehensive Metabolic Core, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Pei Zhu
- https://ror.org/000e0be47 Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- https://ror.org/000e0be47 Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- https://ror.org/000e0be47 Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Abhishek Thakkar
- https://ror.org/000e0be47 Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- https://ror.org/000e0be47 Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- https://ror.org/000e0be47 Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - McKenzi A King
- https://ror.org/000e0be47 Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- https://ror.org/000e0be47 Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- https://ror.org/000e0be47 Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Adam Wt Steffeck
- https://ror.org/000e0be47 Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- https://ror.org/000e0be47 Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- https://ror.org/000e0be47 Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Milad J Alasady
- https://ror.org/000e0be47 Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- https://ror.org/000e0be47 Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- https://ror.org/000e0be47 Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- https://ror.org/000e0be47 Medical Scientist Training Program, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Clara Peek
- https://ror.org/000e0be47 Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- https://ror.org/000e0be47 Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- https://ror.org/000e0be47 Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Jeffrey N Savas
- https://ror.org/000e0be47 Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Marc L Mendillo
- https://ror.org/000e0be47 Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- https://ror.org/000e0be47 Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- https://ror.org/000e0be47 Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
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5
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Fan G, Xie T, Li L, Tang L, Han X, Shi Y. Single-cell and spatial analyses revealed the co-location of cancer stem cells and SPP1+ macrophage in hypoxic region that determines the poor prognosis in hepatocellular carcinoma. NPJ Precis Oncol 2024; 8:75. [PMID: 38521868 PMCID: PMC10960828 DOI: 10.1038/s41698-024-00564-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 03/07/2024] [Indexed: 03/25/2024] Open
Abstract
In hepatocellular carcinoma (HCC), classical cancer stem cells (CSC) markers were shared by normal stem cells, targeting which may hinder hepatic regeneration and cause liver failure. Additionally, the spatial structure of CSC still remained elusive. To address these limitations, we undertook a comprehensive study combining single-cell data (56,022 cells from 20 samples) and spatial data (38,191 spots from eight samples) to obtain CSC signature and uncover its spatial structure. Utilizing the CytoTRACE algorithm, we discretely identified CSC, which displayed upregulated proliferation pathways regulated by HIF1A. A CSC signature of 107 genes was then developed using Weighted Gene Co-expression Network Analysis (WGCNA). Notably, HCC patients with high CSC levels exhibited an accumulation of SPP1+ macrophages (Macro_SPP1) expressing metalloproteinases (MMP9, MMP12, and MMP7) regulated by HIF1A, suggesting a hypoxic tumor region connecting Macro_SPP1 and CSC. Both CSC and Macro_SPP1 correlated with worse prognosis and undesirable immunotherapy response. Spatial analysis revealed the co-location of CSC and Macro_SPP1, with CD8 T cells excluded from the tumor region. The co-location area and non-tumor area of boundary exhibited a high level of hypoxia, with the HAVRC2 checkpoint highly expressed. Within the co-location area, the SPP1 signaling pathway was most active in cell-cell communication, with SPP1-CD44 and SPP1-ITGA/ITGB identified as the main ligand-receptor pairs. This study successfully constructed a CSC signature and demonstrated the co-location of CSC and Macro_SPP1 in a hypoxic region that exacerbates the tumor microenvironment in HCC.
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Affiliation(s)
- Guangyu Fan
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs; No. 17 Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
| | - Tongji Xie
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs; No. 17 Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
| | - Lin Li
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100021, China
| | - Le Tang
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs; No. 17 Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
| | - Xiaohong Han
- Clinical Pharmacology Research Center, Peking Union Medical College Hospital, State Key Laboratory of Complex Severe and Rare Diseases, NMPA Key Laboratory for Clinical Research and Evaluation of Drug, Beijing Key Laboratory of Clinical PK & PD Investigation for Innovative Drugs, Chinese Academy of Medical Sciences & Peking Union Medical College; No.1, Shuaifuyuan, Dongcheng District, Beijing, 100730, China.
| | - Yuankai Shi
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs; No. 17 Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China.
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6
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Mayer MP, Blair L, Blatch GL, Borges TJ, Chadli A, Chiosis G, de Thonel A, Dinkova-Kostova A, Ecroyd H, Edkins AL, Eguchi T, Fleshner M, Foley KP, Fragkostefanakis S, Gestwicki J, Goloubinoff P, Heritz JA, Heske CM, Hibshman JD, Joutsen J, Li W, Lynes M, Mendillo ML, Mivechi N, Mokoena F, Okusha Y, Prahlad V, Repasky E, Sannino S, Scalia F, Shalgi R, Sistonen L, Sontag E, van Oosten-Hawle P, Vihervaara A, Wickramaratne A, Wang SXY, Zininga T. Stress biology: Complexity and multifariousness in health and disease. Cell Stress Chaperones 2024; 29:143-157. [PMID: 38311120 PMCID: PMC10939078 DOI: 10.1016/j.cstres.2024.01.006] [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] [Indexed: 02/06/2024] Open
Abstract
Preserving and regulating cellular homeostasis in the light of changing environmental conditions or developmental processes is of pivotal importance for single cellular and multicellular organisms alike. To counteract an imbalance in cellular homeostasis transcriptional programs evolved, called the heat shock response, unfolded protein response, and integrated stress response, that act cell-autonomously in most cells but in multicellular organisms are subjected to cell-nonautonomous regulation. These transcriptional programs downregulate the expression of most genes but increase the expression of heat shock genes, including genes encoding molecular chaperones and proteases, proteins involved in the repair of stress-induced damage to macromolecules and cellular structures. Sixty-one years after the discovery of the heat shock response by Ferruccio Ritossa, many aspects of stress biology are still enigmatic. Recent progress in the understanding of stress responses and molecular chaperones was reported at the 12th International Symposium on Heat Shock Proteins in Biology, Medicine and the Environment in the Old Town Alexandria, VA, USA from 28th to 31st of October 2023.
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Affiliation(s)
- Matthias P Mayer
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany.
| | - Laura Blair
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Gregory L Blatch
- Biomedical Research and Drug Discovery Research Group, Faculty of Health Sciences, Higher Colleges of Technology, Sharjah, United Arab Emirates; Biomedical Biotechnology Research Unit, Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa
| | - Thiago J Borges
- Department of Surgery, Center for Transplantation Sciences, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02129, USA
| | - Ahmed Chadli
- Georgia Cancer Center, Medical College of Georgia at Augusta University, Augusta, GA 30912, USA
| | - Gabriela Chiosis
- Department of Medicine, Division of Solid Tumors, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Aurélie de Thonel
- CNRS, UMR 7216, 75250 Paris Cedex 13, Paris, France; Univeristy of Paris Diderot, Sorbonne Paris Cité, Paris, France; Département Hospitalo-Universitaire DHU PROTECT, Paris, France
| | - Albena Dinkova-Kostova
- Division of Cellular and Systems Medicine, Jacqui Wood Cancer Centre, School of Medicine, University of Dundee, Dundee, UK
| | - Heath Ecroyd
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Adrienne L Edkins
- Biomedical Biotechnology Research Unit (BioBRU), Department of Biochemistry and Microbiology, Rhodes University, Makhanda, South Africa
| | - Takanori Eguchi
- Department of Dental Pharmacology, Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8525, Japan
| | - Monika Fleshner
- Department of Integrative Physiology, University of Colorado at Boulder, Boulder, CO 80309, USA
| | | | - Sotirios Fragkostefanakis
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University Frankfurt am Main, Frankfurt am Main 60438, Germany
| | - Jason Gestwicki
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA 94158, USA
| | - Pierre Goloubinoff
- Department of Plant Molecular Biology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Jennifer A Heritz
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY 13210, USA; Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Christine M Heske
- Pediatric Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jonathan D Hibshman
- Biology Department, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jenny Joutsen
- Department of Pathology, Lapland Central Hospital, Lapland Wellbeing Services County, Rovaniemi, Finland
| | - Wei Li
- Department of Dermatology and the Norris Comprehensive Cancer Center, University of Southern California Keck Medical Center, Los Angeles, CA 90033, USA
| | - Michael Lynes
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Marc L Mendillo
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Nahid Mivechi
- Molecular Chaperone Biology, Medical College of Georgia, Georgia Cancer Center, Augusta University, Augusta, GA 30912, USA
| | - Fortunate Mokoena
- Department of Biochemistry, North-West University, Mmabatho 2735, South Africa
| | - Yuka Okusha
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Veena Prahlad
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14203, USA
| | - Elizabeth Repasky
- Department of Hematology and Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Sara Sannino
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Federica Scalia
- Department of Biomedicine, Neuroscience and Advanced Diagnostics (BIND), University of Palermo, Palermo, Italy; Euro-Mediterranean Institute of Science and Technology (IEMEST), Palermo, Italy
| | - Reut Shalgi
- Department of Biochemistry, Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 31096, Israel
| | - Lea Sistonen
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland; Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Emily Sontag
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA
| | | | - Anniina Vihervaara
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Anushka Wickramaratne
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shawn Xiang Yang Wang
- Developmental Therapeutics Program, VCU Comprehensive Massey Cancer Center, VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, VA 23298, USA
| | - Tawanda Zininga
- Department of Biochemistry, Stellenbosch University, Stellenbosch 7602, South Africa
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7
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Dorantes-Palma D, Pérez-Mora S, Azuara-Liceaga E, Pérez-Rueda E, Pérez-Ishiwara DG, Coca-González M, Medel-Flores MO, Gómez-García C. Screening and Structural Characterization of Heat Shock Response Elements (HSEs) in Entamoeba histolytica Promoters. Int J Mol Sci 2024; 25:1319. [PMID: 38279319 PMCID: PMC10815948 DOI: 10.3390/ijms25021319] [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: 12/14/2023] [Revised: 01/09/2024] [Accepted: 01/11/2024] [Indexed: 01/28/2024] Open
Abstract
Entamoeba histolytica (E. histolytica) exhibits a remarkable capacity to respond to thermal shock stress through a sophisticated genetic regulation mechanism. This process is carried out via Heat Shock Response Elements (HSEs), which are recognized by Heat Shock Transcription Factors (EhHSTFs), enabling fine and precise control of gene expression. Our study focused on screening for HSEs in the promoters of the E. histolytica genome, specifically analyzing six HSEs, including Ehpgp5, EhrabB1, EhrabB4, EhrabB5, Ehmlbp, and Ehhsp100. We discovered 2578 HSEs, with 1412 in promoters of hypothetical genes and 1166 in coding genes. We observed that a single promoter could contain anywhere from one to five HSEs. Gene ontology analysis revealed the presence of HSEs in essential genes for the amoeba, including cysteine proteinases, ribosomal genes, Myb family DNA-binding proteins, and Rab GTPases, among others. Complementarily, our molecular docking analyses indicate that these HSEs are potentially recognized by EhHSTF5, EhHSTF6, and EhHSTF7 factors in their trimeric conformation. These findings suggest that E. histolytica has the capability to regulate a wide range of critical genes via HSE-EhHSTFs, not only for thermal stress response but also for vital functions of the parasite. This is the first comprehensive study of HSEs in the genome of E. histolytica, significantly contributing to the understanding of its genetic regulation and highlighting the complexity and precision of this mechanism in the parasite's survival.
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Affiliation(s)
- David Dorantes-Palma
- Laboratorio de Biomedicina Molecular 1, ENMyH, Instituto Politécnico Nacional, Mexico City 07320, Mexico; (D.D.-P.); (S.P.-M.); (D.G.P.-I.); (M.C.-G.); (M.O.M.-F.)
| | - Salvador Pérez-Mora
- Laboratorio de Biomedicina Molecular 1, ENMyH, Instituto Politécnico Nacional, Mexico City 07320, Mexico; (D.D.-P.); (S.P.-M.); (D.G.P.-I.); (M.C.-G.); (M.O.M.-F.)
| | - Elisa Azuara-Liceaga
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico City 03100, Mexico;
| | - Ernesto Pérez-Rueda
- Unidad Académica del Estado de Yucatán, Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Mexico City 97302, Mexico;
| | - David Guillermo Pérez-Ishiwara
- Laboratorio de Biomedicina Molecular 1, ENMyH, Instituto Politécnico Nacional, Mexico City 07320, Mexico; (D.D.-P.); (S.P.-M.); (D.G.P.-I.); (M.C.-G.); (M.O.M.-F.)
| | - Misael Coca-González
- Laboratorio de Biomedicina Molecular 1, ENMyH, Instituto Politécnico Nacional, Mexico City 07320, Mexico; (D.D.-P.); (S.P.-M.); (D.G.P.-I.); (M.C.-G.); (M.O.M.-F.)
| | - María Olivia Medel-Flores
- Laboratorio de Biomedicina Molecular 1, ENMyH, Instituto Politécnico Nacional, Mexico City 07320, Mexico; (D.D.-P.); (S.P.-M.); (D.G.P.-I.); (M.C.-G.); (M.O.M.-F.)
| | - Consuelo Gómez-García
- Laboratorio de Biomedicina Molecular 1, ENMyH, Instituto Politécnico Nacional, Mexico City 07320, Mexico; (D.D.-P.); (S.P.-M.); (D.G.P.-I.); (M.C.-G.); (M.O.M.-F.)
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8
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Pessa JC, Joutsen J, Sistonen L. Transcriptional reprogramming at the intersection of the heat shock response and proteostasis. Mol Cell 2024; 84:80-93. [PMID: 38103561 DOI: 10.1016/j.molcel.2023.11.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/16/2023] [Accepted: 11/20/2023] [Indexed: 12/19/2023]
Abstract
Cellular homeostasis is constantly challenged by a myriad of extrinsic and intrinsic stressors. To mitigate the stress-induced damage, cells activate transient survival programs. The heat shock response (HSR) is an evolutionarily well-conserved survival program that is activated in response to proteotoxic stress. The HSR encompasses a dual regulation of transcription, characterized by rapid activation of genes encoding molecular chaperones and concomitant global attenuation of non-chaperone genes. Recent genome-wide approaches have delineated the molecular depth of stress-induced transcriptional reprogramming. The dramatic rewiring of gene and enhancer networks is driven by key transcription factors, including heat shock factors (HSFs), that together with chromatin-modifying enzymes remodel the 3D chromatin architecture, determining the selection of either gene activation or repression. Here, we highlight the current advancements of molecular mechanisms driving transcriptional reprogramming during acute heat stress. We also discuss the emerging implications of HSF-mediated stress signaling in the context of physiological and pathological conditions.
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Affiliation(s)
- Jenny C Pessa
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland; Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Jenny Joutsen
- Department of Pathology, Lapland Central Hospital, Lapland Wellbeing Services County, Rovaniemi, Finland
| | - Lea Sistonen
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland; Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.
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9
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Dastidar SG, De Kumar B, Lauckner B, Parrello D, Perley D, Vlasenok M, Tyagi A, Koney NKK, Abbas A, Nechaev S. Transcriptional responses of cancer cells to heat shock-inducing stimuli involve amplification of robust HSF1 binding. Nat Commun 2023; 14:7420. [PMID: 37973875 PMCID: PMC10654513 DOI: 10.1038/s41467-023-43157-7] [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: 11/23/2022] [Accepted: 11/01/2023] [Indexed: 11/19/2023] Open
Abstract
Responses of cells to stimuli are increasingly discovered to involve the binding of sequence-specific transcription factors outside of known target genes. We wanted to determine to what extent the genome-wide binding and function of a transcription factor are shaped by the cell type versus the stimulus. To do so, we induced the Heat Shock Response pathway in two different cancer cell lines with two different stimuli and related the binding of its master regulator HSF1 to nascent RNA and chromatin accessibility. Here, we show that HSF1 binding patterns retain their identity between basal conditions and under different magnitudes of activation, so that common HSF1 binding is globally associated with distinct transcription outcomes. HSF1-induced increase in DNA accessibility was modest in scale, but occurred predominantly at remote genomic sites. Apart from regulating transcription at existing elements including promoters and enhancers, HSF1 binding amplified during responses to stimuli may engage inactive chromatin.
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Affiliation(s)
- Sayantani Ghosh Dastidar
- Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND, 58202, USA
- Illumina, Inc., San Diego, CA, 92122, USA
| | - Bony De Kumar
- Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND, 58202, USA
- Yale Center for Genome Analysis, Department of Genetics, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Bo Lauckner
- Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND, 58202, USA
| | - Damien Parrello
- Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND, 58202, USA
| | - Danielle Perley
- Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND, 58202, USA
- Canadian Centre for Computational Genomics, McGill Genome Centre, Montreal, QC, H3A0G1, Canada
| | - Maria Vlasenok
- Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND, 58202, USA
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, 121205, Russia
| | - Antariksh Tyagi
- Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND, 58202, USA
- Yale Center for Genome Analysis, Department of Genetics, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Nii Koney-Kwaku Koney
- Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND, 58202, USA
- University of Ghana Medical School, University of Ghana, Accra, Ghana
| | - Ata Abbas
- Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND, 58202, USA
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Sergei Nechaev
- Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND, 58202, USA.
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10
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Heat-Shock Proteins in Leukemia and Lymphoma: Multitargets for Innovative Therapeutic Approaches. Cancers (Basel) 2023; 15:cancers15030984. [PMID: 36765939 PMCID: PMC9913431 DOI: 10.3390/cancers15030984] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/27/2023] [Accepted: 01/31/2023] [Indexed: 02/08/2023] Open
Abstract
Heat-shock proteins (HSPs) are powerful chaperones that provide support for cellular functions under stress conditions but also for the homeostasis of basic cellular machinery. All cancer cells strongly rely on HSPs, as they must continuously adapt to internal but also microenvironmental stresses to survive. In solid tumors, HSPs have been described as helping to correct the folding of misfolded proteins, sustain oncogenic pathways, and prevent apoptosis. Leukemias and lymphomas also overexpress HSPs, which are frequently associated with resistance to therapy. HSPs have therefore been proposed as new therapeutic targets. Given the specific biology of hematological malignancies, it is essential to revise their role in this field, providing a more adaptable and comprehensive picture that would help design future clinical trials. To that end, this review will describe the different pathways and functions regulated by HSP27, HSP70, HSP90, and, not least, HSP110 in leukemias and lymphomas.
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11
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Chin Y, Gumilar KE, Li XG, Tjokroprawiro BA, Lu CH, Lu J, Zhou M, Sobol RW, Tan M. Targeting HSF1 for cancer treatment: mechanisms and inhibitor development. Theranostics 2023; 13:2281-2300. [PMID: 37153737 PMCID: PMC10157728 DOI: 10.7150/thno.82431] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 04/06/2023] [Indexed: 05/10/2023] Open
Abstract
Heat Shock Factor 1 (HSF1) is a master regulator of heat shock responsive signaling. In addition to playing critical roles in cellular heat shock response, emerging evidence suggests that HSF1 also regulates a non-heat shock responsive transcriptional network to handle metabolic, chemical, and genetic stress. The function of HSF1 in cellular transformation and cancer development has been extensively studied in recent years. Due to important roles for HSF1 for coping with various stressful cellular states, research on HSF1 has been very active. New functions and molecular mechanisms underlying these functions have been continuously discovered, providing new targets for novel cancer treatment strategies. In this article, we review the essential roles and mechanisms of HSF1 action in cancer cells, focusing more on recently discovered functions and their underlying mechanisms to reflect the new advances in cancer biology. In addition, we emphasize new advances with regard to HSF1 inhibitors for cancer drug development.
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Affiliation(s)
- Yeh Chin
- Graduate Institute of Biomedical Sciences and Research Center for Cancer Biology, China Medical University, Taichung, Taiwan, R.O.C
| | - Khanisyah E Gumilar
- Graduate Institute of Biomedical Sciences and Research Center for Cancer Biology, China Medical University, Taichung, Taiwan, R.O.C
- The Department of Obstetrics and Gynecology, Medical Faculty, Universitas Airlangga, Surabaya, Indonesia
| | - Xing-Guo Li
- Graduate Institute of Biomedical Sciences and Research Center for Cancer Biology, China Medical University, Taichung, Taiwan, R.O.C
- Institute of Biochemistry & Molecular Biology, China Medical University, Taichung, Taiwan, R.O.C
| | - Brahmana A. Tjokroprawiro
- The Department of Obstetrics and Gynecology, Medical Faculty, Universitas Airlangga, Surabaya, Indonesia
| | - Chien-Hsing Lu
- Department of Gynecology and Obstetrics, Taichung Veterans General Hospital, Taichung, Taiwan, R.O.C
| | - Jianrong Lu
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, USA
| | - Ming Zhou
- Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, China
| | - Robert W. Sobol
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School & Legorreta Cancer Center, Brown University, Providence, USA
| | - Ming Tan
- Graduate Institute of Biomedical Sciences and Research Center for Cancer Biology, China Medical University, Taichung, Taiwan, R.O.C
- Institute of Biochemistry & Molecular Biology, China Medical University, Taichung, Taiwan, R.O.C
- ✉ Corresponding author: Ming Tan, Institute of Biochemistry and Molecular Biology, China Medical University (Taiwan), E-mail:
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12
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Kovács D, Kovács M, Ahmed S, Barna J. Functional diversification of heat shock factors. Biol Futur 2022; 73:427-439. [PMID: 36402935 DOI: 10.1007/s42977-022-00138-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 11/08/2022] [Indexed: 11/21/2022]
Abstract
Heat shock transcription factors (HSFs) are widely known as master regulators of the heat shock response. In invertebrates, a single heat shock factor, HSF1, is responsible for the maintenance of protein homeostasis. In vertebrates, seven members of the HSF family have been identified, namely HSF1, HSF2, HSF3, HSF4, HSF5, HSFX, and HSFY, of which HSF1 and HSF2 are clearly associated with heat shock response, while HSF4 is involved in development. Other members of the family have not yet been studied as extensively. Besides their role in cellular proteostasis, HSFs influence a plethora of biological processes such as aging, development, cell proliferation, and cell differentiation, and they are implicated in several pathologies such as neurodegeneration and cancer. This is achieved by regulating the expression of a great variety of genes including chaperones. Here, we review our current knowledge on the function of HSF family members and important aspects that made possible the functional diversification of HSFs.
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Affiliation(s)
- Dániel Kovács
- Department of Genetics, Institute of Biology, Eötvös Loránd University, Pázmány Péter sétány 1/c, Budapest, H-1117, Hungary
| | - Márton Kovács
- Department of Genetics, Institute of Biology, Eötvös Loránd University, Pázmány Péter sétány 1/c, Budapest, H-1117, Hungary
| | - Saqib Ahmed
- Department of Genetics, Institute of Biology, Eötvös Loránd University, Pázmány Péter sétány 1/c, Budapest, H-1117, Hungary
| | - János Barna
- Department of Genetics, Institute of Biology, Eötvös Loránd University, Pázmány Péter sétány 1/c, Budapest, H-1117, Hungary. .,ELKH-ELTE Genetics Research Group, Pázmány Péter sétány 1/c, Budapest, H-1117, Hungary.
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13
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Tokunaga Y, Otsuyama KI, Kakuta S, Hayashida N. Heat Shock Transcription Factor 2 Is Significantly Involved in Neurodegenerative Diseases, Inflammatory Bowel Disease, Cancer, Male Infertility, and Fetal Alcohol Spectrum Disorder: The Novel Mechanisms of Several Severe Diseases. Int J Mol Sci 2022; 23:ijms232213763. [PMID: 36430241 PMCID: PMC9691173 DOI: 10.3390/ijms232213763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/03/2022] [Accepted: 11/05/2022] [Indexed: 11/10/2022] Open
Abstract
HSF (heat shock transcription factor or heat shock factor) was discovered as a transcription factor indispensable for heat shock response. Although four classical HSFs were discovered in mammals and two major HSFs, HSF1 and HSF2, were cloned in the same year of 1991, only HSF1 was intensively studied because HSF1 can give rise to heat shock response through the induction of various HSPs' expression. On the other hand, HSF2 was not well studied for some time, which was probably due to an underestimate of HSF2 itself. Since the beginning of the 21st century, HSF2 research has progressed and many biologically significant functions of HSF2 have been revealed. For example, the roles of HSF2 in nervous system protection, inflammation, maintenance of mitosis and meiosis, and cancer cell survival and death have been gradually unveiled. However, we feel that the fact HSF2 has a relationship with various factors is not yet widely recognized; therefore, the biological significance of HSF2 has been underestimated. We strongly hope to widely communicate the significance of HSF2 to researchers and readers in broad research fields through this review. In addition, we also hope that many readers will have great interest in the molecular mechanism in which HSF2 acts as an active transcription factor and gene bookmarking mechanism of HSF2 during cell cycle progression, as is summarized in this review.
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Affiliation(s)
- Yasuko Tokunaga
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, Yamaguchi University, Yamaguchi 755-8505, Japan
- Institute of Gene Research, Yamaguchi University Science Research Center, Yamaguchi 755-8505, Japan
| | - Ken-Ichiro Otsuyama
- Department of Clinical Laboratory Science, Faculty of Health Science, Graduate School of Medicine, Yamaguchi University, Yamaguchi 755-8505, Japan
| | - Shigeru Kakuta
- Laboratory of Biomedical Science, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Naoki Hayashida
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, Yamaguchi University, Yamaguchi 755-8505, Japan
- Correspondence: ; Tel.: +81-836-22-2359
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14
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Cugusi S, Bajpe PK, Mitter R, Patel H, Stewart A, Svejstrup JQ. An Important Role for RPRD1B in the Heat Shock Response. Mol Cell Biol 2022; 42:e0017322. [PMID: 36121223 PMCID: PMC9583720 DOI: 10.1128/mcb.00173-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/07/2022] [Accepted: 08/26/2022] [Indexed: 12/25/2022] Open
Abstract
During the heat shock response (HSR), heat shock factor (HSF1 in mammals) binds to target gene promoters, resulting in increased expression of heat shock proteins that help maintain protein homeostasis and ensure cell survival. Besides HSF1, only a relatively few transcription factors with a specific role in ensuring correctly regulated gene expression during the HSR have been described. Here, we use proteomic and genomic (CRISPR) screening to identify a role for RPRD1B in the response to heat shock. Indeed, cells depleted for RPRD1B are heat shock sensitive and show decreased expression of key heat shock proteins (HSPs). These results add to our understanding of the connection between basic gene expression mechanisms and the HSR.
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Affiliation(s)
- Simona Cugusi
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Prashanth Kumar Bajpe
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Richard Mitter
- Bioinformatics and Biostatistics, The Francis Crick Institute, London, United Kingdom
| | - Harshil Patel
- Bioinformatics and Biostatistics, The Francis Crick Institute, London, United Kingdom
| | - Aengus Stewart
- Bioinformatics and Biostatistics, The Francis Crick Institute, London, United Kingdom
| | - Jesper Q. Svejstrup
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, London, United Kingdom
- Department of Cellular and Molecular Medicine, Panum Institute, University of Copenhagen, Copenhagen, Denmark
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15
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Himanen SV, Puustinen MC, Da Silva AJ, Vihervaara A, Sistonen L. HSFs drive transcription of distinct genes and enhancers during oxidative stress and heat shock. Nucleic Acids Res 2022; 50:6102-6115. [PMID: 35687139 PMCID: PMC9226494 DOI: 10.1093/nar/gkac493] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 05/25/2022] [Indexed: 11/13/2022] Open
Abstract
Reprogramming of transcription is critical for the survival under cellular stress. Heat shock has provided an excellent model to investigate nascent transcription in stressed cells, but the molecular mechanisms orchestrating RNA synthesis during other types of stress are unknown. We utilized PRO-seq and ChIP-seq to study how Heat Shock Factors, HSF1 and HSF2, coordinate transcription at genes and enhancers upon oxidative stress and heat shock. We show that pause-release of RNA polymerase II (Pol II) is a universal mechanism regulating gene transcription in stressed cells, while enhancers are activated at the level of Pol II recruitment. Moreover, besides functioning as conventional promoter-binding transcription factors, HSF1 and HSF2 bind to stress-induced enhancers to trigger Pol II pause-release from poised gene promoters. Importantly, HSFs act at distinct genes and enhancers in a stress type-specific manner. HSF1 binds to many chaperone genes upon oxidative and heat stress but activates them only in heat-shocked cells. Under oxidative stress, HSF1 localizes to a unique set of promoters and enhancers to trans-activate oxidative stress-specific genes. Taken together, we show that HSFs function as multi-stress-responsive factors that activate distinct genes and enhancers when encountering changes in temperature and redox state.
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Affiliation(s)
- Samu V Himanen
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, 20520 Turku, Finland.,Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland
| | - Mikael C Puustinen
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, 20520 Turku, Finland.,Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland
| | - Alejandro J Da Silva
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, 20520 Turku, Finland.,Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland
| | - Anniina Vihervaara
- Department of Gene Technology, Science for Life Laboratory, KTH Royal Institute of Technology, 17165 Stockholm, Sweden
| | - Lea Sistonen
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, 20520 Turku, Finland.,Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland
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