1
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Koutsandreas T, Felden B, Chevet E, Chatziioannou A. Protein homeostasis imprinting across evolution. NAR Genom Bioinform 2024; 6:lqae014. [PMID: 38486886 PMCID: PMC10939379 DOI: 10.1093/nargab/lqae014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 10/07/2023] [Accepted: 01/24/2024] [Indexed: 03/17/2024] Open
Abstract
Protein homeostasis (a.k.a. proteostasis) is associated with the primary functions of life, and therefore with evolution. However, it is unclear how cellular proteostasis machines have evolved to adjust protein biogenesis needs to environmental constraints. Herein, we describe a novel computational approach, based on semantic network analysis, to evaluate proteostasis plasticity during evolution. We show that the molecular components of the proteostasis network (PN) are reliable metrics to deconvolute the life forms into Archaea, Bacteria and Eukarya and to assess the evolution rates among species. Semantic graphs were used as new criteria to evaluate PN complexity in 93 Eukarya, 250 Bacteria and 62 Archaea, thus representing a novel strategy for taxonomic classification, which provided information about species divergence. Kingdom-specific PN components were identified, suggesting that PN complexity may correlate with evolution. We found that the gains that occurred throughout PN evolution revealed a dichotomy within both the PN conserved modules and within kingdom-specific modules. Additionally, many of these components contribute to the evolutionary imprinting of other conserved mechanisms. Finally, the current study suggests a new way to exploit the genomic annotation of biomedical ontologies, deriving new knowledge from the semantic comparison of different biological systems.
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Affiliation(s)
- Thodoris Koutsandreas
- Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
- e-NIOS Applications PC, Kallithea-Athens, Greece
| | - Brice Felden
- University of Rennes, INSERM U1230, Rennes, France
| | - Eric Chevet
- INSERM U1242, University of Rennes, Rennes, France
- Centre de Lutte Contre le Cancer Eugène Marquis, Rennes, France
| | - Aristotelis Chatziioannou
- Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
- e-NIOS Applications PC, Kallithea-Athens, Greece
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2
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Liu Y, Huang S, Dong G, Hou C, Zhao Y, Zhang D. Computational identification of DNA damage-relevant lncRNAs for predicting therapeutic efficacy and clinical outcomes in cancer. Comput Biol Med 2024; 171:108107. [PMID: 38412692 DOI: 10.1016/j.compbiomed.2024.108107] [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: 12/12/2023] [Revised: 01/12/2024] [Accepted: 02/04/2024] [Indexed: 02/29/2024]
Abstract
OBJECTIVES The role of long non-coding RNAs (lncRNAs) in cancer treatment, particularly in modulating DNA repair programs, is an emerging field that warrants systematic exploration. This study aimed to systematically identify the lncRNA regulators that potentially regulate DNA damage response (DDR). METHODS Using genome-wide mRNA and lncRNA expression profiles of the same tumor patients, we proposed a novel computational framework. This framework performed Gene Set Variation Analysis to calculate DDR pathway enrichment score, which relies on weighting by tumor purity to obtain DDR activity score for each patient. Then, an in-depth differential expression profiling was conducted to identify pathway activity lncRNAs between high- and low-activity groups, utilizing a bootstrap-based randomization method. RESULTS We comprehensively charted the landscape of DDR-relevant lncRNAs across 23 epithelial-based cancer types. Its effectiveness was validated by assessing the consistency of these lncRNAs within various datasets of the same cancer type (hypergeometric test P < 0.001), examining the expression perturbation of these lncRNAs in response to treatment and demonstrating its application in prioritizing clinically-related lncRNAs. Furthermore, leveraging 820 epithelial ovarian cancer patients from four public datasets, we applied these lncRNAs identified by DDRLnc to establish and validate a risk stratification model to evaluate the benefits of platinum-based adjuvant chemotherapy for the improvement of clinical treatment outcomes. CONCLUSIONS Comprehensive pan-cancer analysis illustrates the utility of computational framework in identifying potentially lncRNAs involved in DDR, thereby offering novel insights into the complex realm of cancer research, and it will become a valuable tool for identifying potential therapeutic targets for cancer.
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Affiliation(s)
- Yixin Liu
- Modern Education Technology Center, Harbin Medical University, Harbin, 150080, China
| | - Shan Huang
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, 150081, China
| | - Guanghui Dong
- College of Computer and Control Engineering, Northeast Forestry University, Harbin, 150040, China
| | - Chang Hou
- College of Computer and Control Engineering, Northeast Forestry University, Harbin, 150040, China
| | - Yuming Zhao
- College of Computer and Control Engineering, Northeast Forestry University, Harbin, 150040, China.
| | - Dandan Zhang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Harbin Medical University, Harbin, 150007, China.
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3
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Isermann T, Schneider KL, Wegwitz F, De Oliveira T, Conradi LC, Volk V, Feuerhake F, Papke B, Stintzing S, Mundt B, Kühnel F, Moll UM, Schulz-Heddergott R. Enhancement of colorectal cancer therapy through interruption of the HSF1-HSP90 axis by p53 activation or cell cycle inhibition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.22.581507. [PMID: 38464125 PMCID: PMC10925225 DOI: 10.1101/2024.02.22.581507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
The stress-associated molecular chaperone system is an actionable target in cancer therapies. It is ubiquitously upregulated in cancer tissues and enables tumorigenicity by stabilizing hundreds of oncoproteins and disturbing the stoichiometry of protein complexes. Most inhibitors target the key component heat-shock protein 90 (HSP90). However, although classical HSP90 inhibitors are highly tumor-selective, they fail in phase 3 clinical oncology trials. These failures are at least partly due to an interference with a negative feedback loop by HSP90 inhibition, known as heat-shock response (HSR): in response to HSP90 inhibition there is compensatory synthesis of stress-inducible chaperones, mediated by the transcription factor heat-shock factor 1 (HSF1). We recently identified that wildtype p53 (p53) actively reduces the HSR by repressing HSF1 via a p21-CDK4/6-MAPK-HSF1 axis. Here we test the hypothesis that in HSP90-based therapies simultaneous p53 activation or direct cell cycle inhibition interrupts the deleterious HSF1-HSR axis and improves the efficiency of HSP90 inhibitors. Indeed, we find that the clinically relevant p53 activator Idasanutlin suppresses the HSF1-HSR activity in HSP90 inhibitor-based therapies. This combination synergistically reduces cell viability and accelerates cell death in p53-proficient colorectal cancer (CRC) cells, murine tumor-derived organoids and patient-derived organoids (PDOs). Mechanistically, upon combination therapy human CRC cells strongly upregulate p53-associated pathways, apoptosis, and inflammatory immune pathways. Likewise, in the chemical AOM/DSS CRC model in mice, dual HSF1-HSP90 inhibition strongly represses tumor growth and remodels immune cell composition, yet displays only minor toxicities in mice and normal mucosa-derived organoids. Importantly, inhibition of the cyclin dependent kinases 4 and 6 (CDK4/6) under HSP90 inhibition phenocopies synergistic repression of the HSR in p53-proficient CRC cells. Even more important, in p53-deficient (mutp53-harboring) CRC cells, an HSP90 inhibition in combination with CDK4/6 inhibitors similarly suppresses the HSF1-HSR system and reduces cancer growth. Likewise, p53-mutated PDOs strongly respond to dual HSF1-HSP90 pathway inhibition and thus, providing a strategy to target CRC independent of the p53 status. In sum, activating p53 (in p53-proficient cancer cells) or inhibiting CDK4/6 (independent of the p53 status) provide new options to improve the clinical outcome of HSP90-based therapies and to enhance colorectal cancer therapy.
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Affiliation(s)
- Tamara Isermann
- Department of Molecular Oncology, University Medical Center Göttingen, Göttingen, Germany
- Charité – Universitätsmedizin Berlin, Institute of Pathology, Laboratory of Molecular Tumor Pathology and Systems Biology, Berlin, Germany
- German Cancer Consortium (DKTK); Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kim Lucia Schneider
- Department of Molecular Oncology, University Medical Center Göttingen, Göttingen, Germany
| | - Florian Wegwitz
- Department of Gynecology and Obstetrics, University Medical Center Göttingen, Göttingen, Germany
| | - Tiago De Oliveira
- Department of General, Visceral, and Pediatric Surgery, University Medical Center Göttingen, Germany
| | - Lena-Christin Conradi
- Department of General, Visceral, and Pediatric Surgery, University Medical Center Göttingen, Germany
| | - Valery Volk
- Institute for Pathology, Hannover Medical School, Hannover, Germany
| | | | - Björn Papke
- Charité – Universitätsmedizin Berlin, Institute of Pathology, Laboratory of Molecular Tumor Pathology and Systems Biology, Berlin, Germany
- German Cancer Consortium (DKTK); Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sebastian Stintzing
- Charité – Universitätsmedizin Berlin, Department of Hematology, Oncology, and Cancer Immunology, Berlin, Germany
| | - Bettina Mundt
- Department of Gastroenterology, Hepatology, Infectious Diseases and Endocrinology, Hannover Medical School, Hannover, Germany
| | - Florian Kühnel
- Department of Gastroenterology, Hepatology, Infectious Diseases and Endocrinology, Hannover Medical School, Hannover, Germany
| | - Ute M. Moll
- Department of Pathology, Stony Brook University, Stony Brook, NY
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4
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Chiosis G, Digwal CS, Trepel JB, Neckers L. Structural and functional complexity of HSP90 in cellular homeostasis and disease. Nat Rev Mol Cell Biol 2023; 24:797-815. [PMID: 37524848 PMCID: PMC10592246 DOI: 10.1038/s41580-023-00640-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/03/2023] [Indexed: 08/02/2023]
Abstract
Heat shock protein 90 (HSP90) is a chaperone with vital roles in regulating proteostasis, long recognized for its function in protein folding and maturation. A view is emerging that identifies HSP90 not as one protein that is structurally and functionally homogeneous but, rather, as a protein that is shaped by its environment. In this Review, we discuss evidence of multiple structural forms of HSP90 in health and disease, including homo-oligomers and hetero-oligomers, also termed epichaperomes, and examine the impact of stress, post-translational modifications and co-chaperones on their formation. We describe how these variations influence context-dependent functions of HSP90 as well as its interaction with other chaperones, co-chaperones and proteins, and how this structural complexity of HSP90 impacts and is impacted by its interaction with small molecule modulators. We close by discussing recent developments regarding the use of HSP90 inhibitors in cancer and how our new appreciation of the structural and functional heterogeneity of HSP90 invites a re-evaluation of how we discover and implement HSP90 therapeutics for disease treatment.
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Affiliation(s)
- Gabriela Chiosis
- Chemical Biology Program, Memorial Sloan Kettering Institute, New York, NY, USA.
- Department of Medicine, Memorial Sloan Kettering Institute, New York, NY, USA.
| | - Chander S Digwal
- Chemical Biology Program, Memorial Sloan Kettering Institute, New York, NY, USA
| | - Jane B Trepel
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Len Neckers
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
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5
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Miles J, Townend S, Milonaitytė D, Smith W, Hodge F, Westhead DR, van Oosten-Hawle P. Transcellular chaperone signaling is an intercellular stress-response distinct from the HSF-1-mediated heat shock response. PLoS Biol 2023; 21:e3001605. [PMID: 36780563 PMCID: PMC9956597 DOI: 10.1371/journal.pbio.3001605] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 02/24/2023] [Accepted: 01/20/2023] [Indexed: 02/15/2023] Open
Abstract
Organismal proteostasis is maintained by intercellular signaling processes including cell nonautonomous stress responses such as transcellular chaperone signaling (TCS). When TCS is activated upon tissue-specific knockdown of hsp-90 in the Caenorhabditis elegans intestine, heat-inducible hsp-70 is induced in muscle cells at the permissive temperature resulting in increased heat stress resistance and lifespan extension. However, our understanding of the molecular mechanism and signaling factors mediating transcellular activation of hsp-70 expression from one tissue to another is still in its infancy. Here, we conducted a combinatorial approach using transcriptome RNA-Seq profiling and a forward genetic mutagenesis screen to elucidate how stress signaling from the intestine to the muscle is regulated. We find that the TCS-mediated "gut-to-muscle" induction of hsp-70 expression is suppressed by HSF-1 and instead relies on transcellular-X-cross-tissue (txt) genes. We identify a key role for the PDZ-domain guanylate cyclase txt-1 and the homeobox transcription factor ceh-58 as signaling hubs in the stress receiving muscle cells to initiate hsp-70 expression and facilitate TCS-mediated heat stress resistance and lifespan extension. Our results provide a new view on cell-nonautonomous regulation of "inter-tissue" stress responses in an organism that highlight a key role for the gut. Our data suggest that the HSF-1-mediated heat shock response is switched off upon TCS activation, in favor of an intercellular stress-signaling route to safeguard survival.
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Affiliation(s)
- Jay Miles
- School of Molecular and Cell Biology & Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Sarah Townend
- School of Molecular and Cell Biology & Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Dovilė Milonaitytė
- School of Molecular and Cell Biology & Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - William Smith
- School of Molecular and Cell Biology & Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Francesca Hodge
- School of Molecular and Cell Biology & Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - David R. Westhead
- School of Molecular and Cell Biology & Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Patricija van Oosten-Hawle
- School of Molecular and Cell Biology & Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
- * E-mail:
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6
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Ginsberg SD, Sharma S, Norton L, Chiosis G. Targeting stressor-induced dysfunctions in protein-protein interaction networks via epichaperomes. Trends Pharmacol Sci 2023; 44:20-33. [PMID: 36414432 PMCID: PMC9789192 DOI: 10.1016/j.tips.2022.10.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/31/2022] [Accepted: 10/31/2022] [Indexed: 11/21/2022]
Abstract
Diseases are manifestations of complex changes in protein-protein interaction (PPI) networks whereby stressors, genetic, environmental, and combinations thereof, alter molecular interactions and perturb the individual from the level of cells and tissues to the entire organism. Targeting stressor-induced dysfunctions in PPI networks has therefore become a promising but technically challenging frontier in therapeutics discovery. This opinion provides a new framework based upon disrupting epichaperomes - pathological entities that enable dysfunctional rewiring of PPI networks - as a mechanism to revert context-specific PPI network dysfunction to a normative state. We speculate on the implications of recent research in this area for a precision medicine approach to detecting and treating complex diseases, including cancer and neurodegenerative disorders.
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Affiliation(s)
- Stephen D Ginsberg
- Center for Dementia Research, Nathan Kline Institute, Orangeburg, NY 10962, USA; Department of Psychiatry, New York University Grossman School of Medicine, New York, NY 10016, USA; Department of Neuroscience and Physiology, New York University Grossman School of Medicine, New York, NY 10016, USA; NYU Neuroscience Institute, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Sahil Sharma
- Program in Chemical Biology, Sloan Kettering Institute, New York, NY 10065, USA
| | - Larry Norton
- Breast Cancer Medicine Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Gabriela Chiosis
- Program in Chemical Biology, Sloan Kettering Institute, New York, NY 10065, USA; Breast Cancer Medicine Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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7
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Mattos DR, Weinman MA, Wan X, Goodall CP, Serrill JD, McPhail KL, Milovancev M, Bracha S, Ishmael JE. Canine osteosarcoma cells exhibit basal accumulation of multiple chaperone proteins and are sensitive to small molecule inhibitors of GRP78 and heat shock protein function. Cell Stress Chaperones 2022; 27:223-239. [PMID: 35244890 PMCID: PMC9106791 DOI: 10.1007/s12192-022-01263-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 02/14/2022] [Accepted: 02/17/2022] [Indexed: 12/12/2022] Open
Abstract
Osteosarcoma is the most common type of bone cancer in dogs and humans, with significant numbers of patients experiencing treatment failure and disease progression. In our search for new approaches to treat osteosarcoma, we previously detected multiple chaperone proteins in the surface-exposed proteome of canine osteosarcoma cells. In the present study, we characterized expression of representative chaperones and find evidence for stress adaptation in canine osteosarcoma cells relative to osteogenic progenitors from normal bone. We compared the cytotoxic potential of direct (HA15) and putative (OSU-03012) inhibitors of Grp78 function and found canine POS and HMPOS osteosarcoma cells to be more sensitive to both compounds than normal cells. HA15 and OSU-03012 increased the thermal stability of Grp78 in intact POS cells at low micromolar concentrations, but each induced distinct patterns in Grp78 expression without significant change in Grp94. Both inhibitors were as effective alone as carboplatin and showed little evidence of synergy in combination treatment. However, HMPOS cells with acquired resistance to carboplatin were sensitive to inhibition of Grp78 (by HA15; OSU-03012), Hsp70 (by VER-155008), and Hsp90 (by 17-AAG) function. These results suggest that multiple nodes within the osteosarcoma chaperome may be relevant chemotherapeutic targets against platinum resistance.
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Affiliation(s)
- Daphne R Mattos
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, 411 Pharmacy Building, Corvallis, OR, 97331, USA
| | - Marcus A Weinman
- Department of Clinical Sciences, College of Veterinary Medicine, Oregon State University, Corvallis, OR, 97331, USA
- CMB Graduate Program, Department of Neurological Sciences, University of Vermont, Burlington, VT, 05405, USA
| | - Xuemei Wan
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, 411 Pharmacy Building, Corvallis, OR, 97331, USA
| | - Cheri P Goodall
- Department of Clinical Sciences, College of Veterinary Medicine, Oregon State University, Corvallis, OR, 97331, USA
| | - Jeffrey D Serrill
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, 411 Pharmacy Building, Corvallis, OR, 97331, USA
| | - Kerry L McPhail
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, 411 Pharmacy Building, Corvallis, OR, 97331, USA
| | - Milan Milovancev
- Department of Clinical Sciences, College of Veterinary Medicine, Oregon State University, Corvallis, OR, 97331, USA.
| | - Shay Bracha
- College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA.
| | - Jane E Ishmael
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, 411 Pharmacy Building, Corvallis, OR, 97331, USA.
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8
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Wong DCS, Seinkmane E, Zeng A, Stangherlin A, Rzechorzek NM, Beale AD, Day J, Reed M, Peak‐Chew SY, Styles CT, Edgar RS, Putker M, O’Neill JS. CRYPTOCHROMES promote daily protein homeostasis. EMBO J 2022; 41:e108883. [PMID: 34842284 PMCID: PMC8724739 DOI: 10.15252/embj.2021108883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 11/07/2021] [Accepted: 11/09/2021] [Indexed: 11/29/2022] Open
Abstract
The daily organisation of most mammalian cellular functions is attributed to circadian regulation of clock-controlled protein expression, driven by daily cycles of CRYPTOCHROME-dependent transcriptional feedback repression. To test this, we used quantitative mass spectrometry to compare wild-type and CRY-deficient fibroblasts under constant conditions. In CRY-deficient cells, we found that temporal variation in protein, phosphopeptide, and K+ abundance was at least as great as wild-type controls. Most strikingly, the extent of temporal variation within either genotype was much smaller than overall differences in proteome composition between WT and CRY-deficient cells. This proteome imbalance in CRY-deficient cells and tissues was associated with increased susceptibility to proteotoxic stress, which impairs circadian robustness, and may contribute to the wide-ranging phenotypes of CRY-deficient mice. Rather than generating large-scale daily variation in proteome composition, we suggest it is plausible that the various transcriptional and post-translational functions of CRY proteins ultimately act to maintain protein and osmotic homeostasis against daily perturbation.
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Affiliation(s)
| | | | - Aiwei Zeng
- MRC Laboratory of Molecular BiologyCambridgeUK
| | | | | | | | - Jason Day
- Department of Earth SciencesUniversity of CambridgeCambridgeUK
| | - Martin Reed
- MRC Laboratory of Molecular BiologyCambridgeUK
| | | | | | - Rachel S Edgar
- Department of Infectious DiseasesImperial CollegeLondonUK
| | - Marrit Putker
- MRC Laboratory of Molecular BiologyCambridgeUK
- Present address:
Crown BioscienceUtrechtthe Netherlands
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9
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Li Z, Wei J, Zheng H, Gan X, Song M, Zhang Y, Kong L, Zhang C, Yang J, Jin Y. m 6A regulator-mediated methylation modification patterns and tumor immune microenvironment in sarcoma. Aging (Albany NY) 2022; 14:330-353. [PMID: 34979500 PMCID: PMC8791212 DOI: 10.18632/aging.203807] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 12/25/2021] [Indexed: 12/02/2022]
Abstract
Background: Studies have shown that the RNA N6-methyladenosine (m6A) modification patterns are extensively involved in the development of multiple tumors. However, the association between the m6A regulator expression patterns and the sarcoma tumor immune microenvironment (TIME) remains unclear. Methods: We systematically evaluated the m6A regulator expression patterns in patients with sarcoma based on known 23 m6A regulators. Different m6A regulator expression patterns were analyzed using gene set variation analysis and a single-sample gene set enrichment analysis algorithm. According to the results of consensus clustering, we classified the patients into four different clusters. Next, we subjected the four clusters to differential genetic analysis and established m6A-related differentially expressed genes (DEGs). We then calculated the m6A-related DEGs score and constructed the m6A-related gene signature, named m6A score. Finally, the 259 sarcoma samples were divided into high- and low-m6A score groups. We further evaluated the TIME landscape between the high- and low-m6A score groups. Results: We identified four different m6A modification clusters and found that each cluster had unique metabolic and immunological characteristics. Based on the 19 prognosis-related DEGs, we calculated the principal component analysis scores for each patient with sarcoma and classified them into high- and low-m6A score groups. Conclusions: The m6A regulator expression patterns and complexity of the sarcoma TIME landscape are closely related to each other. Systematic evaluation of m6A regulator expression patterns and m6A scores in patients with sarcoma will enhance our understanding of TIME characteristics.
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Affiliation(s)
- Zhehong Li
- Traumatology and Orthopedics, Affiliated Hospital of Chengde Medical College, Chengde, Hebei 067000, China
| | - Junqiang Wei
- Department of Bone and Soft Tissue Tumor, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China.,National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China.,Department of Orthopedics, Affiliated Hospital of Chengde Medical College, Chengde, Hebei 067000, China
| | - Honghong Zheng
- General Surgery, Affiliated Hospital of Chengde Medical College, Chengde, Hebei 067000, China
| | - Xintian Gan
- Traumatology and Orthopedics, Affiliated Hospital of Chengde Medical College, Chengde, Hebei 067000, China
| | - Mingze Song
- Traumatology and Orthopedics, Affiliated Hospital of Chengde Medical College, Chengde, Hebei 067000, China
| | - Yafang Zhang
- Traumatology and Orthopedics, Affiliated Hospital of Chengde Medical College, Chengde, Hebei 067000, China
| | - Lingwei Kong
- Traumatology and Orthopedics, Affiliated Hospital of Chengde Medical College, Chengde, Hebei 067000, China
| | - Chao Zhang
- Department of Bone and Soft Tissue Tumor, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China.,National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Jilong Yang
- Department of Bone and Soft Tissue Tumor, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China.,National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Yu Jin
- Traumatology and Orthopedics, Affiliated Hospital of Chengde Medical College, Chengde, Hebei 067000, China
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10
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Ginsberg SD, Joshi S, Sharma S, Guzman G, Wang T, Arancio O, Chiosis G. The penalty of stress - Epichaperomes negatively reshaping the brain in neurodegenerative disorders. J Neurochem 2021; 159:958-979. [PMID: 34657288 PMCID: PMC8688321 DOI: 10.1111/jnc.15525] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/22/2021] [Accepted: 10/13/2021] [Indexed: 02/06/2023]
Abstract
Adaptation to acute and chronic stress and/or persistent stressors is a subject of wide interest in central nervous system disorders. In this context, stress is an effector of change in organismal homeostasis and the response is generated when the brain perceives a potential threat. Herein, we discuss a nuanced and granular view whereby a wide variety of genotoxic and environmental stressors, including aging, genetic risk factors, environmental exposures, and age- and lifestyle-related changes, act as direct insults to cellular, as opposed to organismal, homeostasis. These two concepts of how stressors impact the central nervous system are not mutually exclusive. We discuss how maladaptive stressor-induced changes in protein connectivity through epichaperomes, disease-associated pathologic scaffolds composed of tightly bound chaperones, co-chaperones, and other factors, impact intracellular protein functionality altering phenotypes, that in turn disrupt and remodel brain networks ranging from intercellular to brain connectome levels. We provide an evidence-based view on how these maladaptive changes ranging from stressor to phenotype provide unique precision medicine opportunities for diagnostic and therapeutic development, especially in the context of neurodegenerative disorders including Alzheimer's disease where treatment options are currently limited.
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Affiliation(s)
- Stephen D. Ginsberg
- Center for Dementia Research, Nathan Kline Institute, Orangeburg, New York, USA
- Departments of Psychiatry, Neuroscience & Physiology, the NYU Neuroscience Institute, New York University Grossman School of Medicine, New York City, New York, USA
| | - Suhasini Joshi
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York City, New York, USA
| | - Sahil Sharma
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York City, New York, USA
| | - Gianny Guzman
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York City, New York, USA
| | - Tai Wang
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York City, New York, USA
| | - Ottavio Arancio
- Department of Pathology and Cell Biology, Columbia University, New York City, New York, USA
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University, New York City, New York, USA
| | - Gabriela Chiosis
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York City, New York, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York City, New York, USA
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11
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Joshi S, Gomes ED, Wang T, Corben A, Taldone T, Gandu S, Xu C, Sharma S, Buddaseth S, Yan P, Chan LYL, Gokce A, Rajasekhar VK, Shrestha L, Panchal P, Almodovar J, Digwal CS, Rodina A, Merugu S, Pillarsetty N, Miclea V, Peter RI, Wang W, Ginsberg SD, Tang L, Mattar M, de Stanchina E, Yu KH, Lowery M, Grbovic-Huezo O, O'Reilly EM, Janjigian Y, Healey JH, Jarnagin WR, Allen PJ, Sander C, Erdjument-Bromage H, Neubert TA, Leach SD, Chiosis G. Pharmacologically controlling protein-protein interactions through epichaperomes for therapeutic vulnerability in cancer. Commun Biol 2021; 4:1333. [PMID: 34824367 PMCID: PMC8617294 DOI: 10.1038/s42003-021-02842-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 11/03/2021] [Indexed: 12/03/2022] Open
Abstract
Cancer cell plasticity due to the dynamic architecture of interactome networks provides a vexing outlet for therapy evasion. Here, through chemical biology approaches for systems level exploration of protein connectivity changes applied to pancreatic cancer cell lines, patient biospecimens, and cell- and patient-derived xenografts in mice, we demonstrate interactomes can be re-engineered for vulnerability. By manipulating epichaperomes pharmacologically, we control and anticipate how thousands of proteins interact in real-time within tumours. Further, we can essentially force tumours into interactome hyperconnectivity and maximal protein-protein interaction capacity, a state whereby no rebound pathways can be deployed and where alternative signalling is supressed. This approach therefore primes interactomes to enhance vulnerability and improve treatment efficacy, enabling therapeutics with traditionally poor performance to become highly efficacious. These findings provide proof-of-principle for a paradigm to overcome drug resistance through pharmacologic manipulation of proteome-wide protein-protein interaction networks.
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Affiliation(s)
- Suhasini Joshi
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Erica DaGama Gomes
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Tai Wang
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Adriana Corben
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Tony Taldone
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Srinivasa Gandu
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Chao Xu
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Sahil Sharma
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Salma Buddaseth
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Pengrong Yan
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Lon Yin L Chan
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Askan Gokce
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Vinagolu K Rajasekhar
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Lisa Shrestha
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Palak Panchal
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Justina Almodovar
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Chander S Digwal
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Anna Rodina
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Swathi Merugu
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | | | - Vlad Miclea
- Faculty of Automation and Computer Science, Technical University of Cluj-Napoca, Cluj-Napoca, CJ, 400114, Romania
| | - Radu I Peter
- Faculty of Automation and Computer Science, Technical University of Cluj-Napoca, Cluj-Napoca, CJ, 400114, Romania
| | - Wanyan Wang
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Stephen D Ginsberg
- Center for Dementia Research, Nathan Kline Institute, Orangeburg, NY, 10962, USA
- Departments of Psychiatry, Neuroscience & Physiology, and the NYU Neuroscience Institute, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Laura Tang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Marissa Mattar
- Antitumour Assessment Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Elisa de Stanchina
- Antitumour Assessment Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Kenneth H Yu
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Maeve Lowery
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Olivera Grbovic-Huezo
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Eileen M O'Reilly
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Yelena Janjigian
- Department of Medicine, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY, 10065, USA
| | - John H Healey
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - William R Jarnagin
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Peter J Allen
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Department of Surgery, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Chris Sander
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Hediye Erdjument-Bromage
- Department of Cell Biology, New York University Grossman School of Medicine, New York, NY, 10016, USA
- Kimmel Center for Biology and Medicine at the Skirball Institute, NYU School of Medicine, New York, NY, 10016, USA
| | - Thomas A Neubert
- Department of Cell Biology, New York University Grossman School of Medicine, New York, NY, 10016, USA
- Kimmel Center for Biology and Medicine at the Skirball Institute, NYU School of Medicine, New York, NY, 10016, USA
| | - Steven D Leach
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Dartmouth Geisel School of Medicine and Norris Cotton Cancer Center, Lebanon, NH, 03766, USA
| | - Gabriela Chiosis
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
- Department of Medicine, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY, 10065, USA.
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12
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Herranz-Montoya I, Park S, Djouder N. A comprehensive analysis of prefoldins and their implication in cancer. iScience 2021; 24:103273. [PMID: 34761191 PMCID: PMC8567396 DOI: 10.1016/j.isci.2021.103273] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Prefoldins (PFDNs) are evolutionary conserved co-chaperones, initially discovered in archaea but universally present in eukaryotes. PFDNs are prevalently organized into hetero-hexameric complexes. Although they have been overlooked since their discovery and their functions remain elusive, several reports indicate they act as co-chaperones escorting misfolded or non-native proteins to group II chaperonins. Unlike the eukaryotic PFDNs which interact with cytoskeletal components, the archaeal PFDNs can bind and stabilize a wide range of substrates, possibly due to their great structural diversity. The discovery of the unconventional RPB5 interactor (URI) PFDN-like complex (UPC) suggests that PFDNs have versatile functions and are required for different cellular processes, including an important role in cancer. Here, we summarize their functions across different species. Moreover, a comprehensive analysis of PFDNs genomic alterations across cancer types by using large-scale cancer genomic data indicates that PFDNs are a new class of non-mutated proteins significantly overexpressed in some cancer types.
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Affiliation(s)
- Irene Herranz-Montoya
- Growth Factors, Nutrients and Cancer Group, Molecular Oncology Programme, Centro Nacional de Investigaciones Oncológicas, CNIO, Madrid 28029, Spain
| | - Solip Park
- Computational Cancer Genomics Group, Structural Biology Programme, Centro Nacional de Investigaciones Oncológicas, CNIO, Madrid 28029, Spain
| | - Nabil Djouder
- Growth Factors, Nutrients and Cancer Group, Molecular Oncology Programme, Centro Nacional de Investigaciones Oncológicas, CNIO, Madrid 28029, Spain
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13
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Shkedi A, Adkisson M, Schroeder A, Eckalbar WL, Kuo SY, Neckers L, Gestwicki JE. Inhibitor Combinations Reveal Wiring of the Proteostasis Network in Prostate Cancer Cells. J Med Chem 2021; 64:14809-14821. [PMID: 34606726 PMCID: PMC8806517 DOI: 10.1021/acs.jmedchem.1c01342] [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: 11/29/2022]
Abstract
The protein homeostasis (proteostasis) network is composed of multiple pathways that work together to balance protein folding, stability, and turnover. Cancer cells are particularly reliant on this network; however, it is hypothesized that inhibition of one node might lead to compensation. To better understand these connections, we dosed 22Rv1 prostate cancer cells with inhibitors of four proteostasis targets (Hsp70, Hsp90, proteasome, and p97), either alone or in binary combinations, and measured the effects on cell growth. The results reveal a series of additive, synergistic, and antagonistic relationships, including strong synergy between inhibitors of p97 and the proteasome and striking antagonism between inhibitors of Hsp90 and the proteasome. Based on RNA-seq, these relationships are associated, in part, with activation of stress pathways. Together, these results suggest that cocktails of proteostasis inhibitors might be a powerful way of treating some cancers, although antagonism that blunts the efficacy of both molecules is also possible.
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Affiliation(s)
- Arielle Shkedi
- Department of Pharmaceutical Chemistry and the Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco CA 94158
| | - Michael Adkisson
- Functional Genomics Core, University of California San Francisco, San Francisco, CA 94158
| | - Andrew Schroeder
- Functional Genomics Core, University of California San Francisco, San Francisco, CA 94158
| | - Walter L Eckalbar
- Functional Genomics Core, University of California San Francisco, San Francisco, CA 94158
| | - Szu-Yu Kuo
- Department of Pharmaceutical Chemistry and the Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco CA 94158
| | - Leonard Neckers
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892
| | - Jason E. Gestwicki
- Department of Pharmaceutical Chemistry and the Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco CA 94158
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14
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Chemical tools for epichaperome-mediated interactome dysfunctions of the central nervous system. Nat Commun 2021; 12:4669. [PMID: 34344873 PMCID: PMC8333062 DOI: 10.1038/s41467-021-24821-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 07/07/2021] [Indexed: 12/11/2022] Open
Abstract
Diseases are a manifestation of how thousands of proteins interact. In several diseases, such as cancer and Alzheimer’s disease, proteome-wide disturbances in protein-protein interactions are caused by alterations to chaperome scaffolds termed epichaperomes. Epichaperome-directed chemical probes may be useful for detecting and reversing defective chaperomes. Here we provide structural, biochemical, and functional insights into the discovery of epichaperome probes, with a focus on their use in central nervous system diseases. We demonstrate on-target activity and kinetic selectivity of a radiolabeled epichaperome probe in both cells and mice, together with a proof-of-principle in human patients in an exploratory single group assignment diagnostic study (ClinicalTrials.gov Identifier: NCT03371420). The clinical study is designed to determine the pharmacokinetic parameters and the incidence of adverse events in patients receiving a single microdose of the radiolabeled probe administered by intravenous injection. In sum, we introduce a discovery platform for brain-directed chemical probes that specifically modulate epichaperomes and provide proof-of-principle applications in their use in the detection, quantification, and modulation of the target in complex biological systems. Here, the authors show structural, biochemical, and functional insights into the discovery of epichaperome‐ directed chemical probes for use in central nervous system diseases. Probes emerging from this work have translated to human clinical studies in Alzheimer’s disease and cancer.
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15
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Liu Z, Lu T, Wang Y, Jiao D, Li Z, Wang L, Liu L, Guo C, Zhao Y, Han X. Establishment and experimental validation of an immune miRNA signature for assessing prognosis and immune landscape of patients with colorectal cancer. J Cell Mol Med 2021; 25:6874-6886. [PMID: 34101338 PMCID: PMC8278100 DOI: 10.1111/jcmm.16696] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 05/11/2021] [Accepted: 05/14/2021] [Indexed: 02/06/2023] Open
Abstract
As essential regulators of gene expression, miRNAs are engaged in the initiation and progression of colorectal cancer (CRC), including antitumour immune response. In this study, we proposed an integrated algorithm, ImmuMiRNA, for identifying miRNA modulators of immune‐associated pathways. Based on these immune‐associated miRNAs, we applied the LASSO algorithm to develop a reliable and individualized signature for evaluating overall survival (OS) and inflammatory landscape of CRC patients. An external public data set and qRT‐PCR data from 40 samples were further utilized to validate this signature. As a result, an immune‐associated miRNA prognostic signature (IAMIPS) consisting of three miRNAs (miR‐194‐3P, miR‐216a‐5p and miR‐3677‐3p) was established and validated. Patients in the high‐risk group possessed worse OS. After stratification for clinical factors, the signature remained a powerful independent predictor for OS. IAMIPS displayed much better accuracy than the traditional clinical stage in assessing the prognosis of CRC. Further analysis revealed that patients in the high‐risk group were characterized by inflammatory response, abundance immune cell infiltration, and higher immune checkpoint profiles and tumour mutation burden (TMB). In conclusion, the IAMIPS is highly predictive of OS in patients with CRC, which may serve as a powerful prognostic tool to further optimize immunotherapies for cancer.
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Affiliation(s)
- Zaoqu Liu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Taoyuan Lu
- Department of Cerebrovascular Disease, Zhengzhou University People's Hospital, Zhengzhou, China
| | - Yanli Wang
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Dechao Jiao
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhaonan Li
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Libo Wang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Long Liu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Chunguang Guo
- Department of Endovascular Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yanan Zhao
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xinwei Han
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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16
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Cafe SL, Nixon B, Ecroyd H, Martin JH, Skerrett-Byrne DA, Bromfield EG. Proteostasis in the Male and Female Germline: A New Outlook on the Maintenance of Reproductive Health. Front Cell Dev Biol 2021; 9:660626. [PMID: 33937261 PMCID: PMC8085359 DOI: 10.3389/fcell.2021.660626] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 03/22/2021] [Indexed: 01/07/2023] Open
Abstract
For fully differentiated, long lived cells the maintenance of protein homeostasis (proteostasis) becomes a crucial determinant of cellular function and viability. Neurons are the most well-known example of this phenomenon where the majority of these cells must survive the entire course of life. However, male and female germ cells are also uniquely dependent on the maintenance of proteostasis to achieve successful fertilization. Oocytes, also long-lived cells, are subjected to prolonged periods of arrest and are largely reliant on the translation of stored mRNAs, accumulated during the growth period, to support meiotic maturation and subsequent embryogenesis. Conversely, sperm cells, while relatively ephemeral, are completely reliant on proteostasis due to the absence of both transcription and translation. Despite these remarkable, cell-specific features there has been little focus on understanding protein homeostasis in reproductive cells and how/whether proteostasis is "reset" during embryogenesis. Here, we seek to capture the momentum of this growing field by highlighting novel findings regarding germline proteostasis and how this knowledge can be used to promote reproductive health. In this review we capture proteostasis in the context of both somatic cell and germline aging and discuss the influence of oxidative stress on protein function. In particular, we highlight the contributions of proteostasis changes to oocyte aging and encourage a focus in this area that may complement the extensive analyses of DNA damage and aneuploidy that have long occupied the oocyte aging field. Moreover, we discuss the influence of common non-enzymatic protein modifications on the stability of proteins in the male germline, how these changes affect sperm function, and how they may be prevented to preserve fertility. Through this review we aim to bring to light a new trajectory for our field and highlight the potential to harness the germ cell's natural proteostasis mechanisms to improve reproductive health. This manuscript will be of interest to those in the fields of proteostasis, aging, male and female gamete reproductive biology, embryogenesis, and life course health.
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Affiliation(s)
- Shenae L. Cafe
- Priority Research Centre for Reproductive Science, Faculty of Science, The University of Newcastle, Callaghan, NSW, Australia
| | - Brett Nixon
- Priority Research Centre for Reproductive Science, Faculty of Science, The University of Newcastle, Callaghan, NSW, Australia
| | - Heath Ecroyd
- Molecular Horizons, School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
| | - Jacinta H. Martin
- Department of Human Genetics, McGill University Health Centre Research Institute, Montreal, QC, Canada
| | - David A. Skerrett-Byrne
- Priority Research Centre for Reproductive Science, Faculty of Science, The University of Newcastle, Callaghan, NSW, Australia
| | - Elizabeth G. Bromfield
- Priority Research Centre for Reproductive Science, Faculty of Science, The University of Newcastle, Callaghan, NSW, Australia
- Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
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17
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Shemesh N, Jubran J, Dror S, Simonovsky E, Basha O, Argov C, Hekselman I, Abu-Qarn M, Vinogradov E, Mauer O, Tiago T, Carra S, Ben-Zvi A, Yeger-Lotem E. The landscape of molecular chaperones across human tissues reveals a layered architecture of core and variable chaperones. Nat Commun 2021; 12:2180. [PMID: 33846299 PMCID: PMC8042005 DOI: 10.1038/s41467-021-22369-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 02/23/2021] [Indexed: 12/13/2022] Open
Abstract
The sensitivity of the protein-folding environment to chaperone disruption can be highly tissue-specific. Yet, the organization of the chaperone system across physiological human tissues has received little attention. Through computational analyses of large-scale tissue transcriptomes, we unveil that the chaperone system is composed of core elements that are uniformly expressed across tissues, and variable elements that are differentially expressed to fit with tissue-specific requirements. We demonstrate via a proteomic analysis that the muscle-specific signature is functional and conserved. Core chaperones are significantly more abundant across tissues and more important for cell survival than variable chaperones. Together with variable chaperones, they form tissue-specific functional networks. Analysis of human organ development and aging brain transcriptomes reveals that these functional networks are established in development and decline with age. In this work, we expand the known functional organization of de novo versus stress-inducible eukaryotic chaperones into a layered core-variable architecture in multi-cellular organisms.
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Affiliation(s)
- Netta Shemesh
- Department of Clinical Biochemistry and Pharmacology and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, Israel.,Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Juman Jubran
- Department of Clinical Biochemistry and Pharmacology and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Shiran Dror
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Eyal Simonovsky
- Department of Clinical Biochemistry and Pharmacology and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Omer Basha
- Department of Clinical Biochemistry and Pharmacology and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Chanan Argov
- Department of Clinical Biochemistry and Pharmacology and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Idan Hekselman
- Department of Clinical Biochemistry and Pharmacology and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Mehtap Abu-Qarn
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Ekaterina Vinogradov
- Department of Clinical Biochemistry and Pharmacology and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Omry Mauer
- Department of Clinical Biochemistry and Pharmacology and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Tatiana Tiago
- Centre for Neuroscience and Nanotechnology, Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Serena Carra
- Centre for Neuroscience and Nanotechnology, Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Anat Ben-Zvi
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel.
| | - Esti Yeger-Lotem
- Department of Clinical Biochemistry and Pharmacology and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, Israel.
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18
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Liu Q, Qi Y, Kong X, Wang X, Zhang W, Zhai J, Yang Y, Fang Y, Wang J. Molecular and Clinical Characterization of CCT2 Expression and Prognosis via Large-Scale Transcriptome Profile of Breast Cancer. Front Oncol 2021; 11:614497. [PMID: 33869000 PMCID: PMC8050343 DOI: 10.3389/fonc.2021.614497] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 03/05/2021] [Indexed: 12/13/2022] Open
Abstract
Molecular chaperones play important roles in regulating various cellular processes and malignant transformation. Expression of some subunits of molecular chaperone CCT/TRiC complex have been reported to be correlated with cancer development and patient survival. However, little is known about the expression and prognostic significance of Chaperonin Containing TCP1 Subunit 2 (CCT2). CCT2 is a gene encoding a molecular chaperone that is a member of the chaperonin containing TCP1 complex (CCT), also known as the TCP1 ring complex (TRiC). Through the Cancer Genome Atlas (TCGA) and Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) databases, we systematically reviewed a total of 2,994 cases with transcriptome data and analyzed the functional annotation of CCT2 by Gene ontology and KEGG analysis. Univariate and multivariate survival analysis were performed to investigate the prognostic value of CCT2 in breast cancer. We found CCT2 was significantly upregulated in various tumors. In breast cancer, CCT2 expression was significantly upregulated in HER2-positive (HER2+) group, and more malignant group. In addition, we investigated correlations between CCT2 and other CCT members. Interestingly, almost all CCTs expression were positively correlated with each other, but not CCT6B. Survival analysis suggested that CCT2 overexpression was independently associated with worse prognosis of patients with breast cancer, especially in luminal A subtype. In summary, our results revealed that CCT2 might be involved in regulating cell cycle pathway, and independently predicted worse prognosis in breast cancer patients. These findings may expand understanding of potential anti-CCT2 treatments. To our knowledge, this is the largest and most comprehensive study characterizing the expression pattern of CCT2 together with its prognostic values in breast cancer.
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Affiliation(s)
- Qiang Liu
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yihang Qi
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiangyi Kong
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Massachusetts General Hospital, Harvard Medical School, Harvard University, Boston, MA, United States
| | - Xiangyu Wang
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wenxiang Zhang
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jie Zhai
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yazhe Yang
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yi Fang
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jing Wang
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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19
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Jhaveri KL, Dos Anjos CH, Taldone T, Wang R, Comen E, Fornier M, Bromberg JF, Ma W, Patil S, Rodina A, Pillarsetty N, Duggan S, Khoshi S, Kadija N, Chiosis G, Dunphy MP, Modi S. Measuring Tumor Epichaperome Expression Using [ 124I] PU-H71 Positron Emission Tomography as a Biomarker of Response for PU-H71 Plus Nab-Paclitaxel in HER2-Negative Metastatic Breast Cancer. JCO Precis Oncol 2020; 4:2000273. [PMID: 33283132 DOI: 10.1200/po.20.00273] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/09/2020] [Indexed: 12/13/2022] Open
Abstract
PURPOSE Epichaperome network maintenance is vital to survival of tumors that express it. PU-H71 is an epichaperome inhibitor that binds to the ATP-binding site of HSP90 and has demonstrated antitumor activity in breast cancer xenograft models and clinical safety in patients. PU-positron emission tomography (PET) is a theragnostic imaging tool that allows visualization of the epichaperome target. In this phase Ib trial, we present safety and tolerability for PU-H71 plus nab-paclitaxel in HER2-negative patients with metastatic breast cancer (MBC) and the utility of PU-PET as a noninvasive predictive biomarker. METHODS We performed a 3 + 3 dose-escalation study with escalating PU-H71 doses and standard nab-paclitaxel. The primary objective was to establish safety and determine maximum tolerated dose (MTD)/recommended phase 2 dose. Secondary objectives were to assess pharmacokinetics and clinical efficacy. Patients could enroll in a companion PU-PET protocol to measure epichaperome expression before treatment initiation to allow exploratory correlation with treatment benefit. RESULTS Of the 12 patients enrolled, dose-limiting toxicity occurred in one patient (G3 neutropenic fever) at dose level 1; MTD of PU-H71 was 300 mg/m2 plus nab-paclitaxel 260 mg/m2 administered every 3 weeks. Common toxicities included diarrhea, fatigue, peripheral neuropathy, and nausea. PU-H71 systemic exposure was not altered by nab-paclitaxel administration. Two of 12 patients had partial response (overall response rate, 17%) and the clinical benefit rate was 42% (5 of 12). Time to progression was associated with baseline epichaperome positivity and PU-H71 peak standard uptake value (SUV), with more durable disease control observed with high epichaperome levels. CONCLUSION The combination of PU-H71 and nab-paclitaxel was well tolerated, with evidence of clinical activity. More durable disease control without progression was observed in patients with high baseline epichaperome expression. A phase II trial of this combination with PU-PET as a companion diagnostic for patient selection is currently planned.
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Affiliation(s)
- Komal L Jhaveri
- Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Carlos H Dos Anjos
- Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Tony Taldone
- Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Rui Wang
- Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Elizabeth Comen
- Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Monica Fornier
- Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jacqueline F Bromberg
- Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Weining Ma
- Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sujata Patil
- Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Anna Rodina
- Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Sarhe Khoshi
- Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Nathan Kadija
- Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Gabriela Chiosis
- Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY.,Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Mark P Dunphy
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Shanu Modi
- Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
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20
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Sepulveda-Villegas M, Rojo R, Garza-Hernandez D, de la Rosa-Garza M, Treviño V. A systematic review of genes affecting mitochondrial processes in cancer. Biochim Biophys Acta Mol Basis Dis 2020; 1866:165846. [PMID: 32473387 DOI: 10.1016/j.bbadis.2020.165846] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 05/01/2020] [Accepted: 05/21/2020] [Indexed: 02/07/2023]
Abstract
Malignant conversion of cancer cells requires efficient mitochondria reprogramming orchestrated by hundreds of genes. The transformation includes increased energy demand, biosynthesis of precursors, and reactive oxygen species needed to accelerate cell growth, proliferation, and survival. Reprogramming involves complex gene alterations that have not been methodically curated. Therefore, we systematically analyzed the literature of cancer-related genes in mitochondria. Through the analysis of >2500 PubMed abstracts and >1600 human genes, we identified 228 genes showing clear roles in cancer. Each gene was classified according to their homeostatic function, together with the pathological transitions that contribute to specific cancer hallmarks. The potential clinical relevance of these hallmarks and genes is discussed by representative examples and validated by detecting differences in gene expression levels across 16 different types of cancer. A compendium, including the gene functions and alterations underpinning cancer progression, can be explored at http://bioinformatica.mty.itesm.mx/MitoCancer.
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Affiliation(s)
- Maricruz Sepulveda-Villegas
- Tecnologico de Monterrey, Escuela de Medicina, Cátedra de Bioinformática, Av. Morones Prieto No. 3000, Colonia Los Doctores, Monterrey, Nuevo León 64710, Mexico
| | - Rocio Rojo
- Tecnologico de Monterrey, Escuela de Medicina, Cátedra de Bioinformática, Av. Morones Prieto No. 3000, Colonia Los Doctores, Monterrey, Nuevo León 64710, Mexico
| | - Debora Garza-Hernandez
- Tecnologico de Monterrey, Escuela de Medicina, Cátedra de Bioinformática, Av. Morones Prieto No. 3000, Colonia Los Doctores, Monterrey, Nuevo León 64710, Mexico
| | - Mauricio de la Rosa-Garza
- Tecnologico de Monterrey, Escuela de Medicina, Cátedra de Bioinformática, Av. Morones Prieto No. 3000, Colonia Los Doctores, Monterrey, Nuevo León 64710, Mexico
| | - Victor Treviño
- Tecnologico de Monterrey, Escuela de Medicina, Cátedra de Bioinformática, Av. Morones Prieto No. 3000, Colonia Los Doctores, Monterrey, Nuevo León 64710, Mexico.
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21
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Antonova A, Hummel B, Khavaran A, Redhaber DM, Aprile-Garcia F, Rawat P, Gundel K, Schneck M, Hansen EC, Mitschke J, Mittler G, Miething C, Sawarkar R. Heat-Shock Protein 90 Controls the Expression of Cell-Cycle Genes by Stabilizing Metazoan-Specific Host-Cell Factor HCFC1. Cell Rep 2020; 29:1645-1659.e9. [PMID: 31693902 DOI: 10.1016/j.celrep.2019.09.084] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 08/06/2019] [Accepted: 09/27/2019] [Indexed: 12/18/2022] Open
Abstract
Molecular chaperones such as heat-shock proteins (HSPs) help in protein folding. Their function in the cytosol has been well studied. Notably, chaperones are also present in the nucleus, a compartment where proteins enter after completing de novo folding in the cytosol, and this raises an important question about chaperone function in the nucleus. We performed a systematic analysis of the nuclear pool of heat-shock protein 90. Three orthogonal and independent analyses led us to the core functional interactome of HSP90. Computational and biochemical analyses identify host cell factor C1 (HCFC1) as a transcriptional regulator that depends on HSP90 for its stability. HSP90 was required to maintain the expression of HCFC1-targeted cell-cycle genes. The regulatory nexus between HSP90 and the HCFC1 module identified in this study sheds light on the relevance of chaperones in the transcription of cell-cycle genes. Our study also suggests a therapeutic avenue of combining chaperone and transcription inhibitors for cancer treatment.
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Affiliation(s)
- Aneliya Antonova
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany; Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Barbara Hummel
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Ashkan Khavaran
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany; Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Desiree M Redhaber
- German Consortium for Translational Cancer Research (DKTK), Partner Site Freiburg and German Cancer Research Center (DKFZ), Heidelberg, Germany; Department of Hematology, Oncology and Stem Cell Transplantation, Faculty of Medicine, Medical Center - University of Freiburg, Freiburg, Germany; Faculty of Biology, University of Freiburg, Freiburg, Germany
| | | | - Prashant Rawat
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany; Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Kathrin Gundel
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Megan Schneck
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Erik C Hansen
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Jan Mitschke
- Department of Hematology, Oncology and Stem Cell Transplantation, Faculty of Medicine, Medical Center - University of Freiburg, Freiburg, Germany
| | - Gerhard Mittler
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Cornelius Miething
- German Consortium for Translational Cancer Research (DKTK), Partner Site Freiburg and German Cancer Research Center (DKFZ), Heidelberg, Germany; Department of Hematology, Oncology and Stem Cell Transplantation, Faculty of Medicine, Medical Center - University of Freiburg, Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Ritwick Sawarkar
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany; MRC Toxicology Unit, University of Cambridge, Cambridge, UK.
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22
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Merugu S, Sharma S, Kaner J, Digwal C, Sugita M, Joshi S, Taldone T, Guzman ML, Chiosis G. Chemical probes and methods for single-cell detection and quantification of epichaperomes in hematologic malignancies. Methods Enzymol 2020; 639:289-311. [PMID: 32475406 DOI: 10.1016/bs.mie.2020.04.057] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Detection of protein connectivity dysfunctions in biological samples, i.e., informing on how protein-protein interactions change from a normal to a disease state, is important for both biomedical research and clinical development. The epichaperome is an executor of protein connectivity dysfunction in disease, and thus a surrogate for its detection. This chapter will detail on published methods for epichaperome detection and quantification that combine the advantages of multiparameter flow cytometry with those of the PU-FITC fluorescently labeled epichaperome detection probe. It will offer a comprehensive method description that includes the synthesis and characterization of an epichaperome detection probe and of the negative control probe, the preparation of the biospecimen for epichaperome analysis, the execution of the epichaperome detection and quantification assay and lastly, the data acquisition and analysis. The method provides, at single-cell level, the functional signature of cells, differentiating itself from other single-cell methods that provide a catalog of molecules.
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Affiliation(s)
- Swathi Merugu
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Sahil Sharma
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Justin Kaner
- Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medical College, New York, NY, United States
| | - Chander Digwal
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Mayumi Sugita
- Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medical College, New York, NY, United States
| | - Suhasini Joshi
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Tony Taldone
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States.
| | - Monica L Guzman
- Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medical College, New York, NY, United States.
| | - Gabriela Chiosis
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, United States.
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23
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Taldone T, Wang T, Rodina A, Pillarsetty NVK, Digwal CS, Sharma S, Yan P, Joshi S, Pagare PP, Bolaender A, Roboz GJ, Guzman ML, Chiosis G. A Chemical Biology Approach to the Chaperome in Cancer-HSP90 and Beyond. Cold Spring Harb Perspect Biol 2020; 12:a034116. [PMID: 30936118 PMCID: PMC6773535 DOI: 10.1101/cshperspect.a034116] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Cancer is often associated with alterations in the chaperome, a collection of chaperones, cochaperones, and other cofactors. Changes in the expression levels of components of the chaperome, in the interaction strength among chaperome components, alterations in chaperome constituency, and in the cellular location of chaperome members, are all hallmarks of cancer. Here we aim to provide an overview on how chemical biology has played a role in deciphering such complexity in the biology of the chaperome in cancer and in other diseases. The focus here is narrow and on pathologic changes in the chaperome executed by enhancing the interaction strength between components of distinct chaperome pathways, specifically between those of HSP90 and HSP70 pathways. We will review chemical tools and chemical probe-based assays, with a focus on HSP90. We will discuss how kinetic binding, not classical equilibrium binding, is most appropriate in the development of drugs and probes for the chaperome in disease. We will then present our view on how chaperome inhibitors may become potential drugs and diagnostics in cancer.
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Affiliation(s)
- Tony Taldone
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065
| | - Tai Wang
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065
| | - Anna Rodina
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065
| | | | - Chander S Digwal
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065
| | - Sahil Sharma
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065
| | - Pengrong Yan
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065
| | - Suhasini Joshi
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065
| | - Piyusha P Pagare
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065
| | - Alexander Bolaender
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065
| | - Gail J Roboz
- Division of Hematology and Medical Oncology, Leukemia Program, Weill Cornell Medicine/New York-Presbyterian Hospital, New York, New York 10065
| | - Monica L Guzman
- Division of Hematology and Medical Oncology, Leukemia Program, Weill Cornell Medicine/New York-Presbyterian Hospital, New York, New York 10065
| | - Gabriela Chiosis
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York 10065
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24
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Li Y, Jiang T, Zhou W, Li J, Li X, Wang Q, Jin X, Yin J, Chen L, Zhang Y, Xu J, Li X. Pan-cancer characterization of immune-related lncRNAs identifies potential oncogenic biomarkers. Nat Commun 2020; 11:1000. [PMID: 32081859 PMCID: PMC7035327 DOI: 10.1038/s41467-020-14802-2] [Citation(s) in RCA: 257] [Impact Index Per Article: 64.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 02/03/2020] [Indexed: 12/18/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are emerging as critical regulators of gene expression and they play fundamental roles in immune regulation. Here we introduce an integrated algorithm, ImmLnc, for identifying lncRNA regulators of immune-related pathways. We comprehensively chart the landscape of lncRNA regulation in the immunome across 33 cancer types and show that cancers with similar tissue origin are likely to share lncRNA immune regulators. Moreover, the immune-related lncRNAs are likely to show expression perturbation in cancer and are significantly correlated with immune cell infiltration. ImmLnc can help prioritize cancer-related lncRNAs and further identify three molecular subtypes (proliferative, intermediate, and immunological) of non-small cell lung cancer. These subtypes are characterized by differences in mutation burden, immune cell infiltration, expression of immunomodulatory genes, response to chemotherapy, and prognosis. In summary, the ImmLnc pipeline and the resulting data serve as a valuable resource for understanding lncRNA function and to advance identification of immunotherapy targets.
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Affiliation(s)
- Yongsheng Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, China. .,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, 571199, China. .,College of Biomedical Information and Engineering, Hainan Medical University, Haikou, Hainan, 570100, China.
| | - Tiantongfei Jiang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Weiwei Zhou
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Junyi Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Xinhui Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Qi Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Xiaoyan Jin
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Jiaqi Yin
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Liuxin Chen
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Yunpeng Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Juan Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, China. .,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, 571199, China. .,College of Biomedical Information and Engineering, Hainan Medical University, Haikou, Hainan, 570100, China.
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, China. .,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, 571199, China. .,College of Biomedical Information and Engineering, Hainan Medical University, Haikou, Hainan, 570100, China.
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25
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Investigating Chaperonin-Containing TCP-1 subunit 2 as an essential component of the chaperonin complex for tumorigenesis. Sci Rep 2020; 10:798. [PMID: 31964905 PMCID: PMC6972895 DOI: 10.1038/s41598-020-57602-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 01/03/2020] [Indexed: 12/13/2022] Open
Abstract
Chaperonin-containing TCP-1 (CCT or TRiC) is a multi-subunit complex that folds many of the proteins essential for cancer development. CCT is expressed in diverse cancers and could be an ideal therapeutic target if not for the fact that the complex is encoded by eight distinct genes, complicating the development of inhibitors. Few definitive studies addressed the role of specific subunits in promoting the chaperonin’s function in cancer. To this end, we investigated the activity of CCT2 (CCTβ) by overexpressing or depleting the subunit in breast epithelial and breast cancer cells. We found that increasing total CCT2 in cells by 1.3-1.8-fold using a lentiviral system, also caused CCT3, CCT4, and CCT5 levels to increase. Likewise, silencing cct2 gene expression by ~50% caused other CCT subunits to decrease. Cells expressing CCT2 were more invasive and had a higher proliferative index. CCT2 depletion in a syngeneic murine model of triple negative breast cancer (TNBC) prevented tumor growth. These results indicate that the CCT2 subunit is integral to the activity of the chaperonin and is needed for tumorigenesis. Hence CCT2 could be a viable target for therapeutic development in breast and other cancers.
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26
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The epichaperome is a mediator of toxic hippocampal stress and leads to protein connectivity-based dysfunction. Nat Commun 2020; 11:319. [PMID: 31949159 PMCID: PMC6965647 DOI: 10.1038/s41467-019-14082-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Accepted: 12/16/2019] [Indexed: 12/18/2022] Open
Abstract
Optimal functioning of neuronal networks is critical to the complex cognitive processes of memory and executive function that deteriorate in Alzheimer’s disease (AD). Here we use cellular and animal models as well as human biospecimens to show that AD-related stressors mediate global disturbances in dynamic intra- and inter-neuronal networks through pathologic rewiring of the chaperome system into epichaperomes. These structures provide the backbone upon which proteome-wide connectivity, and in turn, protein networks become disturbed and ultimately dysfunctional. We introduce the term protein connectivity-based dysfunction (PCBD) to define this mechanism. Among most sensitive to PCBD are pathways with key roles in synaptic plasticity. We show at cellular and target organ levels that network connectivity and functional imbalances revert to normal levels upon epichaperome inhibition. In conclusion, we provide proof-of-principle to propose AD is a PCBDopathy, a disease of proteome-wide connectivity defects mediated by maladaptive epichaperomes. The biology of Alzheimer’s disease (AD) remains unknown. We propose AD is a protein connectivity-based dysfunction disorder whereby a switch of the chaperome into epichaperomes rewires proteome-wide connectivity, leading to brain circuitry malfunction that can be corrected by novel therapeutics.
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27
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Yan P, Wang T, Guzman ML, Peter RI, Chiosis G. Chaperome Networks - Redundancy and Implications for Cancer Treatment. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1243:87-99. [PMID: 32297213 PMCID: PMC7279512 DOI: 10.1007/978-3-030-40204-4_6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The chaperome is a large family of proteins composed of chaperones, co-chaperones and a multitude of other factors. Elegant studies in yeast and other organisms have paved the road to how we currently understand the complex organization of this large family into protein networks. The goal of this chapter is to provide an overview of chaperome networks in cancer cells, with a focus on two cellular states defined by chaperome network organization. One state characterized by chaperome networks working in isolation and with little overlap, contains global chaperome networks resembling those of normal, non-transformed, cells. We propose that in this state, redundancy in chaperome networks results in a tumor type unamenable for single-agent chaperome therapy. The second state comprises chaperome networks interconnected in response to cellular stress, such as MYC hyperactivation. This is a state where no redundant pathways can be deployed, and is a state of vulnerability, amenable for chaperome therapy. We conclude by proposing a change in how we discover and implement chaperome inhibitor strategies, and suggest an approach to chaperome therapy where the properties of chaperome networks, rather than genetics or client proteins, are used in chaperome inhibitor implementation.
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Affiliation(s)
- Pengrong Yan
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tai Wang
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Monica L Guzman
- Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Radu I Peter
- Department of Mathematics, Technical University of Cluj-Napoca, Cluj-Napoca, Romania
| | - Gabriela Chiosis
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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28
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Griffiths SG, Ezrin A, Jackson E, Dewey L, Doucette AA. A robust strategy for proteomic identification of biomarkers of invasive phenotype complexed with extracellular heat shock proteins. Cell Stress Chaperones 2019; 24:1197-1209. [PMID: 31650515 PMCID: PMC6882979 DOI: 10.1007/s12192-019-01041-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 10/03/2019] [Accepted: 10/09/2019] [Indexed: 12/17/2022] Open
Abstract
As an extension of their orchestration of intracellular pathways, secretion of extracellular heat shock proteins (HSPs) is an emerging paradigm of homeostasis imperative to multicellular organization. Extracellular HSP is axiomatic to the survival of cells during tumorigenesis; proportional representation of specific HSP family members is indicative of invasive potential and prognosis. Further significance has been added by the knowledge that all cancer-derived exosomes have surface-exposed HSPs that reflect the membrane topology of cells that secrete them. Extracellular HSPs are also characteristic of chronic inflammation and sepsis. Accordingly, interrogation of extracellular HSPs secreted from cell culture models may represent a facile means of identifying translational biomarker signatures for targeting in situ. In the current study, we evaluated a simple peptide-based multivalent HSP affinity approach using the Vn96 peptide for low speed pelleting of HSP complexes from bioreactor cultures of cell lines with varying invasive phenotype in xenotransplant models: U87 (glioblastoma multiforme; invasive); HELA (choriocarcinoma; minimally invasive); HEK293T (virally transformed immortalized; embryonic). Proteomic profiling by bottom-up mass spectrometry revealed a comprehensive range of candidate biomarkers including primary HSP ligands. HSP complexes were associated with additional chaperones of prognostic significance such as protein disulfide isomerases, as well as pleiotropic metabolic enzymes, established as proportionally reflective of invasive phenotype. Biomarkers of inflammatory and mechanotransductive phenotype were restricted to the most invasive cell model U87, including chitinase CHI3L1, lamin C, amyloid derivatives, and histone isoforms.
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Affiliation(s)
| | - Alan Ezrin
- NX Development Corporation, Louisville, KY, USA
| | - Emily Jackson
- David H. Murdock Research Institute, Kannapolis, NC, USA
| | - Lisa Dewey
- David H. Murdock Research Institute, Kannapolis, NC, USA
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29
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Draceni Y, Pechmann S. Pervasive convergent evolution and extreme phenotypes define chaperone requirements of protein homeostasis. Proc Natl Acad Sci U S A 2019; 116:20009-20014. [PMID: 31527276 PMCID: PMC6778244 DOI: 10.1073/pnas.1904611116] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Maintaining protein homeostasis is an essential requirement for cell and organismal viability. An elaborate regulatory system within cells, the protein homeostasis network, safeguards that proteins are correctly folded and functional. At the heart of this regulatory system lies a class of specialized protein quality control enzymes called chaperones that are tasked with assisting proteins in their folding, avoiding aggregation and degradation. Failure and decline of protein homeostasis are directly associated with conditions of aging and aging-related neurodegeneration. However, it is not clear what tips the balance of protein homeostasis and leads to onset of aging and diseases. Here, using a comparative genomics approach we report general principles of maintaining protein homeostasis across the eukaryotic tree of life. Expanding a previous study of 16 eukaryotes to the quantitative analysis of 216 eukaryotic genomes, we find a strong correlation between the composition of eukaryotic chaperone networks and genome complexity that is distinct for different species kingdoms. Organisms with pronounced phenotypes clearly buck this trend. Northobranchius furzeri, the shortest-lived vertebrate and a widely used model for fragile protein homeostasis, is found to be chaperone limited while Heterocephalus glaber as the longest-lived rodent and thus an especially robust organism is characterized by above-average numbers of chaperones. Strikingly, the relative size of chaperone networks is found to generally correlate with longevity in Metazoa. Our results thus indicate that the balance in protein homeostasis may be a key variable in explaining organismal robustness.
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Affiliation(s)
- Yasmine Draceni
- Département de Biochimie, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Sebastian Pechmann
- Département de Biochimie, Université de Montréal, Montréal, QC H3T 1J4, Canada
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Heat Shock Proteins Are Essential Components in Transformation and Tumor Progression: Cancer Cell Intrinsic Pathways and Beyond. Int J Mol Sci 2019; 20:ijms20184507. [PMID: 31514477 PMCID: PMC6769451 DOI: 10.3390/ijms20184507] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 09/06/2019] [Accepted: 09/07/2019] [Indexed: 02/08/2023] Open
Abstract
Heat shock protein (HSP) synthesis is switched on in a remarkably wide range of tumor cells, in both experimental animal systems and in human cancer, in which these proteins accumulate in high levels. In each case, elevated HSP concentrations bode ill for the patient, and are associated with a poor outlook in terms of survival in most cancer types. The significance of elevated HSPs is underpinned by their essential roles in mediating tumor cell intrinsic traits such as unscheduled cell division, escape from programmed cell death and senescence, de novo angiogenesis, and increased invasion and metastasis. An increased HSP expression thus seems essential for tumorigenesis. Perhaps of equal significance is the pronounced interplay between cancer cells and the tumor milieu, with essential roles for intracellular HSPs in the properties of the stromal cells, and their roles in programming malignant cells and in the release of HSPs from cancer cells to influence the behavior of the adjacent tumor and infiltrating the normal cells. These findings of a triple role for elevated HSP expression in tumorigenesis strongly support the targeting of HSPs in cancer, especially given the role of such stress proteins in resistance to conventional therapies.
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Hognon C, Besancenot V, Gruez A, Grandemange S, Monari A. Cooperative Effects of Cytosine Methylation on DNA Structure and Dynamics. J Phys Chem B 2019; 123:7365-7371. [PMID: 31365827 DOI: 10.1021/acs.jpcb.9b05835] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The behavior of the structural parameters of DNA considering different levels of methylation in CpG islands is studied by means of full-atom molecular dynamics simulations and electronic circular dichroism, both in an artificial model system and in a gene promoter sequence. It is demonstrated that methylation although intrinsically brings quite local perturbations may, if its level is high enough, induce cooperative effects that strongly modify the DNA backbone torsional parameters altering the helicity as compared to the nonmethylated case. Because methylation of the CpG island is correlated with the regulation of gene expression, understanding the structural modifications induced in DNA is crucial to characterize all the fine equilibria into play in epigenetics phenomena.
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Affiliation(s)
- Cécilia Hognon
- Université de Lorraine and CNRS, UMR 7019 LPCT , F-54000 Nancy , France
| | | | - Arnaud Gruez
- Université de Lorraine and CNRS, UMR 7356 IMOPA , F-54000 Nancy , France
| | | | - Antonio Monari
- Université de Lorraine and CNRS, UMR 7019 LPCT , F-54000 Nancy , France
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Topf U, Uszczynska-Ratajczak B, Chacinska A. Mitochondrial stress-dependent regulation of cellular protein synthesis. J Cell Sci 2019; 132:132/8/jcs226258. [DOI: 10.1242/jcs.226258] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
ABSTRACT
The production of newly synthesized proteins is vital for all cellular functions and is a determinant of cell growth and proliferation. The synthesis of polypeptide chains from mRNA molecules requires sophisticated machineries and mechanisms that need to be tightly regulated, and adjustable to current needs of the cell. Failures in the regulation of translation contribute to the loss of protein homeostasis, which can have deleterious effects on cellular function and organismal health. Unsurprisingly, the regulation of translation appears to be a crucial element in stress response mechanisms. This review provides an overview of mechanisms that modulate cytosolic protein synthesis upon cellular stress, with a focus on the attenuation of translation in response to mitochondrial stress. We then highlight links between mitochondrion-derived reactive oxygen species and the attenuation of reversible cytosolic translation through the oxidation of ribosomal proteins at their cysteine residues. We also discuss emerging concepts of how cellular mechanisms to stress are adapted, including the existence of alternative ribosomes and stress granules, and the regulation of co-translational import upon organelle stress.
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Affiliation(s)
- Ulrike Topf
- Centre of New Technologies, University of Warsaw, Banacha 2C, Warsaw 02-097, Poland
- Department of Genetics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, Warsaw 02-106, Poland
| | | | - Agnieszka Chacinska
- Centre of New Technologies, University of Warsaw, Banacha 2C, Warsaw 02-097, Poland
- ReMedy International Research Agenda Unit, University of Warsaw, Banacha 2C, Warsaw 02-097, Poland
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Aprile-Garcia F, Tomar P, Hummel B, Khavaran A, Sawarkar R. Nascent-protein ubiquitination is required for heat shock–induced gene downregulation in human cells. Nat Struct Mol Biol 2019; 26:137-146. [DOI: 10.1038/s41594-018-0182-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 12/21/2018] [Indexed: 12/20/2022]
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Voisine C, Brehme M. HSP90 et al.: Chaperome and Proteostasis Deregulation in Human Disease. HEAT SHOCK PROTEINS 2019. [DOI: 10.1007/978-3-030-23158-3_27] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Wang T, Rodina A, Dunphy MP, Corben A, Modi S, Guzman ML, Gewirth DT, Chiosis G. Chaperome heterogeneity and its implications for cancer study and treatment. J Biol Chem 2018; 294:2162-2179. [PMID: 30409908 DOI: 10.1074/jbc.rev118.002811] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The chaperome is the collection of proteins in the cell that carry out molecular chaperoning functions. Changes in the interaction strength between chaperome proteins lead to an assembly that is functionally and structurally distinct from each constituent member. In this review, we discuss the epichaperome, the cellular network that forms when the chaperome components of distinct chaperome machineries come together as stable, functionally integrated, multimeric complexes. In tumors, maintenance of the epichaperome network is vital for tumor survival, rendering them vulnerable to therapeutic interventions that target critical epichaperome network components. We discuss how the epichaperome empowers an approach for precision medicine cancer trials where a new target, biomarker, and relevant drug candidates can be correlated and integrated. We introduce chemical biology methods to investigate the heterogeneity of the chaperome in a given cellular context. Lastly, we discuss how ligand-protein binding kinetics are more appropriate than equilibrium binding parameters to characterize and unravel chaperome targeting in cancer and to gauge the selectivity of ligands for specific tumor-associated chaperome pools.
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Affiliation(s)
- Tai Wang
- From the Chemical Biology Program and
| | | | | | - Adriana Corben
- the Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York 10029
| | - Shanu Modi
- Medicine, Memorial Sloan Kettering Cancer Center, New York, New York 10065
| | - Monica L Guzman
- Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medical College, New York, New York 10065, and
| | - Daniel T Gewirth
- the Hauptman-Woodward Medical Research Institute, Buffalo, New York 14203
| | - Gabriela Chiosis
- From the Chemical Biology Program and .,Medicine, Memorial Sloan Kettering Cancer Center, New York, New York 10065
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Rizzolo K, Houry WA. Multiple functionalities of molecular chaperones revealed through systematic mapping of their interaction networks. J Biol Chem 2018; 294:2142-2150. [PMID: 30194284 DOI: 10.1074/jbc.tm118.002805] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Chaperones are a highly interactive group of proteins that function globally in many cellular processes involved in maintaining protein homeostasis. Traditional biochemical assays typically do not provide a complete view of the intricate networks through which chaperones collaborate to promote proteostasis. Recent advances in high-throughput systematic analyses of chaperone interactions have uncovered that chaperones display a remarkable cooperativity in their interactions with numerous client proteins. This cooperativity has been found to be a fundamental aspect of a properly functioning cell. Aberrant formation or improper regulation of these interactions can easily lead to disease states. Herein, we provide an overview of the use of large-scale interaction assays, whether physical (protein-protein) or genetic (epistatic), to study chaperone interaction networks. Importantly, we discuss the ongoing need for such studies to determine the mechanisms by which protein homeostasis is controlled in the cell.
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Affiliation(s)
- Kamran Rizzolo
- From the Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1 and
| | - Walid A Houry
- From the Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1 and .,the Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
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Abstract
In this Opinion article, we aim to address how cells adapt to stress and the repercussions chronic stress has on cellular function. We consider acute and chronic stress-induced changes at the cellular level, with a focus on a regulator of cellular stress, the chaperome, which is a protein assembly that encompasses molecular chaperones, co-chaperones and other co-factors. We discuss how the chaperome takes on distinct functions under conditions of stress that are executed in ways that differ from the one-on-one cyclic, dynamic functions exhibited by distinct molecular chaperones. We argue that through the formation of multimeric stable chaperome complexes, a state of chaperome hyperconnectivity, or networking, is gained. The role of these chaperome networks is to act as multimolecular scaffolds, a particularly important function in cancer, where they increase the efficacy and functional diversity of several cellular processes. We predict that these concepts will change how we develop and implement drugs targeting the chaperome to treat cancer.
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Affiliation(s)
- Suhasini Joshi
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tai Wang
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Thaís L S Araujo
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sahil Sharma
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jeffrey L Brodsky
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Gabriela Chiosis
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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Zoppino FCM, Guerrero-Gimenez ME, Castro GN, Ciocca DR. Comprehensive transcriptomic analysis of heat shock proteins in the molecular subtypes of human breast cancer. BMC Cancer 2018; 18:700. [PMID: 29954368 PMCID: PMC6022707 DOI: 10.1186/s12885-018-4621-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 06/20/2018] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Heat Shock Proteins (HSPs), a family of genes with key roles in proteostasis, have been extensively associated with cancer behaviour. However, the HSP family is quite large and many of its members have not been investigated in breast cancer (BRCA), particularly in relation with the current molecular BRCA classification. In this work, we performed a comprehensive transcriptomic study of the HSP gene family in BRCA patients from both The Cancer Genome Atlas (TCGA) and the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) cohorts discriminating the BRCA intrinsic molecular subtypes. METHODS We examined gene expression levels of 1097 BRCA tissue samples retrieved from TCGA and 1981 samples of METABRIC, focusing mainly on the HSP family (95 genes). Data were stratified according to the PAM50 gene expression (Luminal A, Luminal B, HER2, Basal, and Normal-like). Transcriptomic analyses include several statistical approaches: differential gene expression, hierarchical clustering and survival analysis. RESULTS Of the 20,531 analysed genes we found that in BRCA almost 30% presented deregulated expression (19% upregulated and 10% downregulated), while of the HSP family 25% appeared deregulated (14% upregulated and 11% downregulated) (|fold change| > 2 comparing BRCA with normal breast tissues). The study revealed the existence of shared HSP genes deregulated in all subtypes of BRCA while other HSPs were deregulated in specific subtypes. Many members of the Chaperonin subfamily were found upregulated while three members (BBS10, BBS12 and CCTB6) were found downregulated. HSPC subfamily had moderate increments of transcripts levels. Various genes of the HSP70 subfamily were upregulated; meanwhile, HSPA12A and HSPA12B appeared strongly downregulated. The strongest downregulation was observed in several HSPB members except for HSPB1. DNAJ members showed heterogeneous expression pattern. We found that 23 HSP genes correlated with overall survival and three HSP-based transcriptional profiles with impact on disease outcome were recognized. CONCLUSIONS We identified shared and specific HSP genes deregulated in BRCA subtypes. This study allowed the recognition of HSP genes not previously associated with BRCA and/or any cancer type, and the identification of three clinically relevant clusters based on HSPs expression patterns with influence on overall survival.
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Affiliation(s)
- Felipe C. M. Zoppino
- Laboratory of Oncology, Institute of Medicine and Experimental Biology of Cuyo (IMBECU), National Scientific and Technical Research Council (CONICET), Av. Dr. Ruiz Leal s/n, Parque General San Martín, 5500 Mendoza, Argentina
| | - Martin E. Guerrero-Gimenez
- Laboratory of Oncology, Institute of Medicine and Experimental Biology of Cuyo (IMBECU), National Scientific and Technical Research Council (CONICET), Av. Dr. Ruiz Leal s/n, Parque General San Martín, 5500 Mendoza, Argentina
| | - Gisela N. Castro
- Laboratory of Oncology, Institute of Medicine and Experimental Biology of Cuyo (IMBECU), National Scientific and Technical Research Council (CONICET), Av. Dr. Ruiz Leal s/n, Parque General San Martín, 5500 Mendoza, Argentina
| | - Daniel R. Ciocca
- Laboratory of Oncology, Institute of Medicine and Experimental Biology of Cuyo (IMBECU), National Scientific and Technical Research Council (CONICET), Av. Dr. Ruiz Leal s/n, Parque General San Martín, 5500 Mendoza, Argentina
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Reisz JA, Barrett AS, Nemkov T, Hansen KC, D'Alessandro A. When nature's robots go rogue: exploring protein homeostasis dysfunction and the implications for understanding human aging disease pathologies. Expert Rev Proteomics 2018; 15:293-309. [PMID: 29540077 PMCID: PMC6174679 DOI: 10.1080/14789450.2018.1453362] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 03/13/2018] [Indexed: 12/19/2022]
Abstract
INTRODUCTION Proteins have been historically regarded as 'nature's robots': Molecular machines that are essential to cellular/extracellular physical mechanical properties and catalyze key reactions for cell/system viability. However, these robots are kept in check by other protein-based machinery to preserve proteome integrity and stability. During aging, protein homeostasis is challenged by oxidation, decreased synthesis, and increasingly inefficient mechanisms responsible for repairing or degrading damaged proteins. In addition, disruptions to protein homeostasis are hallmarks of many neurodegenerative diseases and diseases disproportionately affecting the elderly. Areas covered: Here we summarize age- and disease-related changes to the protein machinery responsible for preserving proteostasis and describe how both aging and disease can each exacerbate damage initiated by the other. We focus on alteration of proteostasis as an etiological or phenomenological factor in neurodegenerative diseases such as Alzheimer's, Parkinson's, and Huntington's, along with Down syndrome, ophthalmic pathologies, and cancer. Expert commentary: Understanding the mechanisms of proteostasis and their dysregulation in health and disease will represent an essential breakthrough in the treatment of many (senescence-associated) pathologies. Strides in this field are currently underway and largely attributable to the introduction of high-throughput omics technologies and their combination with novel approaches to explore structural and cross-link biochemistry.
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Affiliation(s)
- Julie A Reisz
- a Department of Biochemistry and Molecular Genetics , University of Colorado Denver - Anschutz Medical Campus , Aurora , CO , USA
| | - Alexander S Barrett
- a Department of Biochemistry and Molecular Genetics , University of Colorado Denver - Anschutz Medical Campus , Aurora , CO , USA
| | - Travis Nemkov
- a Department of Biochemistry and Molecular Genetics , University of Colorado Denver - Anschutz Medical Campus , Aurora , CO , USA
| | - Kirk C Hansen
- a Department of Biochemistry and Molecular Genetics , University of Colorado Denver - Anschutz Medical Campus , Aurora , CO , USA
| | - Angelo D'Alessandro
- a Department of Biochemistry and Molecular Genetics , University of Colorado Denver - Anschutz Medical Campus , Aurora , CO , USA
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