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Mellis IA, Melzer ME, Bodkin N, Goyal Y. Prevalence of and gene regulatory constraints on transcriptional adaptation in single cells. Genome Biol 2024; 25:217. [PMID: 39135102 PMCID: PMC11320884 DOI: 10.1186/s13059-024-03351-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 07/25/2024] [Indexed: 08/15/2024] Open
Abstract
BACKGROUND Cells and tissues have a remarkable ability to adapt to genetic perturbations via a variety of molecular mechanisms. Nonsense-induced transcriptional compensation, a form of transcriptional adaptation, has recently emerged as one such mechanism, in which nonsense mutations in a gene trigger upregulation of related genes, possibly conferring robustness at cellular and organismal levels. However, beyond a handful of developmental contexts and curated sets of genes, no comprehensive genome-wide investigation of this behavior has been undertaken for mammalian cell types and conditions. How the regulatory-level effects of inherently stochastic compensatory gene networks contribute to phenotypic penetrance in single cells remains unclear. RESULTS We analyze existing bulk and single-cell transcriptomic datasets to uncover the prevalence of transcriptional adaptation in mammalian systems across diverse contexts and cell types. We perform regulon gene expression analyses of transcription factor target sets in both bulk and pooled single-cell genetic perturbation datasets. Our results reveal greater robustness in expression of regulons of transcription factors exhibiting transcriptional adaptation compared to those of transcription factors that do not. Stochastic mathematical modeling of minimal compensatory gene networks qualitatively recapitulates several aspects of transcriptional adaptation, including paralog upregulation and robustness to mutation. Combined with machine learning analysis of network features of interest, our framework offers potential explanations for which regulatory steps are most important for transcriptional adaptation. CONCLUSIONS Our integrative approach identifies several putative hits-genes demonstrating possible transcriptional adaptation-to follow-up on experimentally and provides a formal quantitative framework to test and refine models of transcriptional adaptation.
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Affiliation(s)
- Ian A Mellis
- Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
| | - Madeline E Melzer
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Center for Synthetic Biology, Northwestern University, Chicago, IL, USA
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Nicholas Bodkin
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Center for Synthetic Biology, Northwestern University, Chicago, IL, USA
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Yogesh Goyal
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
- Center for Synthetic Biology, Northwestern University, Chicago, IL, USA.
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
- CZ Biohub Chicago, LLC, Chicago, IL, USA.
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2
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Walia Y, de Bock CE, Huang Y. The landscape of alterations affecting epigenetic regulators in T-cell acute lymphoblastic leukemia: Roles in leukemogenesis and therapeutic opportunities. Int J Cancer 2024; 154:1522-1536. [PMID: 38155420 DOI: 10.1002/ijc.34819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 11/25/2023] [Accepted: 11/28/2023] [Indexed: 12/30/2023]
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive malignancy accounting for 10%-15% of pediatric and 20%-25% of adult ALL cases. Epigenetic irregularities in T-ALL include alterations in both DNA methylation and the post-translational modifications on histones which together play a critical role in the initiation and development of T-ALL. Characterizing the oncogenic mutations that result in these epigenetic changes combined with the reversibility of epigenetic modifications represents an opportunity for the development of epigenetic therapies. Oncogenic mutations and deregulated expression of DNA methyltransferases (DNMTs), Ten-Eleven Translocation dioxygenases (TETs), Histone acetyltransferases (HATs) and members of Polycomb Repressor Complex 2 (PRC2) have all been identified in T-ALL. This review focuses on the current understanding of how these mutations lead to epigenetic changes in T-ALL, their association with disease pathogenesis and the current efforts to exploit these clinically through the development of epigenetic therapies in T-ALL treatment.
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Affiliation(s)
- Yashna Walia
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Kensington, New South Wales, Australia
- School of Clinical Medicine, UNSW Sydney, Kensington, New South Wales, Australia
| | - Charles E de Bock
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Kensington, New South Wales, Australia
- School of Clinical Medicine, UNSW Sydney, Kensington, New South Wales, Australia
| | - Yizhou Huang
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Kensington, New South Wales, Australia
- School of Clinical Medicine, UNSW Sydney, Kensington, New South Wales, Australia
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3
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Gao Y, Feng C, Ma J, Yan Q. Protein arginine methyltransferases (PRMTs): Orchestrators of cancer pathogenesis, immunotherapy dynamics, and drug resistance. Biochem Pharmacol 2024; 221:116048. [PMID: 38346542 DOI: 10.1016/j.bcp.2024.116048] [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: 11/27/2023] [Revised: 01/15/2024] [Accepted: 02/06/2024] [Indexed: 02/16/2024]
Abstract
Protein Arginine Methyltransferases (PRMTs) are a family of enzymes regulating protein arginine methylation, which is a post-translational modification crucial for various cellular processes. Recent studies have highlighted the mechanistic role of PRMTs in cancer pathogenesis, immunotherapy, and drug resistance. PRMTs are involved in diverse oncogenic processes, including cell proliferation, apoptosis, and metastasis. They exert their effects by methylation of histones, transcription factors, and other regulatory proteins, resulting in altered gene expression patterns. PRMT-mediated histone methylation can lead to aberrant chromatin remodeling and epigenetic changes that drive oncogenesis. Additionally, PRMTs can directly interact with key signaling pathways involved in cancer progression, such as the PI3K/Akt and MAPK pathways, thereby modulating cell survival and proliferation. In the context of cancer immunotherapy, PRMTs have emerged as critical regulators of immune responses. They modulate immune checkpoint molecules, including programmed cell death protein 1 (PD-1), through arginine methylation. Drug resistance is a significant challenge in cancer treatment, and PRMTs have been implicated in this phenomenon. PRMTs can contribute to drug resistance through multiple mechanisms, including the epigenetic regulation of drug efflux pumps, altered DNA damage repair, and modulation of cell survival pathways. In conclusion, PRMTs play critical roles in cancer pathogenesis, immunotherapy, and drug resistance. In this overview, we have endeavored to illuminate the mechanistic intricacies of PRMT-mediated processes. Shedding light on these aspects will offer valuable insights into the fundamental biology of cancer and establish PRMTs as promising therapeutic targets.
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Affiliation(s)
- Yihang Gao
- Department of Laboratory Medicine, the Second Hospital of Jilin University, Changchun 130000, China
| | - Chongchong Feng
- Department of Laboratory Medicine, the Second Hospital of Jilin University, Changchun 130000, China.
| | - Jingru Ma
- Department of Laboratory Medicine, the Second Hospital of Jilin University, Changchun 130000, China
| | - Qingzhu Yan
- Department of Ultrasound Medicine, the Second Hospital of Jilin University, Changchun 130000, China
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Mellis IA, Bodkin N, Melzer ME, Goyal Y. Prevalence of and gene regulatory constraints on transcriptional adaptation in single cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.14.553318. [PMID: 37645989 PMCID: PMC10462021 DOI: 10.1101/2023.08.14.553318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Cells and tissues have a remarkable ability to adapt to genetic perturbations via a variety of molecular mechanisms. Nonsense-induced transcriptional compensation, a form of transcriptional adaptation, has recently emerged as one such mechanism, in which nonsense mutations in a gene can trigger upregulation of related genes, possibly conferring robustness at cellular and organismal levels. However, beyond a handful of developmental contexts and curated sets of genes, to date, no comprehensive genome-wide investigation of this behavior has been undertaken for mammalian cell types and contexts. Moreover, how the regulatory-level effects of inherently stochastic compensatory gene networks contribute to phenotypic penetrance in single cells remains unclear. Here we combine computational analysis of existing datasets with stochastic mathematical modeling and machine learning to uncover the widespread prevalence of transcriptional adaptation in mammalian systems and the diverse single-cell manifestations of minimal compensatory gene networks. Regulon gene expression analysis of a pooled single-cell genetic perturbation dataset recapitulates important model predictions. Our integrative approach uncovers several putative hits-genes demonstrating possible transcriptional adaptation-to follow up on experimentally, and provides a formal quantitative framework to test and refine models of transcriptional adaptation.
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Affiliation(s)
- Ian A. Mellis
- Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Nicholas Bodkin
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Center for Synthetic Biology, Northwestern University, Chicago, IL, USA
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Madeline E. Melzer
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Center for Synthetic Biology, Northwestern University, Chicago, IL, USA
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Yogesh Goyal
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Center for Synthetic Biology, Northwestern University, Chicago, IL, USA
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
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5
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Acosta CH, Clemons GA, Citadin CT, Carr WC, Udo MSB, Tesic V, Sanicola HW, Freelin AH, Toms JB, Jordan JD, Guthikonda B, Rodgers KM, Wu CYC, Lee RHC, Lin HW. PRMT7 can prevent neurovascular uncoupling, blood-brain barrier permeability, and mitochondrial dysfunction in repetitive and mild traumatic brain injury. Exp Neurol 2023; 366:114445. [PMID: 37196697 PMCID: PMC10960645 DOI: 10.1016/j.expneurol.2023.114445] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 05/03/2023] [Accepted: 05/12/2023] [Indexed: 05/19/2023]
Abstract
Mild traumatic brain injury (TBI) comprises the largest percentage of TBI-related injuries, with pathophysiological and functional deficits that persist in a subset of TBI patients. In our three-hit paradigm of repetitive and mild traumatic brain injury (rmTBI), we observed neurovascular uncoupling via decreased red blood cell velocity, microvessel diameter, and leukocyte rolling velocity 3 days post-rmTBI via intra-vital two-photon laser scanning microscopy. Furthermore, our data suggest increased blood-brain barrier (BBB) permeability (leakage), with corresponding decrease in junctional protein expression post-rmTBI. Mitochondrial oxygen consumption rates (measured via Seahorse XFe24) were also altered 3 days post-rmTBI, along with disrupted mitochondrial dynamics of fission and fusion. Overall, these pathophysiological findings correlated with decreased protein arginine methyltransferase 7 (PRMT7) protein levels and activity post-rmTBI. Here, we increased PRMT7 levels in vivo to assess the role of the neurovasculature and mitochondria post-rmTBI. In vivo overexpression of PRMT7 using a neuronal specific AAV vector led to restoration of neurovascular coupling, prevented BBB leakage, and promoted mitochondrial respiration, altogether to suggest a protective and functional role of PRMT7 in rmTBI.
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Affiliation(s)
- Christina H Acosta
- Department of Cellular Biology & Anatomy, Louisiana State University Health Sciences Center, Shreveport, LA, United States of America
| | - Garrett A Clemons
- Department of Cellular Biology & Anatomy, Louisiana State University Health Sciences Center, Shreveport, LA, United States of America
| | - Cristiane T Citadin
- Department of Cellular Biology & Anatomy, Louisiana State University Health Sciences Center, Shreveport, LA, United States of America
| | - William C Carr
- Department of Neurology, Louisiana State University Health Sciences Center, Shreveport, LA, United States of America
| | - Mariana Sayuri Berto Udo
- Department of Neurology, Louisiana State University Health Sciences Center, Shreveport, LA, United States of America
| | - Vesna Tesic
- Department of Neurology, Louisiana State University Health Sciences Center, Shreveport, LA, United States of America
| | - Henry W Sanicola
- Department of Neurology, Louisiana State University Health Sciences Center, Shreveport, LA, United States of America; Department of Neurosurgery, Louisiana State University Health Sciences Center, Shreveport, LA, United States of America
| | - Anne H Freelin
- Department of Neurosurgery, Louisiana State University Health Sciences Center, Shreveport, LA, United States of America
| | - Jamie B Toms
- Department of Neurosurgery, Louisiana State University Health Sciences Center, Shreveport, LA, United States of America
| | - J Dedrick Jordan
- Department of Neurology, Louisiana State University Health Sciences Center, Shreveport, LA, United States of America
| | - Bharat Guthikonda
- Department of Neurosurgery, Louisiana State University Health Sciences Center, Shreveport, LA, United States of America
| | - Krista M Rodgers
- Department of Cellular Biology & Anatomy, Louisiana State University Health Sciences Center, Shreveport, LA, United States of America
| | - Celeste Yin-Chieh Wu
- Department of Neurology, Louisiana State University Health Sciences Center, Shreveport, LA, United States of America
| | - Reggie Hui-Chao Lee
- Department of Neurology, Louisiana State University Health Sciences Center, Shreveport, LA, United States of America
| | - Hung Wen Lin
- Department of Cellular Biology & Anatomy, Louisiana State University Health Sciences Center, Shreveport, LA, United States of America; Department of Neurology, Louisiana State University Health Sciences Center, Shreveport, LA, United States of America.
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6
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Conway JRW, Dinç DD, Follain G, Paavolainen O, Kaivola J, Boström P, Hartiala P, Peuhu E, Ivaska J. IGFBP2 secretion by mammary adipocytes limits breast cancer invasion. SCIENCE ADVANCES 2023; 9:eadg1840. [PMID: 37436978 DOI: 10.1126/sciadv.adg1840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 06/08/2023] [Indexed: 07/14/2023]
Abstract
The progression of noninvasive ductal carcinoma in situ to invasive ductal carcinoma for patients with breast cancer results in a significantly poorer prognosis and is the precursor to metastatic disease. In this work, we have identified insulin-like growth factor-binding protein 2 (IGFBP2) as a potent adipocrine factor secreted by healthy breast adipocytes that acts as a barrier against invasive progression. In line with this role, adipocytes differentiated from patient-derived stromal cells were found to secrete IGFBP2, which significantly inhibited breast cancer invasion. This occurred through binding and sequestration of cancer-derived IGF-II. Moreover, depletion of IGF-II in invading cancer cells using small interfering RNAs or an IGF-II-neutralizing antibody ablated breast cancer invasion, highlighting the importance of IGF-II autocrine signaling for breast cancer invasive progression. Given the abundance of adipocytes in the healthy breast, this work exposes the important role they play in suppressing cancer progression and may help expound upon the link between increased mammary density and poorer prognosis.
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Affiliation(s)
- James R W Conway
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520 Turku, Finland
| | - Defne D Dinç
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520 Turku, Finland
- Institute of Biomedicine, and Cancer Research Laboratory FICAN West, University of Turku, FI-20520 Turku, Finland
- Western Finnish Cancer Center (FICAN West), University of Turku and Turku University Hospital, FI-20520 Turku, Finland
| | - Gautier Follain
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520 Turku, Finland
| | - Oona Paavolainen
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520 Turku, Finland
- Institute of Biomedicine, and Cancer Research Laboratory FICAN West, University of Turku, FI-20520 Turku, Finland
- Western Finnish Cancer Center (FICAN West), University of Turku and Turku University Hospital, FI-20520 Turku, Finland
| | - Jasmin Kaivola
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520 Turku, Finland
| | - Pia Boström
- Department of Pathology, Turku University Hospital, 20520 Turku, Finland; University of Turku, 20520 Turku, Finland
| | - Pauliina Hartiala
- Department of Plastic and General Surgery, Turku University Hospital, 20520 Turku, Finland
- Medicity Research Laboratory, InFLAMES Research Flagship, University of Turku, Turku, Finland
| | - Emilia Peuhu
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520 Turku, Finland
- Institute of Biomedicine, and Cancer Research Laboratory FICAN West, University of Turku, FI-20520 Turku, Finland
- Western Finnish Cancer Center (FICAN West), University of Turku and Turku University Hospital, FI-20520 Turku, Finland
| | - Johanna Ivaska
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520 Turku, Finland
- Western Finnish Cancer Center (FICAN West), University of Turku and Turku University Hospital, FI-20520 Turku, Finland
- Department of Life Technologies, University of Turku, FI-20520 Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
- Foundation for the Finnish Cancer Institute, Tukholmankatu 8, FI-00014 Helsinki, Finland
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Sauter C, Simonet J, Guidez F, Dumétier B, Pernon B, Callanan M, Bastie JN, Aucagne R, Delva L. Protein Arginine Methyltransferases as Therapeutic Targets in Hematological Malignancies. Cancers (Basel) 2022; 14:5443. [PMID: 36358861 PMCID: PMC9657843 DOI: 10.3390/cancers14215443] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 10/31/2022] [Accepted: 11/01/2022] [Indexed: 08/02/2023] Open
Abstract
Arginine methylation is a common post-translational modification affecting protein activity and the transcription of target genes when methylation occurs on histone tails. There are nine protein arginine methyltransferases (PRMTs) in mammals, divided into subgroups depending on the methylation they form on a molecule of arginine. During the formation and maturation of the different types of blood cells, PRMTs play a central role by controlling cell differentiation at the transcriptional level. PRMT enzymatic activity is necessary for many cellular processes in hematological malignancies, such as the activation of cell cycle and proliferation, inhibition of apoptosis, DNA repair processes, RNA splicing, and transcription by methylating histone tails' arginine. Chemical tools have been developed to inhibit the activity of PRMTs and have been tested in several models of hematological malignancies, including primary samples from patients, xenografts into immunodeficient mice, mouse models, and human cell lines. They show a significant effect by reducing cell viability and increasing the overall survival of mice. PRMT5 inhibitors have a strong therapeutic potential, as phase I clinical trials in hematological malignancies that use these molecules show promising results, thus, underlining PRMT inhibitors as useful therapeutic tools for cancer treatment in the future.
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Affiliation(s)
- Camille Sauter
- Inserm U1231, Team Epi2THM, LipSTIC Labex, UFR des Sciences de Santé, Université de Bourgogne, Université Bourgogne Franche-Comté, 21000 Dijon, France
| | - John Simonet
- Inserm U1231, Team Epi2THM, LipSTIC Labex, UFR des Sciences de Santé, Université de Bourgogne, Université Bourgogne Franche-Comté, 21000 Dijon, France
| | - Fabien Guidez
- Inserm U1231, Team Epi2THM, LipSTIC Labex, UFR des Sciences de Santé, Université de Bourgogne, Université Bourgogne Franche-Comté, 21000 Dijon, France
| | - Baptiste Dumétier
- Inserm U1231, Team Epi2THM, LipSTIC Labex, UFR des Sciences de Santé, Université de Bourgogne, Université Bourgogne Franche-Comté, 21000 Dijon, France
| | - Baptiste Pernon
- Inserm U1231, Team Epi2THM, LipSTIC Labex, UFR des Sciences de Santé, Université de Bourgogne, Université Bourgogne Franche-Comté, 21000 Dijon, France
| | - Mary Callanan
- Inserm U1231, Team Epi2THM, LipSTIC Labex, UFR des Sciences de Santé, Université de Bourgogne, Université Bourgogne Franche-Comté, 21000 Dijon, France
- Unit for Innovation in Genetics and Epigenetic in Oncology (IGEO)/CRIGEN Core Facility, University Hospital François Mitterrand, 21000 Dijon, France
| | - Jean-Noël Bastie
- Inserm U1231, Team Epi2THM, LipSTIC Labex, UFR des Sciences de Santé, Université de Bourgogne, Université Bourgogne Franche-Comté, 21000 Dijon, France
- Department of Clinical Hematology, University Hospital François Mitterrand, 21000 Dijon, France
| | - Romain Aucagne
- Inserm U1231, Team Epi2THM, LipSTIC Labex, UFR des Sciences de Santé, Université de Bourgogne, Université Bourgogne Franche-Comté, 21000 Dijon, France
- Unit for Innovation in Genetics and Epigenetic in Oncology (IGEO)/CRIGEN Core Facility, University Hospital François Mitterrand, 21000 Dijon, France
| | - Laurent Delva
- Inserm U1231, Team Epi2THM, LipSTIC Labex, UFR des Sciences de Santé, Université de Bourgogne, Université Bourgogne Franche-Comté, 21000 Dijon, France
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