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Tauer JT, Thiele T, Julien C, Ofer L, Zaslansky P, Shahar R, Willie BM. Swim training induces distinct osseous gene expression patterns in anosteocytic and osteocytic teleost fish. Bone 2024; 185:117125. [PMID: 38754573 DOI: 10.1016/j.bone.2024.117125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 05/09/2024] [Accepted: 05/13/2024] [Indexed: 05/18/2024]
Abstract
The traditional understanding of bone mechanosensation implicates osteocytes, canaliculi, and the lacunocanalicular network in biomechanical adaptation. However, recent findings challenge this notion, as shown in advanced teleost fish where anosteocytic bone lacking osteocytes are nevertheless responsive to mechanical load. To investigate specific molecular mechanisms involved in bone mechanoadaptation in osteocytic and anosteocytic fish bone, we conducted a 5-min single swim-training experiment with zebrafish and ricefish, respectively. Through RNASeq analysis of fish spines, analyzed at various time points following swim training, we uncovered distinct gene expression patterns in osteocytic and anosteocytic fish bones. Notably, osteocytic fish bone exhibited an early response to mechanical load, contrasting to a delayed response observed in anosteocytic fish bones, both within 8 h following stimulation. We identified an increase in osteoblast differentiation in anosteocytic bone following training, while chordoblast activity was delayed. This temporal response suggests a time-dependent adaptation in anosteocytic bone, indicating the presence of intricate feedback networks within bone that lacks osteocytes.
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Affiliation(s)
- Josephine T Tauer
- Research Centre, Shriners Hospital for Children-Canada, Montreal, Canada; Faculty of Dental Medicine and Oral Health Sciences, McGill University, Montreal, Canada; Department of Pediatrics and Adolescent Medicine, Johannes Kepler University Linz, Linz, Austria
| | - Tobias Thiele
- Julius Wolff Institute and Berlin Institute of Health Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Catherine Julien
- Research Centre, Shriners Hospital for Children-Canada, Montreal, Canada; Faculty of Dental Medicine and Oral Health Sciences, McGill University, Montreal, Canada
| | - Lior Ofer
- Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University, Rehovot, Israel
| | - Paul Zaslansky
- Department of Operative, Preventive and Pediatric Dentistry, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Ron Shahar
- Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University, Rehovot, Israel
| | - Bettina M Willie
- Research Centre, Shriners Hospital for Children-Canada, Montreal, Canada; Faculty of Dental Medicine and Oral Health Sciences, McGill University, Montreal, Canada.
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Sibai DS, Tremblay MG, Lessard F, Tav C, Sabourin-Félix M, Robinson M, Moss T. TTF1 control of LncRNA synthesis delineates a tumor suppressor pathway directly regulating the ribosomal RNA genes. J Cell Physiol 2024. [PMID: 38764354 DOI: 10.1002/jcp.31303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/29/2024] [Accepted: 05/02/2024] [Indexed: 05/21/2024]
Abstract
The tumor suppressor p14/19ARF regulates ribosomal RNA (rRNA) synthesis by controlling the nucleolar localization of Transcription Termination Factor 1 (TTF1). However, the role played by TTF1 in regulating the rRNA genes and in potentially controlling growth has remained unclear. We now show that TTF1 expression regulates cell growth by determining the cellular complement of ribosomes. Unexpectedly, it achieves this by acting as a "roadblock" to synthesis of the noncoding LncRNA and pRNA that we show are generated from the "Spacer Promoter" duplications present upstream of the 47S pre-rRNA promoter on the mouse and human ribosomal RNA genes. Unexpectedly, the endogenous generation of these noncoding RNAs does not induce CpG methylation or gene silencing. Rather, it acts in cis to suppress 47S preinitiation complex formation and hence de novo pre-rRNA synthesis by a mechanism reminiscent of promoter interference or occlusion. Taken together, our data delineate a pathway from p19ARF to cell growth suppression via the regulation of ribosome biogenesis by noncoding RNAs and validate a key cellular growth law in mammalian cells.
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Affiliation(s)
- Dany S Sibai
- St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Laval University, Quebec City, Quebec, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, Quebec City, Quebec, Canada
- Cancer Research Centre, Laval University, Quebec City, Quebec, Canada
| | - Michel G Tremblay
- St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Laval University, Quebec City, Quebec, Canada
| | - Frédéric Lessard
- St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Laval University, Quebec City, Quebec, Canada
| | - Christophe Tav
- St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Laval University, Quebec City, Quebec, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, Quebec City, Quebec, Canada
- Cancer Research Centre, Laval University, Quebec City, Quebec, Canada
| | - Marianne Sabourin-Félix
- St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Laval University, Quebec City, Quebec, Canada
| | - Mark Robinson
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Tom Moss
- St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Laval University, Quebec City, Quebec, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, Quebec City, Quebec, Canada
- Cancer Research Centre, Laval University, Quebec City, Quebec, Canada
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3
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Amri O, Madore AM, Boucher-Lafleur AM, Laprise C. Genomic analysis of severe COVID-19 considering or not asthma comorbidity: GWAS insights from the BQC19 cohort. BMC Genomics 2024; 25:482. [PMID: 38750426 PMCID: PMC11097529 DOI: 10.1186/s12864-024-10342-x] [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: 03/04/2024] [Accepted: 04/23/2024] [Indexed: 05/18/2024] Open
Abstract
BACKGROUND The severity of COVID-19 is influenced by various factors including the presence of respiratory diseases. Studies have indicated a potential relationship between asthma and COVID-19 severity. OBJECTIVE This study aimed to conduct a genome-wide association study (GWAS) to identify genetic and clinical variants associated with the severity of COVID-19, both among patients with and without asthma. METHODS We analyzed data from 2131 samples sourced from the Biobanque québécoise de la COVID-19 (BQC19), with 1499 samples from patients who tested positive for COVID-19. Among these, 1110 exhibited mild-to-moderate symptoms, 389 had severe symptoms, and 58 had asthma. We conducted a comparative analysis of clinical data from individuals in these three groups and GWAS using a logistic regression model. Phenotypic data analysis resulted in the refined covariates integrated into logistic models for genetic studies. RESULTS Considering a significance threshold of 1 × 10-6, seven genetic variants were associated with severe COVID-19. These variants were located proximal to five genes: sodium voltage-gated channel alpha subunit 1 (SCN10A), desmoplakin (DSP), RP1 axonemal microtubule associated (RP1), IGF like family member 1 (IGFL1), and docking protein 5 (DOK5). The GWAS comparing individuals with severe COVID-19 with asthma to those without asthma revealed four genetic variants in transmembrane protein with EGF like and two follistatin like domains 2 (TMEFF2) and huntingtin interacting protein-1 (HIP1) genes. CONCLUSION This study provides significant insights into the genetic profiles of patients with severe forms of the disease, whether accompanied by asthma or not. These findings enhance our comprehension of the genetic factors that affect COVID-19 severity. KEY MESSAGES Seven genetic variants were associated with the severe form of COVID-19; Four genetic variants were associated with the severe form of COVID-19 in individuals with comorbid asthma; These findings help define the genetic component of the severe form of COVID-19 in relation to asthma as a comorbidity.
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Affiliation(s)
- Omayma Amri
- Centre intersectoriel en santé durable, Université du Québec à Chicoutimi, Saguenay, Québec, G7H 2B1, Canada
- Département des sciences fondamentales, Université du Québec à Chicoutimi, Saguenay, Québec, G7H 2B1, Canada
| | - Anne-Marie Madore
- Centre intersectoriel en santé durable, Université du Québec à Chicoutimi, Saguenay, Québec, G7H 2B1, Canada
- Département des sciences fondamentales, Université du Québec à Chicoutimi, Saguenay, Québec, G7H 2B1, Canada
| | - Anne-Marie Boucher-Lafleur
- Centre intersectoriel en santé durable, Université du Québec à Chicoutimi, Saguenay, Québec, G7H 2B1, Canada
- Département des sciences fondamentales, Université du Québec à Chicoutimi, Saguenay, Québec, G7H 2B1, Canada
| | - Catherine Laprise
- Centre intersectoriel en santé durable, Université du Québec à Chicoutimi, Saguenay, Québec, G7H 2B1, Canada.
- Département des sciences fondamentales, Université du Québec à Chicoutimi, Saguenay, Québec, G7H 2B1, Canada.
- Centre de recherche du Centre intégré universitaire de santé et de services sociaux du Saguenay-Lac-Saint-Jean, Saguenay, Québec, G7H 7K9, Canada.
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Kuzmin E, Baker TM, Lesluyes T, Monlong J, Abe KT, Coelho PP, Schwartz M, Del Corpo J, Zou D, Morin G, Pacis A, Yang Y, Martinez C, Barber J, Kuasne H, Li R, Bourgey M, Fortier AM, Davison PG, Omeroglu A, Guiot MC, Morris Q, Kleinman CL, Huang S, Gingras AC, Ragoussis J, Bourque G, Van Loo P, Park M. Evolution of chromosome-arm aberrations in breast cancer through genetic network rewiring. Cell Rep 2024; 43:113988. [PMID: 38517886 PMCID: PMC11063629 DOI: 10.1016/j.celrep.2024.113988] [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: 09/01/2023] [Revised: 02/02/2024] [Accepted: 03/07/2024] [Indexed: 03/24/2024] Open
Abstract
The basal breast cancer subtype is enriched for triple-negative breast cancer (TNBC) and displays consistent large chromosomal deletions. Here, we characterize evolution and maintenance of chromosome 4p (chr4p) loss in basal breast cancer. Analysis of The Cancer Genome Atlas data shows recurrent deletion of chr4p in basal breast cancer. Phylogenetic analysis of a panel of 23 primary tumor/patient-derived xenograft basal breast cancers reveals early evolution of chr4p deletion. Mechanistically we show that chr4p loss is associated with enhanced proliferation. Gene function studies identify an unknown gene, C4orf19, within chr4p, which suppresses proliferation when overexpressed-a member of the PDCD10-GCKIII kinase module we name PGCKA1. Genome-wide pooled overexpression screens using a barcoded library of human open reading frames identify chromosomal regions, including chr4p, that suppress proliferation when overexpressed in a context-dependent manner, implicating network interactions. Together, these results shed light on the early emergence of complex aneuploid karyotypes involving chr4p and adaptive landscapes shaping breast cancer genomes.
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Affiliation(s)
- Elena Kuzmin
- Rosalind and Morris Goodman Cancer Institute, Montreal, QC H3A 1A3, Canada; Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada.
| | | | | | - Jean Monlong
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; McGill Genome Centre, Montreal, QC H3A 0G1, Canada
| | - Kento T Abe
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health, Toronto, ON M5G 1X5, Canada
| | - Paula P Coelho
- Rosalind and Morris Goodman Cancer Institute, Montreal, QC H3A 1A3, Canada; Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Michael Schwartz
- Rosalind and Morris Goodman Cancer Institute, Montreal, QC H3A 1A3, Canada; Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Joseph Del Corpo
- Department of Biology, Concordia University, Montreal, QC H4B 1R6, Canada
| | - Dongmei Zou
- Rosalind and Morris Goodman Cancer Institute, Montreal, QC H3A 1A3, Canada
| | - Genevieve Morin
- Rosalind and Morris Goodman Cancer Institute, Montreal, QC H3A 1A3, Canada; Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Alain Pacis
- McGill Genome Centre, Montreal, QC H3A 0G1, Canada; Canadian Centre for Computational Genomics (C3G), McGill University, Montreal, QC H3A 0G1, Canada
| | - Yang Yang
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
| | - Constanza Martinez
- Rosalind and Morris Goodman Cancer Institute, Montreal, QC H3A 1A3, Canada; Department of Pathology, McGill University, Montreal, QC H3A 2B4, Canada; Gerald Bronfman Department of Oncology, McGill University, Montreal, QC H4A 3T2, Canada
| | - Jarrett Barber
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Vector Institute, Toronto, ON M5G 1M1, Canada; Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada; Computational and Systems Biology, Sloan Kettering Institute, New York City, NY 10065, USA
| | - Hellen Kuasne
- Rosalind and Morris Goodman Cancer Institute, Montreal, QC H3A 1A3, Canada
| | - Rui Li
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; McGill Genome Centre, Montreal, QC H3A 0G1, Canada
| | - Mathieu Bourgey
- McGill Genome Centre, Montreal, QC H3A 0G1, Canada; Canadian Centre for Computational Genomics (C3G), McGill University, Montreal, QC H3A 0G1, Canada
| | - Anne-Marie Fortier
- Rosalind and Morris Goodman Cancer Institute, Montreal, QC H3A 1A3, Canada
| | - Peter G Davison
- Department of Surgery, McGill University, Montreal, QC H3G 1A4, Canada; McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Atilla Omeroglu
- Department of Pathology, McGill University, Montreal, QC H3A 2B4, Canada
| | | | - Quaid Morris
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Vector Institute, Toronto, ON M5G 1M1, Canada; Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada; Computational and Systems Biology, Sloan Kettering Institute, New York City, NY 10065, USA; Gerstner Sloan Kettering Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Claudia L Kleinman
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; Lady Davis Institute for Medical Research, Montreal, QC H3T 1E2, Canada
| | - Sidong Huang
- Rosalind and Morris Goodman Cancer Institute, Montreal, QC H3A 1A3, Canada; Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada; Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
| | - Anne-Claude Gingras
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health, Toronto, ON M5G 1X5, Canada
| | - Jiannis Ragoussis
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; McGill Genome Centre, Montreal, QC H3A 0G1, Canada
| | - Guillaume Bourque
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; McGill Genome Centre, Montreal, QC H3A 0G1, Canada; Canadian Centre for Computational Genomics (C3G), McGill University, Montreal, QC H3A 0G1, Canada
| | - Peter Van Loo
- The Francis Crick Institute, NW1 1AT London, UK; Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Morag Park
- Rosalind and Morris Goodman Cancer Institute, Montreal, QC H3A 1A3, Canada; Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada; Gerald Bronfman Department of Oncology, McGill University, Montreal, QC H4A 3T2, Canada.
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Giraudo M, Mercier L, Gendron A, Sherry J, Houde M. Transcriptome analyses in juvenile yellow perch (Perca flavescens) exposed in vivo to clothianidin and chlorantraniliprole: Possible sampling bias. PLoS One 2024; 19:e0302126. [PMID: 38625968 PMCID: PMC11020500 DOI: 10.1371/journal.pone.0302126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 03/28/2024] [Indexed: 04/18/2024] Open
Abstract
The St. Lawrence River is an important North American waterway that is subject to anthropogenic pressures including intensive urbanization, and agricultural development. Pesticides are widely used for agricultural activities in fields surrounding the yellow perch (Perca flavescens) habitat in Lake St. Pierre (Quebec, Canada), a fluvial lake of the river where the perch population has collapsed. Clothianidin and chlorantraniliprole were two of the most detected insecticides in surface waters near perch spawning areas. The objectives of the present study were to evaluate the transcriptional and biochemical effects of these two pesticides on juvenile yellow perch exposed for 28d to environmental doses of each compound alone and in a mixture under laboratory/aquaria conditions. Hepatic mRNA-sequencing revealed an effect of chlorantraniliprole alone (37 genes) and combined with clothianidin (251 genes), but no effects of clothianidin alone were observed in perch. Dysregulated genes were mostly related to circadian rhythms and to Ca2+ signaling, the latter effect has been previously associated with chlorantraniliprole mode of action in insects. Moreover, chronic exposure to clothianidin increased the activity of acetylcholinesterase in the brain of exposed fish, suggesting a potential non-target effect of this insecticide. Further analyses of three clock genes by qRT-PCR suggested that part of the observed effects of chlorantraniliprole on the circadian gene regulation of juvenile perch could be the result of time-of-day of sacrifice. These results provide insight into biological effects of insecticides in juvenile perch and highlight the importance of considering the circadian rhythm in experimental design and results analyses.
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Affiliation(s)
- Maeva Giraudo
- Environment and Climate Change Canada, Aquatic Contaminants Research Division, Montreal, Quebec, Canada
| | - Laurie Mercier
- Environment and Climate Change Canada, Aquatic Contaminants Research Division, Montreal, Quebec, Canada
| | - Andrée Gendron
- Environment and Climate Change Canada, Aquatic Contaminants Research Division, Montreal, Quebec, Canada
| | - Jim Sherry
- Environment and Climate Change Canada, Aquatic Contaminants Research Division, Burlington, Ontario, Canada
| | - Magali Houde
- Environment and Climate Change Canada, Aquatic Contaminants Research Division, Montreal, Quebec, Canada
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O’Dowd K, Isham IM, Vatandour S, Boulianne M, Dozois CM, Gagnon CA, Barjesteh N, Abdul-Careem MF. Host Immune Response Modulation in Avian Coronavirus Infection: Tracheal Transcriptome Profiling In Vitro and In Vivo. Viruses 2024; 16:605. [PMID: 38675946 PMCID: PMC11053446 DOI: 10.3390/v16040605] [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: 03/21/2024] [Revised: 04/05/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
Infectious bronchitis virus (IBV) is a highly contagious Gammacoronavirus causing moderate to severe respiratory infection in chickens. Understanding the initial antiviral response in the respiratory mucosa is crucial for controlling viral spread. We aimed to characterize the impact of IBV Delmarva (DMV)/1639 and IBV Massachusetts (Mass) 41 at the primary site of infection, namely, in chicken tracheal epithelial cells (cTECs) in vitro and the trachea in vivo. We hypothesized that some elements of the induced antiviral responses are distinct in both infection models. We inoculated cTECs and infected young specific pathogen-free (SPF) chickens with IBV DMV/1639 or IBV Mass41, along with mock-inoculated controls, and studied the transcriptome using RNA-sequencing (RNA-seq) at 3 and 18 h post-infection (hpi) for cTECs and at 4 and 11 days post-infection (dpi) in the trachea. We showed that IBV DMV/1639 and IBV Mass41 replicate in cTECs in vitro and the trachea in vivo, inducing host mRNA expression profiles that are strain- and time-dependent. We demonstrated the different gene expression patterns between in vitro and in vivo tracheal IBV infection. Ultimately, characterizing host-pathogen interactions with various IBV strains reveals potential mechanisms for inducing and modulating the immune response during IBV infection in the chicken trachea.
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Affiliation(s)
- Kelsey O’Dowd
- Health Research Innovation Centre, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; (K.O.); (I.M.I.)
| | - Ishara M. Isham
- Health Research Innovation Centre, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; (K.O.); (I.M.I.)
| | - Safieh Vatandour
- Department of Animal and Poultry Science, Islamic Azad University, Qaemshahr Branch, Qaem Shahr 4765161964, Iran;
| | - Martine Boulianne
- Swine and Poultry Infectious Diseases Research Centre–Fonds de Recherche du Québec (CRIPA-FRQ), Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC J2S 2M2, Canada; (M.B.); (C.M.D.); (C.A.G.); (N.B.)
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC J2S 2M2, Canada
| | - Charles M. Dozois
- Swine and Poultry Infectious Diseases Research Centre–Fonds de Recherche du Québec (CRIPA-FRQ), Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC J2S 2M2, Canada; (M.B.); (C.M.D.); (C.A.G.); (N.B.)
- Institut National de Recherche Scientifique-Centre Armand-Frappier Santé Biotechnologie, Laval, QC H7V 1B7, Canada
| | - Carl A. Gagnon
- Swine and Poultry Infectious Diseases Research Centre–Fonds de Recherche du Québec (CRIPA-FRQ), Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC J2S 2M2, Canada; (M.B.); (C.M.D.); (C.A.G.); (N.B.)
- Molecular Diagnostic and Virology Laboratories, Centre de Diagnostic Vétérinaire de l’Université de Montréal (CDVUM), Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC J2S 2M2, Canada
| | - Neda Barjesteh
- Swine and Poultry Infectious Diseases Research Centre–Fonds de Recherche du Québec (CRIPA-FRQ), Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC J2S 2M2, Canada; (M.B.); (C.M.D.); (C.A.G.); (N.B.)
| | - Mohamed Faizal Abdul-Careem
- Health Research Innovation Centre, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; (K.O.); (I.M.I.)
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7
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Dorion MF, Casas D, Shlaifer I, Yaqubi M, Fleming P, Karpilovsky N, Chen CXQ, Nicouleau M, Piscopo VEC, MacDougall EJ, Alluli A, Goldsmith TM, Schneider A, Dorion S, Aprahamian N, MacDonald A, Thomas RA, Dudley RWR, Hall JA, Fon EA, Antel JP, Stratton JA, Durcan TM, La Piana R, Healy LM. An adapted protocol to derive microglia from stem cells and its application in the study of CSF1R-related disorders. Mol Neurodegener 2024; 19:31. [PMID: 38576039 PMCID: PMC10996091 DOI: 10.1186/s13024-024-00723-x] [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: 09/11/2023] [Accepted: 03/17/2024] [Indexed: 04/06/2024] Open
Abstract
BACKGROUND Induced pluripotent stem cell-derived microglia (iMGL) represent an excellent tool in studying microglial function in health and disease. Yet, since differentiation and survival of iMGL are highly reliant on colony-stimulating factor 1 receptor (CSF1R) signaling, it is difficult to use iMGL to study microglial dysfunction associated with pathogenic defects in CSF1R. METHODS Serial modifications to an existing iMGL protocol were made, including but not limited to changes in growth factor combination to drive microglial differentiation, until successful derivation of microglia-like cells from an adult-onset leukoencephalopathy with axonal spheroids and pigmented glia (ALSP) patient carrying a c.2350G > A (p.V784M) CSF1R variant. Using healthy control lines, the quality of the new iMGL protocol was validated through cell yield assessment, measurement of microglia marker expression, transcriptomic comparison to primary microglia, and evaluation of inflammatory and phagocytic activities. Similarly, molecular and functional characterization of the ALSP patient-derived iMGL was carried out in comparison to healthy control iMGL. RESULTS The newly devised protocol allowed the generation of iMGL with enhanced transcriptomic similarity to cultured primary human microglia and with higher scavenging and inflammatory competence at ~ threefold greater yield compared to the original protocol. Using this protocol, decreased CSF1R autophosphorylation and cell surface expression was observed in iMGL derived from the ALSP patient compared to those derived from healthy controls. Additionally, ALSP patient-derived iMGL presented a migratory defect accompanying a temporal reduction in purinergic receptor P2Y12 (P2RY12) expression, a heightened capacity to internalize myelin, as well as heightened inflammatory response to Pam3CSK4. Poor P2RY12 expression was confirmed to be a consequence of CSF1R haploinsufficiency, as this feature was also observed following CSF1R knockdown or inhibition in mature control iMGL, and in CSF1RWT/KO and CSF1RWT/E633K iMGL compared to their respective isogenic controls. CONCLUSIONS We optimized a pre-existing iMGL protocol, generating a powerful tool to study microglial involvement in human neurological diseases. Using the optimized protocol, we have generated for the first time iMGL from an ALSP patient carrying a pathogenic CSF1R variant, with preliminary characterization pointing toward functional alterations in migratory, phagocytic and inflammatory activities.
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Affiliation(s)
- Marie-France Dorion
- Neuroimmunology Unit, Montreal Neurological Institute-Hospital, McGill University, Montreal, H3A 2B4, Canada
- Early Drug Discovery Unit, Montreal Neurological Institute-Hospital, McGill University, Montreal, H3A 2B4, Canada
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, H3A 2B4, Canada
| | - Diana Casas
- Neuroimmunology Unit, Montreal Neurological Institute-Hospital, McGill University, Montreal, H3A 2B4, Canada
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, H3A 2B4, Canada
| | - Irina Shlaifer
- Early Drug Discovery Unit, Montreal Neurological Institute-Hospital, McGill University, Montreal, H3A 2B4, Canada
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, H3A 2B4, Canada
| | - Moein Yaqubi
- Neuroimmunology Unit, Montreal Neurological Institute-Hospital, McGill University, Montreal, H3A 2B4, Canada
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, H3A 2B4, Canada
| | - Peter Fleming
- Neuroimmunology Unit, Montreal Neurological Institute-Hospital, McGill University, Montreal, H3A 2B4, Canada
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, H3A 2B4, Canada
| | - Nathan Karpilovsky
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, H3A 2B4, Canada
- McGill Parkinson Program and Neurodegenerative Disorders Research Group, Montreal Neurological Institute-Hospital, McGill University, Montreal, H3A 2B4, Canada
| | - Carol X-Q Chen
- Early Drug Discovery Unit, Montreal Neurological Institute-Hospital, McGill University, Montreal, H3A 2B4, Canada
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, H3A 2B4, Canada
| | - Michael Nicouleau
- Early Drug Discovery Unit, Montreal Neurological Institute-Hospital, McGill University, Montreal, H3A 2B4, Canada
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, H3A 2B4, Canada
| | - Valerio E C Piscopo
- Early Drug Discovery Unit, Montreal Neurological Institute-Hospital, McGill University, Montreal, H3A 2B4, Canada
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, H3A 2B4, Canada
| | - Emma J MacDougall
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, H3A 2B4, Canada
- McGill Parkinson Program and Neurodegenerative Disorders Research Group, Montreal Neurological Institute-Hospital, McGill University, Montreal, H3A 2B4, Canada
| | - Aeshah Alluli
- Early Drug Discovery Unit, Montreal Neurological Institute-Hospital, McGill University, Montreal, H3A 2B4, Canada
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, H3A 2B4, Canada
| | - Taylor M Goldsmith
- Early Drug Discovery Unit, Montreal Neurological Institute-Hospital, McGill University, Montreal, H3A 2B4, Canada
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, H3A 2B4, Canada
| | - Alexandria Schneider
- Early Drug Discovery Unit, Montreal Neurological Institute-Hospital, McGill University, Montreal, H3A 2B4, Canada
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, H3A 2B4, Canada
| | - Samuel Dorion
- Faculty of Arts and Sciences, Université de Montréal, Montreal, H3T 1NB, Canada
| | - Nathalia Aprahamian
- Early Drug Discovery Unit, Montreal Neurological Institute-Hospital, McGill University, Montreal, H3A 2B4, Canada
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, H3A 2B4, Canada
| | - Adam MacDonald
- Neuroimmunology Unit, Montreal Neurological Institute-Hospital, McGill University, Montreal, H3A 2B4, Canada
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, H3A 2B4, Canada
| | - Rhalena A Thomas
- Early Drug Discovery Unit, Montreal Neurological Institute-Hospital, McGill University, Montreal, H3A 2B4, Canada
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, H3A 2B4, Canada
- McGill Parkinson Program and Neurodegenerative Disorders Research Group, Montreal Neurological Institute-Hospital, McGill University, Montreal, H3A 2B4, Canada
| | - Roy W R Dudley
- Department of Pediatric Surgery, Division of Neurosurgery, Montreal Children's Hospital, McGill University Health Centers, Montreal, H4A 3J1, Canada
| | - Jeffrey A Hall
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, H3A 2B4, Canada
| | - Edward A Fon
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, H3A 2B4, Canada
- McGill Parkinson Program and Neurodegenerative Disorders Research Group, Montreal Neurological Institute-Hospital, McGill University, Montreal, H3A 2B4, Canada
| | - Jack P Antel
- Neuroimmunology Unit, Montreal Neurological Institute-Hospital, McGill University, Montreal, H3A 2B4, Canada
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, H3A 2B4, Canada
| | - Jo Anne Stratton
- Neuroimmunology Unit, Montreal Neurological Institute-Hospital, McGill University, Montreal, H3A 2B4, Canada
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, H3A 2B4, Canada
| | - Thomas M Durcan
- Early Drug Discovery Unit, Montreal Neurological Institute-Hospital, McGill University, Montreal, H3A 2B4, Canada
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, H3A 2B4, Canada
| | - Roberta La Piana
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, H3A 2B4, Canada.
| | - Luke M Healy
- Neuroimmunology Unit, Montreal Neurological Institute-Hospital, McGill University, Montreal, H3A 2B4, Canada.
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, H3A 2B4, Canada.
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8
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Ghosh A, Leung YH, Yu J, Sladek R, Chénier I, Oppong AK, Peyot ML, Madiraju SRM, Al-Khairi I, Thanaraj TA, Abubaker J, Al-Mulla F, Prentki M, Abu-Farha M. Silencing ANGPTL8 reduces mouse preadipocyte differentiation and insulin signaling. Biochim Biophys Acta Mol Cell Biol Lipids 2024; 1869:159461. [PMID: 38272177 DOI: 10.1016/j.bbalip.2024.159461] [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: 12/04/2023] [Revised: 01/12/2024] [Accepted: 01/19/2024] [Indexed: 01/27/2024]
Abstract
ANGPTL8, expressed mainly in the liver and adipose tissue, regulates the activity of lipoprotein lipase (LPL) present in the extracellular space and triglyceride (TG) metabolism through its interaction with ANGPTL3 and ANGPTL4. Whether intracellular ANGPTL8 can also exert effects in tissues where it is expressed is uncertain. ANGPTL8 expression was low in preadipocytes and much increased during differentiation. To better understand the role of intracellular ANGPTL8 in adipocytes and assess whether it may play a role in adipocyte differentiation, we knocked down its expression in normal mouse subcutaneous preadipocytes. ANGPTL8 knockdown reduced adipocyte differentiation, cellular TG accumulation and also isoproterenol-stimulated lipolysis at day 7 of differentiation. RNA-Seq analysis of ANGPTL8 siRNA or control siRNA transfected SC preadipocytes on days 0, 2, 4 and 7 of differentiation showed that ANGPTL8 knockdown impeded the early (day 2) expression of adipogenic and insulin signaling genes, PPARγ, as well as genes related to extracellular matrix and NF-κB signaling. Insulin mediated Akt phosphorylation was reduced at an early stage during adipocyte differentiation. This study based on normal primary cells shows that ANGPTL8 has intracellular actions in addition to effects in the extracellular space, like modulating LPL activity. Preadipocyte ANGPTL8 expression modulates their differentiation possibly via changes in insulin signaling gene expression.
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Affiliation(s)
- Anindya Ghosh
- Departments of Nutrition, Biochemistry and Molecular Medicine, University of Montreal, and Montreal Diabetes Research Center, Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC, Canada
| | - Yat Hei Leung
- Departments of Nutrition, Biochemistry and Molecular Medicine, University of Montreal, and Montreal Diabetes Research Center, Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC, Canada
| | - Jeffrey Yu
- Department of Medicine, McGill University, Montréal, QC, Canada
| | - Robert Sladek
- Department of Medicine, McGill University, Montréal, QC, Canada
| | - Isabelle Chénier
- Departments of Nutrition, Biochemistry and Molecular Medicine, University of Montreal, and Montreal Diabetes Research Center, Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC, Canada
| | - Abel K Oppong
- Departments of Nutrition, Biochemistry and Molecular Medicine, University of Montreal, and Montreal Diabetes Research Center, Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC, Canada
| | - Marie-Line Peyot
- Departments of Nutrition, Biochemistry and Molecular Medicine, University of Montreal, and Montreal Diabetes Research Center, Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC, Canada
| | - S R Murthy Madiraju
- Departments of Nutrition, Biochemistry and Molecular Medicine, University of Montreal, and Montreal Diabetes Research Center, Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC, Canada
| | | | | | | | | | - Marc Prentki
- Departments of Nutrition, Biochemistry and Molecular Medicine, University of Montreal, and Montreal Diabetes Research Center, Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC, Canada.
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9
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Maure A, Lawarée E, Fiorentino F, Pawlik A, Gona S, Giraud-Gatineau A, Eldridge MJG, Danckaert A, Hardy D, Frigui W, Keck C, Gutierrez C, Neyrolles O, Aulner N, Mai A, Hamon M, Barreiro LB, Brodin P, Brosch R, Rotili D, Tailleux L. A host-directed oxadiazole compound potentiates antituberculosis treatment via zinc poisoning in human macrophages and in a mouse model of infection. PLoS Biol 2024; 22:e3002259. [PMID: 38683873 PMCID: PMC11081512 DOI: 10.1371/journal.pbio.3002259] [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: 07/05/2023] [Revised: 05/09/2024] [Accepted: 03/13/2024] [Indexed: 05/02/2024] Open
Abstract
Antituberculosis drugs, mostly developed over 60 years ago, combined with a poorly effective vaccine, have failed to eradicate tuberculosis. More worryingly, multiresistant strains of Mycobacterium tuberculosis (MTB) are constantly emerging. Innovative strategies are thus urgently needed to improve tuberculosis treatment. Recently, host-directed therapy has emerged as a promising strategy to be used in adjunct with existing or future antibiotics, by improving innate immunity or limiting immunopathology. Here, using high-content imaging, we identified novel 1,2,4-oxadiazole-based compounds, which allow human macrophages to control MTB replication. Genome-wide gene expression analysis revealed that these molecules induced zinc remobilization inside cells, resulting in bacterial zinc intoxication. More importantly, we also demonstrated that, upon treatment with these novel compounds, MTB became even more sensitive to antituberculosis drugs, in vitro and in vivo, in a mouse model of tuberculosis. Manipulation of heavy metal homeostasis holds thus great promise to be exploited to develop host-directed therapeutic interventions.
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Affiliation(s)
- Alexandra Maure
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Unit for Integrated Mycobacterial Pathogenomics, Paris, France
| | - Emeline Lawarée
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Unit for Integrated Mycobacterial Pathogenomics, Paris, France
| | - Francesco Fiorentino
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Rome, Italy
| | - Alexandre Pawlik
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Unit for Integrated Mycobacterial Pathogenomics, Paris, France
| | - Saideep Gona
- Department of Genetic Medicine, University of Chicago, Chicago, Illinois, United States of America
| | | | | | - Anne Danckaert
- Institut Pasteur, Université Paris Cité, UTechS BioImaging-C2RT, Paris, France
| | - David Hardy
- Institut Pasteur, Université Paris Cité, Histopathology Platform, Paris, France
| | - Wafa Frigui
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Unit for Integrated Mycobacterial Pathogenomics, Paris, France
| | - Camille Keck
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Unit for Integrated Mycobacterial Pathogenomics, Paris, France
| | - Claude Gutierrez
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Olivier Neyrolles
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Nathalie Aulner
- Institut Pasteur, Université Paris Cité, UTechS BioImaging-C2RT, Paris, France
| | - Antonello Mai
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Rome, Italy
- Pasteur Institute, Cenci-bolognetti Foundation, Sapienza University of Rome, Rome, Italy
| | - Mélanie Hamon
- Institut Pasteur, Université Paris Cité, Chromatine et Infection unit, Paris, France
| | - Luis B. Barreiro
- Department of Genetic Medicine, University of Chicago, Chicago, Illinois, United States of America
| | - Priscille Brodin
- Université de Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, Lille, France
| | - Roland Brosch
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Unit for Integrated Mycobacterial Pathogenomics, Paris, France
| | - Dante Rotili
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Rome, Italy
| | - Ludovic Tailleux
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Unit for Integrated Mycobacterial Pathogenomics, Paris, France
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10
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Martínez Duncker Rebolledo E, Chan D, Christensen KE, Reagan AM, Howell GR, Rozen R, Trasler J. Sperm DNA methylation defects in a new mouse model of the 5,10-methylenetetrahydrofolate reductase 677C>T variant and correction with moderate dose folic acid supplementation. Mol Hum Reprod 2024; 30:gaae008. [PMID: 38366926 PMCID: PMC10980591 DOI: 10.1093/molehr/gaae008] [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: 07/20/2023] [Revised: 01/30/2024] [Indexed: 02/19/2024] Open
Abstract
5,10-Methylenetetrahydrofolate reductase (MTHFR) is an enzyme that plays a key role in providing methyl groups for DNA methylation, including during spermatogenesis. A common genetic variant in humans (MTHFR 677C>T) results in reduced enzyme activity and has been linked to various disorders, including male infertility. A new animal model has been created by reproducing the human equivalent of the polymorphism in mice using CRISPR/Cas9. Biochemical parameters in the Mthfr 677TT mice recapitulate alterations found in MTHFR 677TT men. Our aims were to characterize the sperm DNA methylome of the Mthfr 677CC and TT mice on a control diet (2 mg folic acid/kg diet) and assess the effects of folic acid supplementation (10 mg/kg diet) on the sperm DNA methylome. Body and reproductive organ weights, testicular sperm counts, and histology were examined. DNA methylation in sperm was assessed using bisulfite pyrosequencing and whole-genome bisulfite sequencing (WGBS). Reproductive parameters and locus-specific imprinted gene methylation were unaffected by genotype or diet. Using WGBS, sperm from 677TT mice had 360 differentially methylated tiles as compared to 677CC mice, predominantly hypomethylation (60% of tiles). Folic acid supplementation mostly caused hypermethylation in sperm of males of both genotypes and was found to partially correct the DNA methylation alterations in sperm associated with the TT genotype. The new mouse model will be useful in understanding the role of MTHFR deficiency in male fertility and in designing folate supplementation regimens for the clinic.
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Affiliation(s)
- Edgar Martínez Duncker Rebolledo
- Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Donovan Chan
- Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Karen E Christensen
- Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | | | - Gareth R Howell
- The Jackson Laboratory, Bar Harbor, ME, USA
- Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA, USA
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME, USA
| | - Rima Rozen
- Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Department of Pediatrics, McGill University, Montreal, QC, Canada
| | - Jacquetta Trasler
- Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Department of Pediatrics, McGill University, Montreal, QC, Canada
- Department of Pharmacology & Therapeutics, Montreal, QC, Canada
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11
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Aracena KA, Lin YL, Luo K, Pacis A, Gona S, Mu Z, Yotova V, Sindeaux R, Pramatarova A, Simon MM, Chen X, Groza C, Lougheed D, Gregoire R, Brownlee D, Boye C, Pique-Regi R, Li Y, He X, Bujold D, Pastinen T, Bourque G, Barreiro LB. Epigenetic variation impacts individual differences in the transcriptional response to influenza infection. Nat Genet 2024; 56:408-419. [PMID: 38424460 DOI: 10.1038/s41588-024-01668-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 01/16/2024] [Indexed: 03/02/2024]
Abstract
Humans display remarkable interindividual variation in their immune response to identical challenges. Yet, our understanding of the genetic and epigenetic factors contributing to such variation remains limited. Here we performed in-depth genetic, epigenetic and transcriptional profiling on primary macrophages derived from individuals of European and African ancestry before and after infection with influenza A virus. We show that baseline epigenetic profiles are strongly predictive of the transcriptional response to influenza A virus across individuals. Quantitative trait locus (QTL) mapping revealed highly coordinated genetic effects on gene regulation, with many cis-acting genetic variants impacting concomitantly gene expression and multiple epigenetic marks. These data reveal that ancestry-associated differences in the epigenetic landscape can be genetically controlled, even more than gene expression. Lastly, among QTL variants that colocalized with immune-disease loci, only 7% were gene expression QTL, while the remaining genetic variants impact epigenetic marks, stressing the importance of considering molecular phenotypes beyond gene expression in disease-focused studies.
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Affiliation(s)
| | - Yen-Lung Lin
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Kaixuan Luo
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Alain Pacis
- Canadian Centre for Computational Genomics, McGill University, Montreal, Quebec, Canada
| | - Saideep Gona
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Zepeng Mu
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Vania Yotova
- Department of Genetics, CHU Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - Renata Sindeaux
- Department of Genetics, CHU Sainte-Justine Research Center, Montreal, Quebec, Canada
| | | | | | - Xun Chen
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
| | - Cristian Groza
- Quantitative Life Sciences, McGill University, Montreal, Quebec, Canada
| | - David Lougheed
- Canadian Centre for Computational Genomics, McGill University, Montreal, Quebec, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Romain Gregoire
- Canadian Centre for Computational Genomics, McGill University, Montreal, Quebec, Canada
| | - David Brownlee
- Canadian Centre for Computational Genomics, McGill University, Montreal, Quebec, Canada
| | - Carly Boye
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA
| | - Roger Pique-Regi
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, USA
| | - Yang Li
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Xin He
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - David Bujold
- Canadian Centre for Computational Genomics, McGill University, Montreal, Quebec, Canada
- McGill Genome Centre, Montreal, Quebec, Canada
| | - Tomi Pastinen
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Genomic Medicine Center, Children's Mercy, Kansas City, MO, USA
| | - Guillaume Bourque
- Canadian Centre for Computational Genomics, McGill University, Montreal, Quebec, Canada.
- McGill Genome Centre, Montreal, Quebec, Canada.
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan.
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.
| | - Luis B Barreiro
- Department of Human Genetics, University of Chicago, Chicago, IL, USA.
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA.
- Committee on Immunology, University of Chicago, Chicago, IL, USA.
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12
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Fournelle D, Mostefai F, Brunet-Ratnasingham E, Poujol R, Grenier JC, Gálvez JH, Pagliuzza A, Levade I, Moreira S, Benlarbi M, Beaudoin-Bussières G, Gendron-Lepage G, Bourassa C, Tauzin A, Grandjean Lapierre S, Chomont N, Finzi A, Kaufmann DE, Craig M, Hussin JG. Intra-Host Evolution Analyses in an Immunosuppressed Patient Supports SARS-CoV-2 Viral Reservoir Hypothesis. Viruses 2024; 16:342. [PMID: 38543708 PMCID: PMC10974702 DOI: 10.3390/v16030342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 02/17/2024] [Accepted: 02/20/2024] [Indexed: 05/23/2024] Open
Abstract
Throughout the SARS-CoV-2 pandemic, several variants of concern (VOCs) have been identified, many of which share recurrent mutations in the spike glycoprotein's receptor-binding domain (RBD). This region coincides with known epitopes and can therefore have an impact on immune escape. Protracted infections in immunosuppressed patients have been hypothesized to lead to an enrichment of such mutations and therefore drive evolution towards VOCs. Here, we present the case of an immunosuppressed patient that developed distinct populations with immune escape mutations throughout the course of their infection. Notably, by investigating the co-occurrence of substitutions on individual sequencing reads in the RBD, we found quasispecies harboring mutations that confer resistance to known monoclonal antibodies (mAbs) such as S:E484K and S:E484A. These mutations were acquired without the patient being treated with mAbs nor convalescent sera and without them developing a detectable immune response to the virus. We also provide additional evidence for a viral reservoir based on intra-host phylogenetics, which led to a viral substrain that evolved elsewhere in the patient's body, colonizing their upper respiratory tract (URT). The presence of SARS-CoV-2 viral reservoirs can shed light on protracted infections interspersed with periods where the virus is undetectable, and potential explanations for long-COVID cases.
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Affiliation(s)
- Dominique Fournelle
- Research Centre Montreal Heart Institute, Montréal, QC H1T 1C8, Canada; (D.F.); (F.M.); (R.P.); (J.-C.G.)
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Fatima Mostefai
- Research Centre Montreal Heart Institute, Montréal, QC H1T 1C8, Canada; (D.F.); (F.M.); (R.P.); (J.-C.G.)
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Elsa Brunet-Ratnasingham
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC H2X 0A9, Canada; (E.B.-R.); (A.P.); (M.B.); (G.B.-B.); (G.G.-L.); (C.B.); (A.T.); (S.G.L.); (N.C.); (D.E.K.)
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Raphaël Poujol
- Research Centre Montreal Heart Institute, Montréal, QC H1T 1C8, Canada; (D.F.); (F.M.); (R.P.); (J.-C.G.)
| | - Jean-Christophe Grenier
- Research Centre Montreal Heart Institute, Montréal, QC H1T 1C8, Canada; (D.F.); (F.M.); (R.P.); (J.-C.G.)
| | - José Héctor Gálvez
- Canadian Centre for Computational Genomics, Montréal, QC H3A 0G1, Canada;
| | - Amélie Pagliuzza
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC H2X 0A9, Canada; (E.B.-R.); (A.P.); (M.B.); (G.B.-B.); (G.G.-L.); (C.B.); (A.T.); (S.G.L.); (N.C.); (D.E.K.)
| | - Inès Levade
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC H9X 3R5, Canada; (I.L.)
| | - Sandrine Moreira
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC H9X 3R5, Canada; (I.L.)
| | - Mehdi Benlarbi
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC H2X 0A9, Canada; (E.B.-R.); (A.P.); (M.B.); (G.B.-B.); (G.G.-L.); (C.B.); (A.T.); (S.G.L.); (N.C.); (D.E.K.)
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Guillaume Beaudoin-Bussières
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC H2X 0A9, Canada; (E.B.-R.); (A.P.); (M.B.); (G.B.-B.); (G.G.-L.); (C.B.); (A.T.); (S.G.L.); (N.C.); (D.E.K.)
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Gabrielle Gendron-Lepage
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC H2X 0A9, Canada; (E.B.-R.); (A.P.); (M.B.); (G.B.-B.); (G.G.-L.); (C.B.); (A.T.); (S.G.L.); (N.C.); (D.E.K.)
| | - Catherine Bourassa
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC H2X 0A9, Canada; (E.B.-R.); (A.P.); (M.B.); (G.B.-B.); (G.G.-L.); (C.B.); (A.T.); (S.G.L.); (N.C.); (D.E.K.)
| | - Alexandra Tauzin
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC H2X 0A9, Canada; (E.B.-R.); (A.P.); (M.B.); (G.B.-B.); (G.G.-L.); (C.B.); (A.T.); (S.G.L.); (N.C.); (D.E.K.)
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Simon Grandjean Lapierre
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC H2X 0A9, Canada; (E.B.-R.); (A.P.); (M.B.); (G.B.-B.); (G.G.-L.); (C.B.); (A.T.); (S.G.L.); (N.C.); (D.E.K.)
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Nicolas Chomont
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC H2X 0A9, Canada; (E.B.-R.); (A.P.); (M.B.); (G.B.-B.); (G.G.-L.); (C.B.); (A.T.); (S.G.L.); (N.C.); (D.E.K.)
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Andrés Finzi
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC H2X 0A9, Canada; (E.B.-R.); (A.P.); (M.B.); (G.B.-B.); (G.G.-L.); (C.B.); (A.T.); (S.G.L.); (N.C.); (D.E.K.)
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Daniel E. Kaufmann
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC H2X 0A9, Canada; (E.B.-R.); (A.P.); (M.B.); (G.B.-B.); (G.G.-L.); (C.B.); (A.T.); (S.G.L.); (N.C.); (D.E.K.)
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC H3C 3J7, Canada
- Centre Hospitalier de l’Université de Montréal (CHUM), Montréal, QC H2X 0C1, Canada
- Division of Infectious Diseases, Department of Medicine, University Hospital and University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Morgan Craig
- Research Centre, Centre Hospitalier UniversitaireSainte-Justine, Montréal, QC H3T 1C5, Canada;
- Département de Mathématiques et de Statistique, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Julie G. Hussin
- Research Centre Montreal Heart Institute, Montréal, QC H1T 1C8, Canada; (D.F.); (F.M.); (R.P.); (J.-C.G.)
- Département de Médecine, Université de Montréal, Montréal, QC H3C 3J7, Canada
- Mila-Quebec AI Institute, Montréal, QC H2S 3H1, Canada
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13
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Pomerleau M, Charron-Lamoureux V, Léonard L, Grenier F, Rodrigue S, Beauregard PB. Adaptive laboratory evolution reveals regulators involved in repressing biofilm development as key players in Bacillus subtilis root colonization. mSystems 2024; 9:e0084323. [PMID: 38206029 PMCID: PMC10878085 DOI: 10.1128/msystems.00843-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 12/04/2023] [Indexed: 01/12/2024] Open
Abstract
Root-associated microorganisms play an important role in plant health, such as plant growth-promoting rhizobacteria (PGPR) from the Bacillus and Pseudomonas genera. Although bacterial consortia including these two genera would represent a promising avenue to efficient biofertilizer formulation, we observed that Bacillus subtilis root colonization is decreased by the presence of Pseudomonas fluorescens and Pseudomonas protegens. To determine if B. subtilis can adapt to the inhibitory effect of Pseudomonas on roots, we conducted adaptative laboratory evolution experiments with B. subtilis in mono-association or co-cultured with P. fluorescens on tomato plant roots. Evolved isolates with various colony morphology and stronger colonization capacity of both tomato plant and Arabidopsis thaliana roots emerged rapidly from the two evolution experiments. Certain evolved isolates also had better fitness on the root in the presence of other Pseudomonas species. In all independent lineages, whole-genome resequencing revealed non-synonymous mutations in genes ywcC or sinR encoding regulators involved in repressing biofilm development, suggesting their involvement in enhanced root colonization. These findings provide insights into the molecular mechanisms underlying B. subtilis adaptation to root colonization and highlight the potential of directed evolution to enhance the beneficial traits of PGPR.IMPORTANCEIn this study, we aimed to enhance the abilities of the plant-beneficial bacterium Bacillus subtilis to colonize plant roots in the presence of competing Pseudomonas bacteria. To achieve this, we conducted adaptive laboratory experiments, allowing Bacillus to evolve in a defined environment. We successfully obtained strains of Bacillus that were more effective at colonizing plant roots than the ancestor strain. To identify the genetic changes driving this improvement, we sequenced the genomes of these evolved strains. Interestingly, mutations that facilitated the formation of robust biofilms on roots were predominant. Many of these evolved Bacillus isolates also displayed the remarkable ability to outcompete Pseudomonas species. Our research sheds light on the mutational paths selected in Bacillus subtilis to thrive in root environments and offers exciting prospects for improving beneficial traits in plant growth-promoting microorganisms. Ultimately, this could pave the way for the development of more effective biofertilizers and sustainable agricultural practices.
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Affiliation(s)
- Maude Pomerleau
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | | | - Lucille Léonard
- Département de Génie Biologique, Université de Technologie de Compiègne, Compiègne, France
| | - Frédéric Grenier
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Sébastien Rodrigue
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Pascale B. Beauregard
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada
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14
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Dorion MF, Yaqubi M, Senkevich K, Kieran NW, MacDonald A, Chen CXQ, Luo W, Wallis A, Shlaifer I, Hall JA, Dudley RWR, Glass IA, Stratton JA, Fon EA, Bartels T, Antel JP, Gan-or Z, Durcan TM, Healy LM. MerTK is a mediator of alpha-synuclein fibril uptake by human microglia. Brain 2024; 147:427-443. [PMID: 37671615 PMCID: PMC10834256 DOI: 10.1093/brain/awad298] [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: 03/08/2023] [Revised: 07/26/2023] [Accepted: 08/29/2023] [Indexed: 09/07/2023] Open
Abstract
Mer tyrosine kinase (MerTK) is a receptor tyrosine kinase that mediates non-inflammatory, homeostatic phagocytosis of diverse types of cellular debris. Highly expressed on the surface of microglial cells, MerTK is of importance in brain development, homeostasis, plasticity and disease. Yet, involvement of this receptor in the clearance of protein aggregates that accumulate with ageing and in neurodegenerative diseases has yet to be defined. The current study explored the function of MerTK in the microglial uptake of alpha-synuclein fibrils which play a causative role in the pathobiology of synucleinopathies. Using human primary and induced pluripotent stem cell-derived microglia, the MerTK-dependence of alpha-synuclein fibril internalization was investigated in vitro. Relevance of this pathway in synucleinopathies was assessed through burden analysis of MERTK variants and analysis of MerTK expression in patient-derived cells and tissues. Pharmacological inhibition of MerTK and siRNA-mediated MERTK knockdown both caused a decreased rate of alpha-synuclein fibril internalization by human microglia. Consistent with the non-inflammatory nature of MerTK-mediated phagocytosis, alpha-synuclein fibril internalization was not observed to induce secretion of pro-inflammatory cytokines such as IL-6 or TNF, and downmodulated IL-1β secretion from microglia. Burden analysis in two independent patient cohorts revealed a significant association between rare functionally deleterious MERTK variants and Parkinson's disease in one of the cohorts (P = 0.002). Despite a small upregulation in MERTK mRNA expression in nigral microglia from Parkinson's disease/Lewy body dementia patients compared to those from non-neurological control donors in a single-nuclei RNA-sequencing dataset (P = 5.08 × 10-21), no significant upregulation in MerTK protein expression was observed in human cortex and substantia nigra lysates from Lewy body dementia patients compared to controls. Taken together, our findings define a novel role for MerTK in mediating the uptake of alpha-synuclein fibrils by human microglia, with possible involvement in limiting alpha-synuclein spread in synucleinopathies such as Parkinson's disease. Upregulation of this pathway in synucleinopathies could have therapeutic values in enhancing alpha-synuclein fibril clearance in the brain.
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Affiliation(s)
- Marie-France Dorion
- Early Drug Discovery Unit, Montreal Neurological Institute-Hospital, McGill University, Montreal H3A 2B4, Canada
- Neuroimmunology Unit, Montreal Neurological Institute-Hospital, McGill University, Montreal H3A 2B4, Canada
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal H3A 2B4, Canada
| | - Moein Yaqubi
- Neuroimmunology Unit, Montreal Neurological Institute-Hospital, McGill University, Montreal H3A 2B4, Canada
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal H3A 2B4, Canada
| | - Konstantin Senkevich
- McGill Parkinson Program and Neurodegenerative Diseases Group, Montreal Neurological Institute-Hospital, McGill University, Montreal H3A 2B4, Canada
- Department of Human Genetics, McGill University, Montreal H3A 0C7, Canada
| | - Nicholas W Kieran
- Neuroimmunology Unit, Montreal Neurological Institute-Hospital, McGill University, Montreal H3A 2B4, Canada
| | - Adam MacDonald
- Neuroimmunology Unit, Montreal Neurological Institute-Hospital, McGill University, Montreal H3A 2B4, Canada
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal H3A 2B4, Canada
| | - Carol X Q Chen
- Early Drug Discovery Unit, Montreal Neurological Institute-Hospital, McGill University, Montreal H3A 2B4, Canada
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal H3A 2B4, Canada
| | - Wen Luo
- Early Drug Discovery Unit, Montreal Neurological Institute-Hospital, McGill University, Montreal H3A 2B4, Canada
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal H3A 2B4, Canada
| | - Amber Wallis
- UK Dementia Research Institute, University College London, London WC1E 6BT, UK
| | - Irina Shlaifer
- Early Drug Discovery Unit, Montreal Neurological Institute-Hospital, McGill University, Montreal H3A 2B4, Canada
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal H3A 2B4, Canada
| | - Jeffery A Hall
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal H3A 2B4, Canada
| | - Roy W R Dudley
- Department of Pediatric Surgery, Division of Neurosurgery, Montreal Children's Hospital, McGill University Health Centers, Montreal H4A 3J1, Canada
| | - Ian A Glass
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | | | - Jo Anne Stratton
- Neuroimmunology Unit, Montreal Neurological Institute-Hospital, McGill University, Montreal H3A 2B4, Canada
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal H3A 2B4, Canada
| | - Edward A Fon
- Early Drug Discovery Unit, Montreal Neurological Institute-Hospital, McGill University, Montreal H3A 2B4, Canada
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal H3A 2B4, Canada
- McGill Parkinson Program and Neurodegenerative Diseases Group, Montreal Neurological Institute-Hospital, McGill University, Montreal H3A 2B4, Canada
| | - Tim Bartels
- UK Dementia Research Institute, University College London, London WC1E 6BT, UK
| | - Jack P Antel
- Neuroimmunology Unit, Montreal Neurological Institute-Hospital, McGill University, Montreal H3A 2B4, Canada
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal H3A 2B4, Canada
| | - Ziv Gan-or
- McGill Parkinson Program and Neurodegenerative Diseases Group, Montreal Neurological Institute-Hospital, McGill University, Montreal H3A 2B4, Canada
- Department of Human Genetics, McGill University, Montreal H3A 0C7, Canada
| | - Thomas M Durcan
- Early Drug Discovery Unit, Montreal Neurological Institute-Hospital, McGill University, Montreal H3A 2B4, Canada
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal H3A 2B4, Canada
| | - Luke M Healy
- Neuroimmunology Unit, Montreal Neurological Institute-Hospital, McGill University, Montreal H3A 2B4, Canada
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal H3A 2B4, Canada
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15
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Legault LM, Breton-Larrivée M, Langford-Avelar A, Lemieux A, McGraw S. Sex-based disparities in DNA methylation and gene expression in late-gestation mouse placentas. Biol Sex Differ 2024; 15:2. [PMID: 38183126 PMCID: PMC10770955 DOI: 10.1186/s13293-023-00577-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 12/18/2023] [Indexed: 01/07/2024] Open
Abstract
BACKGROUND The placenta is vital for fetal development and its contributions to various developmental issues, such as pregnancy complications, fetal growth restriction, and maternal exposure, have been extensively studied in mice. The placenta forms mainly from fetal tissue and therefore has the same biological sex as the fetus it supports. Extensive research has delved into the placenta's involvement in pregnancy complications and future offspring development, with a notable emphasis on exploring sex-specific disparities. However, despite these investigations, sex-based disparities in epigenetic (e.g., DNA methylation) and transcriptomic features of the late-gestation mouse placenta remain largely unknown. METHODS We collected male and female mouse placentas at late gestation (E18.5, n = 3/sex) and performed next-generation sequencing to identify genome-wide sex differences in transcription and DNA methylation. RESULTS Our comparison between male and female revealed 358 differentially expressed genes (DEGs) on autosomes, which were associated with signaling pathways involved in transmembrane transport and the responses to viruses and external stimuli. X chromosome DEGs (n = 39) were associated with different pathways, including those regulating chromatin modification and small GTPase-mediated signal transduction. Differentially methylated regions (DMRs) were more common on the X chromosomes (n = 3756) than on autosomes (n = 1705). Interestingly, while most X chromosome DMRs had higher DNA methylation levels in female placentas and tended to be included in CpG dinucleotide-rich regions, 73% of autosomal DMRs had higher methylation levels in male placentas and were distant from CpG-rich regions. Several DEGs were correlated with DMRs. A subset of the DMRs present in late-stage placentas were already established in mid-gestation (E10.5) placentas (n = 348 DMRs on X chromosome and 19 DMRs on autosomes), while others were acquired later in placental development. CONCLUSION Our study provides comprehensive lists of DEGs and DMRs between male and female that collectively cause profound differences in the DNA methylation and gene expression profiles of late-gestation mouse placentas. Our results demonstrate the importance of incorporating sex-specific analyses into epigenetic and transcription studies to enhance the accuracy and comprehensiveness of their conclusions and help address the significant knowledge gap regarding how sex differences influence placental function.
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Affiliation(s)
- Lisa-Marie Legault
- CHU Ste-Justine Research Center, 3175 Chemin de La Côte-Sainte-Catherine, Montréal, QC, H3T 1C5, Canada
- Department of Biochemistry and Molecular Medicine, Université de Montréal, 2900 Boulevard Edouard‑Montpetit, Montréal, QC, H3T 1J4, Canada
| | - Mélanie Breton-Larrivée
- CHU Ste-Justine Research Center, 3175 Chemin de La Côte-Sainte-Catherine, Montréal, QC, H3T 1C5, Canada
- Department of Biochemistry and Molecular Medicine, Université de Montréal, 2900 Boulevard Edouard‑Montpetit, Montréal, QC, H3T 1J4, Canada
| | - Alexandra Langford-Avelar
- CHU Ste-Justine Research Center, 3175 Chemin de La Côte-Sainte-Catherine, Montréal, QC, H3T 1C5, Canada
- Department of Biochemistry and Molecular Medicine, Université de Montréal, 2900 Boulevard Edouard‑Montpetit, Montréal, QC, H3T 1J4, Canada
| | - Anthony Lemieux
- CHU Ste-Justine Research Center, 3175 Chemin de La Côte-Sainte-Catherine, Montréal, QC, H3T 1C5, Canada
| | - Serge McGraw
- CHU Ste-Justine Research Center, 3175 Chemin de La Côte-Sainte-Catherine, Montréal, QC, H3T 1C5, Canada.
- Department of Biochemistry and Molecular Medicine, Université de Montréal, 2900 Boulevard Edouard‑Montpetit, Montréal, QC, H3T 1J4, Canada.
- Department of Obstetrics and Gynecology, Université de Montréal, 2900 Boulevard Edouard‑Montpetit, Montréal, QC, H3T 1J4, Canada.
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16
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Lismer A, Shao X, Dumargne MC, Lafleur C, Lambrot R, Chan D, Toft G, Bonde JP, MacFarlane AJ, Bornman R, Aneck-Hahn N, Patrick S, Bailey JM, de Jager C, Dumeaux V, Trasler JM, Kimmins S. The Association between Long-Term DDT or DDE Exposures and an Altered Sperm Epigenome-a Cross-Sectional Study of Greenlandic Inuit and South African VhaVenda Men. ENVIRONMENTAL HEALTH PERSPECTIVES 2024; 132:17008. [PMID: 38294233 PMCID: PMC10829569 DOI: 10.1289/ehp12013] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/26/2023] [Accepted: 12/20/2023] [Indexed: 02/01/2024]
Abstract
BACKGROUND The organochlorine dichlorodiphenyltrichloroethane (DDT) is banned worldwide owing to its negative health effects. It is exceptionally used as an insecticide for malaria control. Exposure occurs in regions where DDT is applied, as well as in the Arctic, where its endocrine disrupting metabolite, p , p ' -dichlorodiphenyldichloroethylene (p , p ' -DDE) accumulates in marine mammals and fish. DDT and p , p ' -DDE exposures are linked to birth defects, infertility, cancer, and neurodevelopmental delays. Of particular concern is the potential of DDT use to impact the health of generations to come via the heritable sperm epigenome. OBJECTIVES The objective of this study was to assess the sperm epigenome in relation to p , p ' -DDE serum levels between geographically diverse populations. METHODS In the Limpopo Province of South Africa, we recruited 247 VhaVenda South African men and selected 50 paired blood serum and semen samples, and 47 Greenlandic Inuit blood and semen paired samples were selected from a total of 193 samples from the biobank of the INUENDO cohort, an EU Fifth Framework Programme Research and Development project. Sample selection was based on obtaining a range of p , p ' -DDE serum levels (mean = 870.734 ± 134.030 ng / mL ). We assessed the sperm epigenome in relation to serum p , p ' -DDE levels using MethylC-Capture-sequencing (MCC-seq) and chromatin immunoprecipitation followed by sequencing (ChIP-seq). We identified genomic regions with altered DNA methylation (DNAme) and differential enrichment of histone H3 lysine 4 trimethylation (H3K4me3) in sperm. RESULTS Differences in DNAme and H3K4me3 enrichment were identified at transposable elements and regulatory regions involved in fertility, disease, development, and neurofunction. A subset of regions with sperm DNAme and H3K4me3 that differed between exposure groups was predicted to persist in the preimplantation embryo and to be associated with embryonic gene expression. DISCUSSION These findings suggest that DDT and p , p ' -DDE exposure impacts the sperm epigenome in a dose-response-like manner and may negatively impact the health of future generations through epigenetic mechanisms. Confounding factors, such as other environmental exposures, genetic diversity, and selection bias, cannot be ruled out. https://doi.org/10.1289/EHP12013.
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Affiliation(s)
- Ariane Lismer
- Department of Pharmacology and Therapeutics, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada
| | - Xiaojian Shao
- Digital Technologies Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Marie-Charlotte Dumargne
- Department of Animal Science, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Quebec, Canada
| | - Christine Lafleur
- University of Montreal Hospital Research Centre, Montreal, Quebec, Canada
| | - Romain Lambrot
- University of Montreal Hospital Research Centre, Montreal, Quebec, Canada
| | - Donovan Chan
- Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Gunnar Toft
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark
| | - Jens Peter Bonde
- Department of Occupational and Environmental Medicine, Bispebjerg University Hospital, Copenhagen, Denmark
- Institute of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Amanda J. MacFarlane
- Agriculture Food and Nutrition Evidence Center, Texas A&M University, Fort Worth, Texas, USA
| | - Riana Bornman
- Environmental Chemical Pollution and Health Research Unit, School of Health Systems and Public Health, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
- University of Pretoria Institute for Sustainable Malaria Control, School of Health Systems and Public Health, Faculty of Health Sciences, University of Pretoria, South Africa
| | - Natalie Aneck-Hahn
- University of Pretoria Institute for Sustainable Malaria Control, School of Health Systems and Public Health, Faculty of Health Sciences, University of Pretoria, South Africa
| | - Sean Patrick
- University of Pretoria Institute for Sustainable Malaria Control, School of Health Systems and Public Health, Faculty of Health Sciences, University of Pretoria, South Africa
| | - Janice M. Bailey
- Research Centre on Reproduction and Intergenerational Health, Department of Animal Sciences, Université Laval, Quebec, Quebec, Canada
| | - Christiaan de Jager
- Environmental Chemical Pollution and Health Research Unit, School of Health Systems and Public Health, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
- University of Pretoria Institute for Sustainable Malaria Control, School of Health Systems and Public Health, Faculty of Health Sciences, University of Pretoria, South Africa
| | - Vanessa Dumeaux
- Department of Anatomy and Cell Biology, Western University, London, Ontario, Canada
- Department of Oncology, Western University, London, Ontario, Canada
| | - Jacquetta M. Trasler
- Department of Pharmacology and Therapeutics, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada
- Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
- Department of Human Genetics, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
- Department of Pediatrics, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - Sarah Kimmins
- Department of Pharmacology and Therapeutics, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada
- University of Montreal Hospital Research Centre, Montreal, Quebec, Canada
- Department of Pathology and Cell Biology, Faculty of Medicine, University of Montreal, Quebec, Canada
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17
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Berthold M, Albrecht M, Campbell DA, Omar NM. Draft genomes of 3 cyanobacteria strains and 17 co-habiting proteobacteria assembled from metagenomes. Microbiol Resour Announc 2023; 12:e0046023. [PMID: 37943043 PMCID: PMC10720521 DOI: 10.1128/mra.00460-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 10/12/2023] [Indexed: 11/10/2023] Open
Abstract
Cyanobium and Synechococcus are prominent, globally distributed cyanobacteria genera with ecological significance. Here, we report the genomes of the marine Synechococcus sp. CCMP836 and two strains of Cyanobium (CZS25K and CZS48M) along with the genomes of 17 co-occurring proteobacteria. These genomes will improve the strain-specific ecological positions.
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Affiliation(s)
| | - Martin Albrecht
- Institute of Biological Sciences, University of Rostock, Rostock, Germany
| | | | - Naaman M. Omar
- Department of Biology, Mount Allison University, Sackville, Canada
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18
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Apostolides M, Li M, Arnoldo A, Ku M, Husić M, Ramani AK, Brudno M, Turinsky A, Hawkins C, Siddaway R. Clinical Implementation of MetaFusion for Accurate Cancer-Driving Fusion Detection from RNA Sequencing. J Mol Diagn 2023; 25:921-931. [PMID: 37748705 DOI: 10.1016/j.jmoldx.2023.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 08/15/2023] [Accepted: 09/07/2023] [Indexed: 09/27/2023] Open
Abstract
Oncogenic fusion genes may be identified from next-generation sequencing data, typically RNA-sequencing. However, in a clinical setting, identifying these alterations is challenging against a background of nonrelevant fusion calls that reduce workflow precision and specificity. Furthermore, although numerous algorithms have been developed to detect fusions in RNA-sequencing, there are variations in their individual sensitivities. Here this problem was addressed by introducing MetaFusion into clinical use. Its utility was illustrated when applied to both whole-transcriptome and targeted sequencing data sets. MetaFusion combines ensemble fusion calls from eight individual fusion-calling algorithms with practice-informed identification of gene fusions that are known to be clinically relevant. In doing so, it allows oncogenic fusions to be identified with near-perfect sensitivity and high precision and specificity, significantly outperforming the individual fusion callers it uses as well as existing clinical-grade software. MetaFusion enhances clinical yield over existing methods and is able to identify fusions that have patient relevance for the purposes of diagnosis, prognosis, and treatment.
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Affiliation(s)
- Michael Apostolides
- Centre for Computational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Michael Li
- Centre for Computational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Anthony Arnoldo
- Division of Pathology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Michelle Ku
- The Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Ontario, Canada; Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Mia Husić
- Centre for Computational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Arun K Ramani
- Centre for Computational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Michael Brudno
- Centre for Computational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada; Department of Computer Science, University of Toronto, Toronto, Ontario, Canada; University Health Network, Toronto, Ontario, Canada
| | - Andrei Turinsky
- Centre for Computational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Cynthia Hawkins
- Division of Pathology, Hospital for Sick Children, Toronto, Ontario, Canada; The Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Ontario, Canada; Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.
| | - Robert Siddaway
- Division of Pathology, Hospital for Sick Children, Toronto, Ontario, Canada; The Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Ontario, Canada; Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada.
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19
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Beaumont RN, Flatley C, Vaudel M, Wu X, Chen J, Moen GH, Skotte L, Helgeland Ø, Solé-Navais P, Banasik K, Albiñana C, Ronkainen J, Fadista J, Stinson SE, Trajanoska K, Wang CA, Westergaard D, Srinivasan S, Sánchez-Soriano C, Bilbao JR, Allard C, Groleau M, Kuulasmaa T, Leirer DJ, White F, Jacques PÉ, Cheng H, Hao K, Andreassen OA, Åsvold BO, Atalay M, Bhatta L, Bouchard L, Brumpton BM, Brunak S, Bybjerg-Grauholm J, Ebbing C, Elliott P, Engelbrechtsen L, Erikstrup C, Estarlich M, Franks S, Gaillard R, Geller F, Grove J, Hougaard DM, Kajantie E, Morgen CS, Nohr EA, Nyegaard M, Palmer CNA, Pedersen OB, Rivadeneira F, Sebert S, Shields BM, Stoltenberg C, Surakka I, Thørner LW, Ullum H, Vaarasmaki M, Vilhjalmsson BJ, Willer CJ, Lakka TA, Gybel-Brask D, Bustamante M, Hansen T, Pearson ER, Reynolds RM, Ostrowski SR, Pennell CE, Jaddoe VWV, Felix JF, Hattersley AT, Melbye M, Lawlor DA, Hveem K, Werge T, Nielsen HS, Magnus P, Evans DM, Jacobsson B, Järvelin MR, Zhang G, Hivert MF, Johansson S, Freathy RM, Feenstra B, Njølstad PR. Genome-wide association study of placental weight identifies distinct and shared genetic influences between placental and fetal growth. Nat Genet 2023; 55:1807-1819. [PMID: 37798380 PMCID: PMC10632150 DOI: 10.1038/s41588-023-01520-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 08/31/2023] [Indexed: 10/07/2023]
Abstract
A well-functioning placenta is essential for fetal and maternal health throughout pregnancy. Using placental weight as a proxy for placental growth, we report genome-wide association analyses in the fetal (n = 65,405), maternal (n = 61,228) and paternal (n = 52,392) genomes, yielding 40 independent association signals. Twenty-six signals are classified as fetal, four maternal and three fetal and maternal. A maternal parent-of-origin effect is seen near KCNQ1. Genetic correlation and colocalization analyses reveal overlap with birth weight genetics, but 12 loci are classified as predominantly or only affecting placental weight, with connections to placental development and morphology, and transport of antibodies and amino acids. Mendelian randomization analyses indicate that fetal genetically mediated higher placental weight is causally associated with preeclampsia risk and shorter gestational duration. Moreover, these analyses support the role of fetal insulin in regulating placental weight, providing a key link between fetal and placental growth.
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Affiliation(s)
- Robin N Beaumont
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Christopher Flatley
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Genetics and Bioinformatics, Health Data and Digitalization, Norwegian Institute of Public Health, Oslo, Norway
| | - Marc Vaudel
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Xiaoping Wu
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Jing Chen
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Gunn-Helen Moen
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Frazer Institute, The University of Queensland, Brisbane, Queensland, Australia
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Line Skotte
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Øyvind Helgeland
- Department of Genetics and Bioinformatics, Health Data and Digitalization, Norwegian Institute of Public Health, Oslo, Norway
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Pol Solé-Navais
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Karina Banasik
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Clara Albiñana
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
| | | | - João Fadista
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
- Department of Clinical Sciences, Lund University Diabetes Centre, Malmö, Sweden
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Sara Elizabeth Stinson
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Katerina Trajanoska
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
| | - Carol A Wang
- School of Medicine and Public Health, College of Medicine, Public Health and Wellbeing, The University of Newcastle, Newcastle, New South Wales, Australia
- Hunter Medical Research Institute, New Lambton Heights, Newcastle, New South Wales, Australia
| | - David Westergaard
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
- Department of Obstetrics and Gynecology, Copenhagen University Hospital, Hvidovre, Denmark
- Methods and Analysis, Statistics Denmark, Copenhagen, Denmark
| | - Sundararajan Srinivasan
- Division of Population Health and Genomics, School of Medicine, University of Dundee, Dundee, UK
| | | | - Jose Ramon Bilbao
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain
- Biobizkaia Health Research Institute, Barakaldo, Spain
- Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Barcelona, Spain
| | - Catherine Allard
- Centre de recherche du Centre Hospitalier de l'Universite de Sherbrooke, Sherbrooke, Québec, Canada
| | - Marika Groleau
- Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Teemu Kuulasmaa
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio Campus, Kuopio, Finland
| | - Daniel J Leirer
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Frédérique White
- Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Pierre-Étienne Jacques
- Centre de recherche du Centre Hospitalier de l'Universite de Sherbrooke, Sherbrooke, Québec, Canada
- Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Haoxiang Cheng
- Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Ke Hao
- Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Ole A Andreassen
- NORMENT Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Bjørn Olav Åsvold
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- HUNT Research Centre, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Levanger, Norway
- Department of Endocrinology, Clinic of Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Mustafa Atalay
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio Campus, Kuopio, Finland
| | - Laxmi Bhatta
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
| | - Luigi Bouchard
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada
- Clinical Department of Laboratory Medicine, Centre intégré universitaire de santé et de services sociaux (CIUSSS) du Saguenay-Lac-St-Jean-Hôpital Universitaire de Chicoutimi, Saguenay, Québec, Canada
| | - Ben Michael Brumpton
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- HUNT Research Centre, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Levanger, Norway
- Clinic of Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Jonas Bybjerg-Grauholm
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
| | - Cathrine Ebbing
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Gynecology and Obstetrics, Haukeland University Hospital, Bergen, Norway
| | - Paul Elliott
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Line Engelbrechtsen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Obstetrics and Gynecology, Herlev Hospital, Herlev, Denmark
| | - Christian Erikstrup
- Department Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
- Department Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Marisa Estarlich
- Faculty of Nursing and Chiropody, Universitat de València, C/Menendez Pelayo, Valencia, Spain
- Epidemiology and Environmental Health Joint Research Unit, Foundation for the Promotion of Health and Biomedical Research in the Valencian Region, FISABIO-Public Health, FISABIO-Universitat Jaume I-Universitat de València, Valencia, Spain
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Stephen Franks
- Institute of Reproductive and Developmental Biology, Imperial College London, London, UK
| | - Romy Gaillard
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Frank Geller
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Jakob Grove
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Department of Biomedicine-Human Genetics and the iSEQ Center, Aarhus University, Aarhus, Denmark
- Center for Genomics and Personalized Medicine, Aarhus, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - David M Hougaard
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
| | - Eero Kajantie
- Research Unit of Clinical Medicine, Medical Research Center, University of Oulu, Oulu, Finland
- Population Health Unit, Finnish Institute for Health and Welfare, Helsinki and Oulu, Oulu, Finland
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Camilla S Morgen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- National Institute of Public Health, University of Southern Denmark, Copenhagen, Denmark
| | - Ellen A Nohr
- Institute of Clinical research, University of Southern Denmark, Odense, Denmark
| | - Mette Nyegaard
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Colin N A Palmer
- Division of Population Health and Genomics, School of Medicine, University of Dundee, Dundee, UK
| | - Ole Birger Pedersen
- Department of Clinical Immunology, Zealand University Hospital, Køge, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Fernando Rivadeneira
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Sylvain Sebert
- Research Unit of Population Health, University of Oulu, Oulu, Finland
| | - Beverley M Shields
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Camilla Stoltenberg
- Norwegian Institute of Public Health, Oslo, Norway
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Ida Surakka
- Department of Internal Medicine, Division of Cardiology, University of Michigan, Ann Arbor, MI, USA
| | - Lise Wegner Thørner
- Department of Clinical Immunology, Copenhagen University Hospital-Rigshospitalet, Copenhagen, Denmark
| | | | - Marja Vaarasmaki
- Research Unit of Clinical Medicine, Medical Research Center, University of Oulu, Oulu, Finland
- Department of Obstetrics and Gynaecology, Oulu University Hospital, Oulu, Finland
| | - Bjarni J Vilhjalmsson
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Cristen J Willer
- Department of Internal Medicine, Division of Cardiology, University of Michigan, Ann Arbor, MI, USA
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Timo A Lakka
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio Campus, Kuopio, Finland
- Department of Clinical Physiology and Nuclear Medicine, Kuopio University Hospital, Kuopio, Finland
- Foundation for Research in Health Exercise and Nutrition, Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
| | - Dorte Gybel-Brask
- Psychotherapeutic Outpatient Clinic, Mental Health Services, Capital Region, Copenhagen, Denmark
| | - Mariona Bustamante
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Madrid, Spain
- ISGlobal, Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ewan R Pearson
- Division of Population Health and Genomics, School of Medicine, University of Dundee, Dundee, UK
| | - Rebecca M Reynolds
- Centre for Cardiovascular Science, The University of Edinburgh, Edinburgh, UK
| | - Sisse R Ostrowski
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Immunology, Copenhagen University Hospital-Rigshospitalet, Copenhagen, Denmark
| | - Craig E Pennell
- School of Medicine and Public Health, College of Medicine, Public Health and Wellbeing, The University of Newcastle, Newcastle, New South Wales, Australia
- Hunter Medical Research Institute, New Lambton Heights, Newcastle, New South Wales, Australia
| | - Vincent W V Jaddoe
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Janine F Felix
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Andrew T Hattersley
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Mads Melbye
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Danish Cancer Institute, Copenhagen, Denmark
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Deborah A Lawlor
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Kristian Hveem
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- HUNT Research Centre, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Levanger, Norway
| | - Thomas Werge
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, Copenhagen, Denmark
- Lundbeck Center for Geogenetics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Henriette Svarre Nielsen
- Department of Obstetrics and Gynecology, Copenhagen University Hospital, Hvidovre, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Per Magnus
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - David M Evans
- Frazer Institute, The University of Queensland, Brisbane, Queensland, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Bo Jacobsson
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Genetics and Bioinformatics, Health Data and Digitalization, Norwegian Institute of Public Health, Oslo, Norway
| | - Marjo-Riitta Järvelin
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
- Center for Life Course Health Research, University of Oulu, Oulu, Finland
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
- Unit of Primary Health Care, Oulu University Hospital, OYS, Oulu, Finland
| | - Ge Zhang
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- March of Dimes Prematurity Research Center Ohio Collaborative, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Marie-France Hivert
- Department of Population Medicine, Harvard Medical School, Harvard Pilgrim Health Care Institute, Boston, MA, USA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Stefan Johansson
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway.
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway.
| | - Rachel M Freathy
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK.
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK.
| | - Bjarke Feenstra
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark.
- Department of Clinical Immunology, Copenhagen University Hospital-Rigshospitalet, Copenhagen, Denmark.
| | - Pål R Njølstad
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway.
- Children and Youth Clinic, Haukeland University Hospital, Bergen, Norway.
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20
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Hooker JC, Smith M, Zapata G, Charette M, Luckert D, Mohr RM, Daba KA, Warkentin TD, Hadinezhad M, Barlow B, Hou A, Lefebvre F, Golshani A, Cober ER, Samanfar B. Differential gene expression provides leads to environmentally regulated soybean seed protein content. FRONTIERS IN PLANT SCIENCE 2023; 14:1260393. [PMID: 37790790 PMCID: PMC10544915 DOI: 10.3389/fpls.2023.1260393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 08/23/2023] [Indexed: 10/05/2023]
Abstract
Soybean is an important global source of plant-based protein. A persistent trend has been observed over the past two decades that soybeans grown in western Canada have lower seed protein content than soybeans grown in eastern Canada. In this study, 10 soybean genotypes ranging in average seed protein content were grown in an eastern location (control) and three western locations (experimental) in Canada. Seed protein and oil contents were measured for all lines in each location. RNA-sequencing and differential gene expression analysis were used to identify differentially expressed genes that may account for relatively low protein content in western-grown soybeans. Differentially expressed genes were enriched for ontologies and pathways that included amino acid biosynthesis, circadian rhythm, starch metabolism, and lipid biosynthesis. Gene ontology, pathway mapping, and quantitative trait locus (QTL) mapping collectively provide a close inspection of mechanisms influencing nitrogen assimilation and amino acid biosynthesis between soybeans grown in the East and West. It was found that western-grown soybeans had persistent upregulation of asparaginase (an asparagine hydrolase) and persistent downregulation of asparagine synthetase across 30 individual differential expression datasets. This specific difference in asparagine metabolism between growing environments is almost certainly related to the observed differences in seed protein content because of the positive correlation between seed protein content at maturity and free asparagine in the developing seed. These results provided pointed information on seed protein-related genes influenced by environment. This information is valuable for breeding programs and genetic engineering of geographically optimized soybeans.
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Affiliation(s)
- Julia C. Hooker
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON, Canada
| | - Myron Smith
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON, Canada
| | - Gerardo Zapata
- Canadian Centre for Computational Genomics, Montréal, QC, Canada
| | - Martin Charette
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Doris Luckert
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Ramona M. Mohr
- Brandon Research Centre, Agriculture and Agri-Food Canada, Brandon, MB, Canada
| | - Ketema A. Daba
- Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | | | - Mehri Hadinezhad
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Brent Barlow
- Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Anfu Hou
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, Canada
| | | | - Ashkan Golshani
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON, Canada
| | - Elroy R. Cober
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Bahram Samanfar
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON, Canada
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21
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Liao J, Song S, Gusscott S, Fu Z, VanderKolk I, Busscher BM, Lau KH, Brind’Amour J, Szabó PE. Establishment of paternal methylation imprint at the H19/Igf2 imprinting control region. SCIENCE ADVANCES 2023; 9:eadi2050. [PMID: 37672574 PMCID: PMC10482337 DOI: 10.1126/sciadv.adi2050] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 08/02/2023] [Indexed: 09/08/2023]
Abstract
The insulator model explains the workings of the H19 and Igf2 imprinted domain in the soma, where insulation of the Igf2 promoter from its enhancers occurs by CTCF in the maternally inherited unmethylated chromosome but not the paternally inherited methylated allele. The molecular mechanism that targets paternal methylation imprint establishment to the imprinting control region (ICR) in the male germline is unknown. We tested the function of prospermatogonia-specific broad low-level transcription in this process using mouse genetics. Paternal imprint establishment was abnormal when transcription was stopped at the entry point to the ICR. The germline epimutation persisted into the paternal allele of the soma, resulting in reduced Igf2 in fetal organs and reduced fetal growth, consistent with the insulator model and insulin-like growth factor 2 (IGF2)'s role as fetal growth factor. These results collectively support the role of broad low-level transcription through the H19/Igf2 ICR in the establishment of its paternal methylation imprint in the male germ line, with implications for Silver-Russell syndrome.
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Affiliation(s)
- Ji Liao
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Sangmin Song
- Division of Molecular and Cellular Biology, City of Hope Cancer Center, Duarte, CA 91010, USA
| | - Samuel Gusscott
- Département de Biomédecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, Quebec J2S, Canada
| | - Zhen Fu
- Bioinformatics and Biostatistics Core, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Ivan VanderKolk
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | | | - Kin H. Lau
- Bioinformatics and Biostatistics Core, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Julie Brind’Amour
- Département de Biomédecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, Quebec J2S, Canada
| | - Piroska E. Szabó
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
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22
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Kumar A, Schwab M, Laborit Labrada B, Silveira MAD, Goudreault M, Fournier É, Bellmann K, Beauchemin N, Gingras AC, Bilodeau S, Laplante M, Marette A. SHP-1 phosphatase acts as a coactivator of PCK1 transcription to control gluconeogenesis. J Biol Chem 2023; 299:105164. [PMID: 37595871 PMCID: PMC10504565 DOI: 10.1016/j.jbc.2023.105164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 07/25/2023] [Accepted: 07/28/2023] [Indexed: 08/20/2023] Open
Abstract
We previously reported that the protein-tyrosine phosphatase SHP-1 (PTPN6) negatively regulates insulin signaling, but its impact on hepatic glucose metabolism and systemic glucose control remains poorly understood. Here, we use co-immunoprecipitation assays, chromatin immunoprecipitation sequencing, in silico methods, and gluconeogenesis assay, and found a new mechanism whereby SHP-1 acts as a coactivator for transcription of the phosphoenolpyruvate carboxykinase 1 (PCK1) gene to increase liver gluconeogenesis. SHP-1 is recruited to the regulatory regions of the PCK1 gene and interacts with RNA polymerase II. The recruitment of SHP-1 to chromatin is dependent on its association with the transcription factor signal transducer and activator of transcription 5 (STAT5). Loss of SHP-1 as well as STAT5 decrease RNA polymerase II recruitment to the PCK1 promoter and consequently PCK1 mRNA levels leading to blunted gluconeogenesis. This work highlights a novel nuclear role of SHP-1 as a key transcriptional regulator of hepatic gluconeogenesis adding a new mechanism to the repertoire of SHP-1 functions in metabolic control.
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Affiliation(s)
- Amit Kumar
- Faculté de Médecine, Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (CRIUCPQ), Université Laval, Québec, Quebec, Canada
| | - Michael Schwab
- Faculté de Médecine, Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (CRIUCPQ), Université Laval, Québec, Quebec, Canada
| | - Beisy Laborit Labrada
- Faculté de Médecine, Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (CRIUCPQ), Université Laval, Québec, Quebec, Canada
| | - Maruhen Amir Datsch Silveira
- Centre de Recherche du CHU de Québec - Université Laval, Axe Oncologie, Québec, Quebec, Canada; Centre de Recherche sur le Cancer de l'Université Laval, Québec, Quebec, Canada; Département de biologie moléculaire, biochimie médicale et pathologie, Faculté de Médecine, Université Laval, Québec, Quebec, Canada
| | - Marilyn Goudreault
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Quebec, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada
| | - Éric Fournier
- Centre de Recherche du CHU de Québec - Université Laval, Axe Oncologie, Québec, Quebec, Canada; Centre de Recherche sur le Cancer de l'Université Laval, Québec, Quebec, Canada; Département de biologie moléculaire, biochimie médicale et pathologie, Faculté de Médecine, Université Laval, Québec, Quebec, Canada; Centre de recherche en données massives de l'Université Laval, Québec, Quebec, Canada
| | - Kerstin Bellmann
- Faculté de Médecine, Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (CRIUCPQ), Université Laval, Québec, Quebec, Canada
| | - Nicole Beauchemin
- Department of Oncology, Medicine and Biochemistry, Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, Quebec, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Steve Bilodeau
- Centre de Recherche du CHU de Québec - Université Laval, Axe Oncologie, Québec, Quebec, Canada; Centre de Recherche sur le Cancer de l'Université Laval, Québec, Quebec, Canada; Département de biologie moléculaire, biochimie médicale et pathologie, Faculté de Médecine, Université Laval, Québec, Quebec, Canada; Centre de recherche en données massives de l'Université Laval, Québec, Quebec, Canada
| | - Mathieu Laplante
- Faculté de Médecine, Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (CRIUCPQ), Université Laval, Québec, Quebec, Canada; Centre de Recherche sur le Cancer de l'Université Laval, Québec, Quebec, Canada
| | - André Marette
- Faculté de Médecine, Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (CRIUCPQ), Université Laval, Québec, Quebec, Canada; Institute of Nutrition and Functional Foods, Laval University, Québec, Quebec, Canada.
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23
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He Y, Goyette MA, Chapelle J, Boufaied N, Al Rahbani J, Schonewolff M, Danek EI, Muller WJ, Labbé DP, Côté JF, Lamarche-Vane N. CdGAP is a talin-binding protein and a target of TGF-β signaling that promotes HER2-positive breast cancer growth and metastasis. Cell Rep 2023; 42:112936. [PMID: 37552602 DOI: 10.1016/j.celrep.2023.112936] [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: 05/10/2022] [Revised: 05/10/2023] [Accepted: 07/20/2023] [Indexed: 08/10/2023] Open
Abstract
Epithelial-to-mesenchymal transition (EMT) plays a crucial role in metastasis, which is the leading cause of death in breast cancer patients. Here, we show that Cdc42 GTPase-activating protein (CdGAP) promotes tumor formation and metastasis to lungs in the HER2-positive (HER2+) murine breast cancer model. CdGAP facilitates intravasation, extravasation, and growth at metastatic sites. CdGAP depletion in HER2+ murine primary tumors mediates crosstalk with a Dlc1-RhoA pathway and is associated with a transforming growth factor β (TGF-β)-induced EMT transcriptional signature. CdGAP is positively regulated by TGF-β signaling during EMT and interacts with the adaptor talin to modulate focal adhesion dynamics and integrin activation. Moreover, HER2+ breast cancer patients with high CdGAP mRNA expression combined with a high TGF-β-EMT signature are more likely to present lymph node invasion. Our results suggest CdGAP as a candidate therapeutic target for HER2+ metastatic breast cancer by inhibiting TGF-β and integrin/talin signaling pathways.
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Affiliation(s)
- Yi He
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montréal, QC H4A 3J1, Canada; Department of Anatomy and Cell Biology, McGill University, Montréal, QC H3A 0C7, Canada
| | - Marie-Anne Goyette
- Institut de Recherches Cliniques de Montréal, Université de Montréal, Montréal, QC H2W 1R7, Canada
| | - Jennifer Chapelle
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montréal, QC H4A 3J1, Canada; Department of Anatomy and Cell Biology, McGill University, Montréal, QC H3A 0C7, Canada
| | - Nadia Boufaied
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montréal, QC H4A 3J1, Canada
| | - Jalal Al Rahbani
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montréal, QC H4A 3J1, Canada; Department of Anatomy and Cell Biology, McGill University, Montréal, QC H3A 0C7, Canada
| | - Maribel Schonewolff
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montréal, QC H4A 3J1, Canada; Department of Anatomy and Cell Biology, McGill University, Montréal, QC H3A 0C7, Canada
| | - Eric I Danek
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montréal, QC H4A 3J1, Canada; Department of Anatomy and Cell Biology, McGill University, Montréal, QC H3A 0C7, Canada
| | - William J Muller
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montréal, QC H3A 1A3, Canada
| | - David P Labbé
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montréal, QC H4A 3J1, Canada; Department of Anatomy and Cell Biology, McGill University, Montréal, QC H3A 0C7, Canada; Division of Urology, Department of Surgery, McGill University, Montréal, QC H4A 3J1, Canada
| | - Jean-François Côté
- Department of Anatomy and Cell Biology, McGill University, Montréal, QC H3A 0C7, Canada; Institut de Recherches Cliniques de Montréal, Université de Montréal, Montréal, QC H2W 1R7, Canada
| | - Nathalie Lamarche-Vane
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montréal, QC H4A 3J1, Canada; Department of Anatomy and Cell Biology, McGill University, Montréal, QC H3A 0C7, Canada.
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Borges-Martins ANC, Ferreira-Neto JRC, da Silva MD, Morais DADL, Pandolfi V, Silva RLDO, de Melo ALTM, da Costa AF, Benko-Iseppon AM. Unlocking Cowpea's Defense Responses: Conserved Transcriptional Signatures in the Battle against CABMV and CPSMV Viruses. Life (Basel) 2023; 13:1747. [PMID: 37629606 PMCID: PMC10455494 DOI: 10.3390/life13081747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/04/2023] [Accepted: 08/10/2023] [Indexed: 08/27/2023] Open
Abstract
Cowpea aphid-borne mosaic virus (CABMV) and Cowpea severe mosaic virus (CPSMV) threaten cowpea commercial production. This study aimed to analyze Conserved Transcriptional Signatures (CTS) in cowpea's genotypes that are resistant to these viruses. CTS covered up- (UR) or down-regulated (DR) cowpea transcripts in response to CABMV and CPSMV mechanical inoculations. The conservation of cowpea's UR defense response was primarily observed with the one hpi treatments, with decreased CTS representatives as time elapsed. This suggests that cowpea utilizes generic mechanisms during its early interaction with the studied viruses, and subsequently employs more specialized strategies for each viral agent. The potential action of the CTS-UR emphasizes the importance of redox balance, ethylene and jasmonic acid pathways. Additionally, the CTS-UR provides evidence for the involvement of R genes, PR proteins, and PRRs receptors-extensively investigated in combating bacterial and fungal pathogens-in the defense against viral inoculation. AP2-ERF, WRKY, and MYB transcription factors, as well as PIP aquaporins and MAPK cascades, also emerged as significant molecular players. The presented work represents the first study investigating conserved mechanisms in the cowpea defense response to viral inoculations, highlighting relevant processes for initial defense responses.
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Affiliation(s)
- Artemisa Nazaré Costa Borges-Martins
- Departamento de Ensino, Instituto Federal do Maranhão, Buriticupu 65393-000, Brazil;
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife 50670-901, Brazil; (M.D.d.S.); (V.P.); (A.L.T.M.d.M.)
| | - José Ribamar Costa Ferreira-Neto
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife 50670-901, Brazil; (M.D.d.S.); (V.P.); (A.L.T.M.d.M.)
| | - Manassés Daniel da Silva
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife 50670-901, Brazil; (M.D.d.S.); (V.P.); (A.L.T.M.d.M.)
| | | | - Valesca Pandolfi
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife 50670-901, Brazil; (M.D.d.S.); (V.P.); (A.L.T.M.d.M.)
| | | | - Ana Luiza Trajano Mangueira de Melo
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife 50670-901, Brazil; (M.D.d.S.); (V.P.); (A.L.T.M.d.M.)
| | | | - Ana Maria Benko-Iseppon
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife 50670-901, Brazil; (M.D.d.S.); (V.P.); (A.L.T.M.d.M.)
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Dort J, Orfi Z, Fiscaletti M, Campeau PM, Dumont NA. Gpr18 agonist dampens inflammation, enhances myogenesis, and restores muscle function in models of Duchenne muscular dystrophy. Front Cell Dev Biol 2023; 11:1187253. [PMID: 37645248 PMCID: PMC10461444 DOI: 10.3389/fcell.2023.1187253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 07/24/2023] [Indexed: 08/31/2023] Open
Abstract
Introduction: Muscle wasting in Duchenne Muscular Dystrophy is caused by myofiber fragility and poor regeneration that lead to chronic inflammation and muscle replacement by fibrofatty tissue. Our recent findings demonstrated that Resolvin-D2, a bioactive lipid derived from omega-3 fatty acids, has the capacity to dampen inflammation and stimulate muscle regeneration to alleviate disease progression. This therapeutic avenue has many advantages compared to glucocorticoids, the current gold-standard treatment for Duchenne Muscular Dystrophy. However, the use of bioactive lipids as therapeutic drugs also faces many technical challenges such as their instability and poor oral bioavailability. Methods: Here, we explored the potential of PSB-KD107, a synthetic agonist of the resolvin-D2 receptor Gpr18, as a therapeutic alternative for Duchenne Muscular Dystrophy. Results and discussion: We showed that PSB-KD107 can stimulate the myogenic capacity of patient iPSC-derived myoblasts in vitro. RNAseq analysis revealed an enrichment in biological processes related to fatty acid metabolism, lipid biosynthesis, small molecule biosynthesis, and steroid-related processes in PSB-KD107-treated mdx myoblasts, as well as signaling pathways such as Peroxisome proliferator-activated receptors, AMP-activated protein kinase, mammalian target of rapamycin, and sphingolipid signaling pathways. In vivo, the treatment of dystrophic mdx mice with PSB-KD107 resulted in reduced inflammation, enhanced myogenesis, and improved muscle function. The positive impact of PSB-KD107 on muscle function is similar to the one of Resolvin-D2. Overall, our findings provide a proof-of concept that synthetic analogs of bioactive lipid receptors hold therapeutic potential for the treatment of Duchenne Muscular Dystrophy.
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Affiliation(s)
- Junio Dort
- CHU Sainte-Justine Research Center, Montreal, QC, Canada
- School of Rehabilitation, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
| | - Zakaria Orfi
- CHU Sainte-Justine Research Center, Montreal, QC, Canada
- Department of Pharmacology and Physiology, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
| | - Melissa Fiscaletti
- CHU Sainte-Justine Research Center, Montreal, QC, Canada
- Department of Pediatrics, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
| | - Philippe M. Campeau
- CHU Sainte-Justine Research Center, Montreal, QC, Canada
- Department of Pediatrics, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
| | - Nicolas A. Dumont
- CHU Sainte-Justine Research Center, Montreal, QC, Canada
- School of Rehabilitation, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
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Hughes CHK, Smith OE, Meinsohn MC, Brunelle M, Gévry N, Murphy BD. Steroidogenic factor 1 (SF-1; Nr5a1) regulates the formation of the ovarian reserve. Proc Natl Acad Sci U S A 2023; 120:e2220849120. [PMID: 37494420 PMCID: PMC10410717 DOI: 10.1073/pnas.2220849120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 06/12/2023] [Indexed: 07/28/2023] Open
Abstract
The ovarian follicle reserve, formed pre- or perinatally, comprises all oocytes for lifetime reproduction. Depletion of this reserve results in infertility. Steroidogenic factor 1 (SF-1; Nr5a1) and liver receptor homolog 1 (LRH-1; Nr5a2) are two orphan nuclear receptors that regulate adult endocrine function, but their role in follicle formation is unknown. We developed models of conditional depletion of SF-1 or LRH-1 from prenatal ovaries. Depletion of SF-1, but not LRH-1, resulted in dramatically smaller ovaries and fewer primordial follicles. This was mediated by increased oocyte death, resulting from increased ovarian inflammation and increased Notch signaling. Major dysregulated genes were Iroquois homeobox 3 and 5 and their downstream targets involved in the establishment of the ovarian laminin matrix and oocyte-granulosa cell gap junctions. Disruptions of these pathways resulted in follicles with impaired basement membrane formation and compromised oocyte-granulosa communication networks, believed to render them more prone to atresia. This study identifies SF-1 as a key regulator of the formation of the ovarian reserve.
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Affiliation(s)
- Camilla H. K. Hughes
- Centre de recherche en reproduction et fertilité, Faculté de médecine vétérinaire, Université de Montréal, St-Hyacinthe, QCJ2S 2M2, Canada
| | - Olivia E. Smith
- Centre de recherche en reproduction et fertilité, Faculté de médecine vétérinaire, Université de Montréal, St-Hyacinthe, QCJ2S 2M2, Canada
| | - Marie-Charlotte Meinsohn
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, MA02114
- Department of Surgery, Harvard Medical School, Boston, MA02115
| | - Mylène Brunelle
- Département de biologie, Université de Sherbrooke, Sherbrooke, QCJ1K 0A5, Canada
| | - Nicolas Gévry
- Département de biologie, Université de Sherbrooke, Sherbrooke, QCJ1K 0A5, Canada
| | - Bruce D. Murphy
- Centre de recherche en reproduction et fertilité, Faculté de médecine vétérinaire, Université de Montréal, St-Hyacinthe, QCJ2S 2M2, Canada
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Zwaig M, Johnston MJ, Lee JJ, Farooq H, Gallo M, Jabado N, Taylor MD, Ragoussis J. Linked-read based analysis of the medulloblastoma genome. Front Oncol 2023; 13:1221611. [PMID: 37576901 PMCID: PMC10419201 DOI: 10.3389/fonc.2023.1221611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 07/06/2023] [Indexed: 08/15/2023] Open
Abstract
Introduction Medulloblastoma is the most common type of malignant pediatric brain tumor with group 4 medulloblastomas (G4 MBs) accounting for 40% of cases. However, the molecular mechanisms that underlie this subgroup are still poorly understood. Point mutations are detected in a large number of genes at low incidence per gene while the detection of complex structural variants in recurrently affected genes typically requires the application of long-read technologies. Methods Here, we applied linked-read sequencing, which combines the long-range genome information of long-read sequencing with the high base pair accuracy of short read sequencing and very low sample input requirements. Results We demonstrate the detection of complex structural variants and point mutations in these tumors, and, for the first time, the detection of extrachromosomal DNA (ecDNA) with linked-reads. We provide further evidence for the high heterogeneity of somatic mutations in G4 MBs and add new complex events associated with it. Discussion We detected several enhancer-hijacking events, an ecDNA containing the MYCN gene, and rare structural rearrangements, such a chromothripsis in a G4 medulloblastoma, chromoplexy involving 8 different chromosomes, a TERT gene rearrangement, and a PRDM6 duplication.
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Affiliation(s)
- Melissa Zwaig
- Victor Phillip Dahdaleh Institute of Genomic Medicine and Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Michael J. Johnston
- Alberta Children’s Hospital Research Institute, Arnie Charbonneau Cancer Institute, and Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - John J.Y. Lee
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
- Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA, United States
| | | | - Marco Gallo
- Alberta Children’s Hospital Research Institute, Arnie Charbonneau Cancer Institute, and Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Nada Jabado
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- The Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Department of Pediatrics, McGill University, Montreal, QC, Canada
| | - Michael D. Taylor
- Division of Neurosurgery, The Arthur and Sonia Labatt Brain Tumour Research Centre and the Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Texas Children’s Cancer Center , Hematology-Oncology Section and Department of Pediatrics – Hematology/Oncology and Neurosurgery, Baylor College of Medicine, Houston, TX, United States
| | - Jiannis Ragoussis
- Victor Phillip Dahdaleh Institute of Genomic Medicine and Department of Human Genetics, McGill University, Montreal, QC, Canada
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Tav C, Fournier É, Fournier M, Khadangi F, Baguette A, Côté MC, Silveira MAD, Bérubé-Simard FA, Bourque G, Droit A, Bilodeau S. Glucocorticoid stimulation induces regionalized gene responses within topologically associating domains. Front Genet 2023; 14:1237092. [PMID: 37576549 PMCID: PMC10413275 DOI: 10.3389/fgene.2023.1237092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 07/07/2023] [Indexed: 08/15/2023] Open
Abstract
Transcription-factor binding to cis-regulatory regions regulates the gene expression program of a cell, but occupancy is often a poor predictor of the gene response. Here, we show that glucocorticoid stimulation led to the reorganization of transcriptional coregulators MED1 and BRD4 within topologically associating domains (TADs), resulting in active or repressive gene environments. Indeed, we observed a bias toward the activation or repression of a TAD when their activities were defined by the number of regions gaining and losing MED1 and BRD4 following dexamethasone (Dex) stimulation. Variations in Dex-responsive genes at the RNA levels were consistent with the redistribution of MED1 and BRD4 at the associated cis-regulatory regions. Interestingly, Dex-responsive genes without the differential recruitment of MED1 and BRD4 or binding by the glucocorticoid receptor were found within TADs, which gained or lost MED1 and BRD4, suggesting a role of the surrounding environment in gene regulation. However, the amplitude of the response of Dex-regulated genes was higher when the differential recruitment of the glucocorticoid receptor and transcriptional coregulators was observed, reaffirming the role of transcription factor-driven gene regulation and attributing a lesser role to the TAD environment. These results support a model where a signal-induced transcription factor induces a regionalized effect throughout the TAD, redefining the notion of direct and indirect effects of transcription factors on target genes.
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Affiliation(s)
- Christophe Tav
- Centre de Recherche du CHU de Québec—Université Laval, Axe Oncologie, Québec, QC, Canada
- Centre de Recherche sur le Cancer de l’Université Laval, Québec, QC, Canada
- Centre de Recherche en Données Massives de l’Université Laval, Québec, QC, Canada
| | - Éric Fournier
- Centre de Recherche du CHU de Québec—Université Laval, Axe Oncologie, Québec, QC, Canada
- Centre de Recherche sur le Cancer de l’Université Laval, Québec, QC, Canada
- Centre de Recherche en Données Massives de l’Université Laval, Québec, QC, Canada
| | - Michèle Fournier
- Centre de Recherche du CHU de Québec—Université Laval, Axe Oncologie, Québec, QC, Canada
- Centre de Recherche sur le Cancer de l’Université Laval, Québec, QC, Canada
| | - Fatemeh Khadangi
- Centre de Recherche du CHU de Québec—Université Laval, Axe Oncologie, Québec, QC, Canada
- Centre de Recherche sur le Cancer de l’Université Laval, Québec, QC, Canada
| | - Audrey Baguette
- Department of Human Genetics, Faculty of Medicine, McGill University, Montréal, QC, Canada
| | - Maxime C. Côté
- Centre de Recherche du CHU de Québec—Université Laval, Axe Oncologie, Québec, QC, Canada
- Centre de Recherche sur le Cancer de l’Université Laval, Québec, QC, Canada
| | - Maruhen A. D. Silveira
- Centre de Recherche du CHU de Québec—Université Laval, Axe Oncologie, Québec, QC, Canada
- Centre de Recherche sur le Cancer de l’Université Laval, Québec, QC, Canada
| | - Félix-Antoine Bérubé-Simard
- Centre de Recherche du CHU de Québec—Université Laval, Axe Oncologie, Québec, QC, Canada
- Centre de Recherche sur le Cancer de l’Université Laval, Québec, QC, Canada
| | - Guillaume Bourque
- Department of Human Genetics, Faculty of Medicine, McGill University, Montréal, QC, Canada
- Canadian Center for Computational Genomics, McGill University, Montréal, QC, Canada
| | - Arnaud Droit
- Centre de Recherche sur le Cancer de l’Université Laval, Québec, QC, Canada
- Centre de Recherche en Données Massives de l’Université Laval, Québec, QC, Canada
- Centre de Recherche du CHU de Québec—Université Laval, Axe Endocrinologie et Néphrologie, Québec, QC, Canada
- Département de Médecine Moléculaire, Faculté de Médecine, Université Laval, Québec, QC, Canada
| | - Steve Bilodeau
- Centre de Recherche du CHU de Québec—Université Laval, Axe Oncologie, Québec, QC, Canada
- Centre de Recherche sur le Cancer de l’Université Laval, Québec, QC, Canada
- Centre de Recherche en Données Massives de l’Université Laval, Québec, QC, Canada
- Département de Biologie Moléculaire, Biochimie Médicale et Pathologie, Faculté de Médecine, Université Laval, Québec, QC, Canada
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Casimir L, Zimmer S, Racine-Brassard F, Goudreau F, Jacques PÉ, Maréchal A. Chronic treatment with ATR and CHK1 inhibitors does not substantially increase the mutational burden of human cells. Mutat Res 2023; 827:111834. [PMID: 37531716 DOI: 10.1016/j.mrfmmm.2023.111834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 07/13/2023] [Accepted: 07/19/2023] [Indexed: 08/04/2023]
Abstract
DNA replication stress (RS) entails the frequent slow down and arrest of replication forks by a variety of conditions that hinder accurate and processive genome duplication. Elevated RS leads to genome instability, replication catastrophe and eventually cell death. RS is particularly prevalent in cancer cells and its exacerbation to unsustainable levels by chemotherapeutic agents remains a cornerstone of cancer treatments. The adverse consequences of RS are normally prevented by the ATR and CHK1 checkpoint kinases that stabilize stressed forks, suppress origin firing and promote cell cycle arrest when replication is perturbed. Specific inhibitors of these kinases have been developed and shown to potentiate RS and cell death in multiple in vitro cancer settings. Ongoing clinical trials are now probing their efficacy against various cancer types, either as single agents or in combination with mainstay chemotherapeutics. Despite their promise as valuable additions to the anti-cancer pharmacopoeia, we still lack a genome-wide view of the potential mutagenicity of these new drugs. To investigate this question, we performed chronic long-term treatments of TP53-depleted human cancer cells with ATR and CHK1 inhibitors (ATRi, AZD6738/ceralasertib and CHK1i, MK8776/SCH-900776). ATR or CHK1 inhibition did not significantly increase the mutational burden of cells, nor generate specific mutational signatures. Indeed, no notable changes in the numbers of base substitutions, short insertions/deletions and larger scale rearrangements were observed despite induction of replication-associated DNA breaks during treatments. Interestingly, ATR inhibition did induce a slight increase in closely-spaced mutations, a feature previously attributed to translesion synthesis DNA polymerases. The results suggest that ATRi and CHK1i do not have substantial mutagenic effects in vitro when used as standalone agents.
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Affiliation(s)
- Lisa Casimir
- Département de Biologie, Université de Sherbrooke, Sherbrooke J1K 2R1, QC, Canada; Institut de Recherche sur le Cancer de l'Université de Sherbrooke (IRCUS), Sherbrooke J1K 2R1, QC, Canada
| | - Samuel Zimmer
- Département de Biologie, Université de Sherbrooke, Sherbrooke J1K 2R1, QC, Canada; Institut de Recherche sur le Cancer de l'Université de Sherbrooke (IRCUS), Sherbrooke J1K 2R1, QC, Canada
| | - Félix Racine-Brassard
- Département de Biologie, Université de Sherbrooke, Sherbrooke J1K 2R1, QC, Canada; Institut de Recherche sur le Cancer de l'Université de Sherbrooke (IRCUS), Sherbrooke J1K 2R1, QC, Canada
| | - Félix Goudreau
- Département de Biologie, Université de Sherbrooke, Sherbrooke J1K 2R1, QC, Canada; Institut de Recherche sur le Cancer de l'Université de Sherbrooke (IRCUS), Sherbrooke J1K 2R1, QC, Canada
| | - Pierre-Étienne Jacques
- Département de Biologie, Université de Sherbrooke, Sherbrooke J1K 2R1, QC, Canada; Institut de Recherche sur le Cancer de l'Université de Sherbrooke (IRCUS), Sherbrooke J1K 2R1, QC, Canada; Centre de recherche du Centre hospitalier universitaire de Sherbrooke (CRCHUS), Sherbrooke J1H 5N3, QC, Canada.
| | - Alexandre Maréchal
- Département de Biologie, Université de Sherbrooke, Sherbrooke J1K 2R1, QC, Canada; Institut de Recherche sur le Cancer de l'Université de Sherbrooke (IRCUS), Sherbrooke J1K 2R1, QC, Canada; Centre de recherche du Centre hospitalier universitaire de Sherbrooke (CRCHUS), Sherbrooke J1H 5N3, QC, Canada.
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Laurent J, Le Berre I, Armengaud J, Kailasam S, Couteau J, Waeles M, Le Floch S, Laroche J, Pichereau V. Integration of environmental signatures and omics-based approaches on the European flounder to assist with health assessment of estuarine ecosystems in Brittany, France. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 878:163195. [PMID: 37003335 DOI: 10.1016/j.scitotenv.2023.163195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/21/2023] [Accepted: 03/27/2023] [Indexed: 05/13/2023]
Abstract
This study aimed to develop a multidisciplinary approach to assess the ecological status of six moderate-sized French estuaries. For each estuary, we gathered geographical information, hydrobiological data, chemistry of pollutants and fish biology, including integration of proteomics and transcriptomics data. This integrative study covered the entire hydrological system studied, from the watershed to the estuary, and considered all the anthropogenic factors that can impact this environment. To reach this goal, European flounder (Platichthys flesus) were collected from six estuaries in September, which ensures a minimum residence time of five months within an estuary. Geographical metrics are used to characterize land use in each watershed. The concentrations of nitrite, nitrate, organic pollutants, and trace elements were measured in water, sediments and biota. All of these environmental parameters allowed to set up a typology of estuaries. Classical fish biomarkers, coupled with molecular data from transcriptomics and shotgun proteomics, highlighted the flounder's responses to stressors in its environment. We analysed the protein abundances and gene expression levels in the liver of fish from the different estuaries. We showed clear positive deregulation of proteins associated with xenobiotic detoxification in a system characterized by a large population density and industrial activity, as well as in a predominantly agricultural catchment area (mostly cultures of vegetables and pig breeding) mainly impacted by pesticides. Fish from the latter estuary also displayed strong deregulation of the urea cycle, most probably related to high nitrogen load. Proteomic and transcriptomic data also revealed a deregulation of proteins and genes related to the response to hypoxia, and a probable endocrine disruption in some estuaries. Coupling these data allowed the precise identification of the main stressors interacting within each hydrosystem.
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Affiliation(s)
- Jennifer Laurent
- LEMAR UMR 6539 CNRS/UBO/IRD/Ifremer, IUEM-Université de Bretagne Occidentale, Rue Dumont D'Urville, 29280 Plouzané, France; CEDRE, 715 rue Alain Colas, 29200 Brest, France.
| | - Iwan Le Berre
- LETG-Brest GEOMER, UMR 6554 CNRS, IUEM-Université de Bretagne Occidentale, Rue Dumont D'Urville, 29280 Plouzané, France
| | - Jean Armengaud
- Laboratoire Innovations Technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRAe, F-30207 Bagnols-sur-Cèze, France
| | - Senthilkumar Kailasam
- Canadian Centre for Computational Genomics, McGill University, Montreal, Quebec H3A 0G1, Canada; Department of Human Genetics, McGill University, Montréal, Québec, Canada
| | - Jérôme Couteau
- TOXEM, 12 rue des 4 saisons, 76290 Montivilliers, France
| | - Matthieu Waeles
- LEMAR UMR 6539 CNRS/UBO/IRD/Ifremer, IUEM-Université de Bretagne Occidentale, Rue Dumont D'Urville, 29280 Plouzané, France
| | | | - Jean Laroche
- LEMAR UMR 6539 CNRS/UBO/IRD/Ifremer, IUEM-Université de Bretagne Occidentale, Rue Dumont D'Urville, 29280 Plouzané, France
| | - Vianney Pichereau
- LEMAR UMR 6539 CNRS/UBO/IRD/Ifremer, IUEM-Université de Bretagne Occidentale, Rue Dumont D'Urville, 29280 Plouzané, France.
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Shaw DG, Aguirre-Gamboa R, Vieira MC, Gona S, DiNardi N, Wang A, Dumaine A, Gelderloos-Arends J, Earley ZM, Meckel KR, Ciszewski C, Castillo A, Monroe K, Torres J, Shah SC, Colombel JF, Itzkowitz S, Newberry R, Cohen RD, Rubin DT, Quince C, Cobey S, Jonkers IH, Weber CR, Pekow J, Wilson PC, Barreiro LB, Jabri B. Antigen-driven colonic inflammation is associated with development of dysplasia in primary sclerosing cholangitis. Nat Med 2023; 29:1520-1529. [PMID: 37322120 PMCID: PMC10287559 DOI: 10.1038/s41591-023-02372-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 04/26/2023] [Indexed: 06/17/2023]
Abstract
Primary sclerosing cholangitis (PSC) is an immune-mediated disease of the bile ducts that co-occurs with inflammatory bowel disease (IBD) in almost 90% of cases. Colorectal cancer is a major complication of patients with PSC and IBD, and these patients are at a much greater risk compared to patients with IBD without concomitant PSC. Combining flow cytometry, bulk and single-cell transcriptomics, and T and B cell receptor repertoire analysis of right colon tissue from 65 patients with PSC, 108 patients with IBD and 48 healthy individuals we identified a unique adaptive inflammatory transcriptional signature associated with greater risk and shorter time to dysplasia in patients with PSC. This inflammatory signature is characterized by antigen-driven interleukin-17A (IL-17A)+ forkhead box P3 (FOXP3)+ CD4 T cells that express a pathogenic IL-17 signature, as well as an expansion of IgG-secreting plasma cells. These results suggest that the mechanisms that drive the emergence of dysplasia in PSC and IBD are distinct and provide molecular insights that could guide prevention of colorectal cancer in individuals with PSC.
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Affiliation(s)
- Dustin G Shaw
- Committee on Immunology, University of Chicago, Chicago, IL, USA
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Raúl Aguirre-Gamboa
- Department of Medicine, University of Chicago, Chicago, IL, USA
- Committee on Genetics, Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Marcos C Vieira
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Saideep Gona
- Department of Medicine, University of Chicago, Chicago, IL, USA
- Committee on Genetics, Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Nicholas DiNardi
- Committee on Immunology, University of Chicago, Chicago, IL, USA
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Anni Wang
- Committee on Immunology, University of Chicago, Chicago, IL, USA
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Anne Dumaine
- Department of Medicine, University of Chicago, Chicago, IL, USA
- Committee on Genetics, Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Jody Gelderloos-Arends
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Zachary M Earley
- Committee on Immunology, University of Chicago, Chicago, IL, USA
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | | | - Cezary Ciszewski
- Committee on Immunology, University of Chicago, Chicago, IL, USA
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Anabella Castillo
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kelly Monroe
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Joana Torres
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Gastroenterology, Hospital Beatriz Ângelo, Loures, Portugal
- Division of Gastroenterology, Hospital Luz, Lisboa, Portugal
- Faculty of Medicine, Universidade de Lisboa, Lisboa, Portugal
| | - Shailja C Shah
- Division of Gastroenterology, University of California San Diego, San Diego, CA, USA
- Jennifer Moreno VA San Diego Healthcare System, San Diego, CA, USA
| | - Jean-Frédéric Colombel
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Steven Itzkowitz
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rodney Newberry
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Russell D Cohen
- University of Chicago Inflammatory Bowel Disease Center, Chicago, IL, USA
| | - David T Rubin
- University of Chicago Inflammatory Bowel Disease Center, Chicago, IL, USA
| | - Christopher Quince
- Organisms and Ecosystems, Earlham Institute, Norwich, NR4 7UZ, UK
- Warwick Medical School, University of Warwick, Coventry, CV4 7HL, UK
- Gut Microbes and Health, Quadram Institute, Norwich, NR4 7UQ, UK
| | - Sarah Cobey
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Iris H Jonkers
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | | | - Joel Pekow
- University of Chicago Inflammatory Bowel Disease Center, Chicago, IL, USA
| | - Patrick C Wilson
- Committee on Immunology, University of Chicago, Chicago, IL, USA
- Department of Medicine, University of Chicago, Chicago, IL, USA
- Section of Rheumatology, University of Chicago, Chicago, IL, USA
| | - Luis B Barreiro
- Committee on Immunology, University of Chicago, Chicago, IL, USA.
- Department of Medicine, University of Chicago, Chicago, IL, USA.
- Committee on Genetics, Genomics and Systems Biology, University of Chicago, Chicago, IL, USA.
| | - Bana Jabri
- Committee on Immunology, University of Chicago, Chicago, IL, USA.
- Department of Medicine, University of Chicago, Chicago, IL, USA.
- Department of Pathology, University of Chicago, Chicago, IL, USA.
- Department of Pediatrics, University of Chicago, Chicago, IL, USA.
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32
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Rahimi S, Shao X, Chan D, Martel J, Bérard A, Fraser WD, Simon MM, Kwan T, Bourque G, Trasler J. Capturing sex-specific and hypofertility-linked effects of assisted reproductive technologies on the cord blood DNA methylome. Clin Epigenetics 2023; 15:82. [PMID: 37170172 PMCID: PMC10176895 DOI: 10.1186/s13148-023-01497-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 05/02/2023] [Indexed: 05/13/2023] Open
Abstract
BACKGROUND Children conceived through assisted reproduction are at an increased risk for growth and genomic imprinting disorders, often linked to DNA methylation defects. It has been suggested that assisted reproductive technology (ART) and underlying parental infertility can induce epigenetic instability, specifically interfering with DNA methylation reprogramming events during germ cell and preimplantation development. To date, human studies exploring the association between ART and DNA methylation defects have reported inconsistent or inconclusive results, likely due to population heterogeneity and the use of technologies with limited coverage of the epigenome. In our study, we explored the epigenetic risk of ART by comprehensively profiling the DNA methylome of 73 human cord blood samples of singleton pregnancies (n = 36 control group, n = 37 ART/hypofertile group) from a human prospective longitudinal birth cohort, the 3D (Design, Develop, Discover) Study, using a high-resolution sequencing-based custom capture panel that examines over 2.4 million autosomal CpGs in the genome. RESULTS We identified evidence of sex-specific effects of ART/hypofertility on cord blood DNA methylation patterns. Our genome-wide analyses identified ~ 46% more CpGs affected by ART/hypofertility in female than in male infant cord blood. We performed a detailed analysis of three imprinted genes which have been associated with altered DNA methylation following ART (KCNQ1OT1, H19/IGF2 and GNAS) and found that female infant cord blood was associated with DNA hypomethylation. When compared to less invasive procedures such as intrauterine insemination, more invasive ARTs (in vitro fertilization, intracytoplasmic sperm injection, embryo culture) resulted in more marked and distinct effects on the cord blood DNA methylome. In the in vitro group, we found a close to fourfold higher proportion of significantly enriched Gene Ontology terms involved in development than in the in vivo group. CONCLUSIONS Our study highlights the ability of a sensitive, targeted, sequencing-based approach to uncover DNA methylation perturbations in cord blood associated with hypofertility and ART and influenced by offspring sex and ART technique invasiveness.
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Affiliation(s)
- Sophia Rahimi
- Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Xiaojian Shao
- Digital Technologies Research Centre, National Research Council Canada, Ottawa, ON, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
| | - Donovan Chan
- Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Josée Martel
- Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Anick Bérard
- Research Unit On Medications and Pregnancy, Research Centre, CHU Sainte-Justine, Montreal, Canada
- Faculty of Pharmacy, Université de Montréal, Montreal, QC, Canada
- Faculty of Medicine, Université Claude Bernard Lyon 1, Lyon, France
| | - William D Fraser
- Department of Obstetrics and Gynecology, Université de Sherbrooke and Centre de Recherche du CHUS, Sherbrooke, QC, Canada
| | | | - Tony Kwan
- McGill University Genome Centre, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Guillaume Bourque
- McGill University Genome Centre, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Jacquetta Trasler
- Research Institute of the McGill University Health Centre, Montreal, QC, Canada.
- Department of Human Genetics, McGill University, Montreal, QC, Canada.
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada.
- Department of Pediatrics, McGill University, Montreal, QC, Canada.
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33
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Dorion MF, Yaqubi M, Murdoch HJ, Hall JA, Dudley R, Antel JP, Durcan TM, Healy LM. Systematic comparison of culture media uncovers phenotypic shift of primary human microglia defined by reduced reliance to CSF1R signaling. Glia 2023; 71:1278-1293. [PMID: 36680780 DOI: 10.1002/glia.24338] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 11/17/2022] [Accepted: 01/02/2023] [Indexed: 01/22/2023]
Abstract
Efforts to understand microglia function in health and diseases have been hindered by the lack of culture models that recapitulate in situ cellular properties. In recent years, the use of serum-free media with brain-derived growth factors (colony stimulating factor 1 receptor [CSF1R] ligands and TGF-β1/2) have been favored for the maintenance of rodent microglia as they promote morphological features observed in situ. Here we study the functional and transcriptomic impacts of such media on human microglia (hMGL). Media formulation had little impact on microglia transcriptome assessed by RNA sequencing which was sufficient to significantly alter microglia capacity to phagocytose myelin debris and to elicit an inflammatory response to lipopolysaccharide. When compared to immediately ex vivo microglia from the same donors, the addition of fetal bovine serum to culture media, but not growth factors, was found to aid in the maintenance of key signature genes including those involved in phagocytic processes. A phenotypic shift characterized by CSF1R downregulation in culture correlated with a lack of reliance on CSF1R signaling for survival. Consequently, no improvement in cell survival was observed following culture supplementation with CSF1R ligands. Our study provides better understanding of hMGL in culture, with observations that diverge from those previously made in rodent microglia.
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Affiliation(s)
- Marie-France Dorion
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Québec, Canada
| | - Moein Yaqubi
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Québec, Canada
| | - Hunter J Murdoch
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Québec, Canada
| | - Jeffery A Hall
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Québec, Canada
| | - Roy Dudley
- Department of Pediatric Neurosurgery, Montreal Children's Hospital, Montreal, Canada
| | - Jack P Antel
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Québec, Canada
| | - Thomas Martin Durcan
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Québec, Canada
| | - Luke Michael Healy
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Québec, Canada
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34
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Vasudev NS, Scelo G, Glennon KI, Wilson M, Letourneau L, Eveleigh R, Nourbehesht N, Arseneault M, Paccard A, Egevad L, Viksna J, Celms E, Jackson SM, Abedi-Ardekani B, Warren AY, Selby PJ, Trainor S, Kimuli M, Cartledge J, Soomro N, Adeyoju A, Patel PM, Wozniak MB, Holcatova I, Brisuda A, Janout V, Chanudet E, Zaridze D, Moukeria A, Shangina O, Foretova L, Navratilova M, Mates D, Jinga V, Bogdanovic L, Kovacevic B, Cambon-Thomsen A, Bourque G, Brazma A, Tost J, Brennan P, Lathrop M, Riazalhosseini Y, Banks RE. Application of Genomic Sequencing to Refine Patient Stratification for Adjuvant Therapy in Renal Cell Carcinoma. Clin Cancer Res 2023; 29:1220-1231. [PMID: 36815791 PMCID: PMC10068441 DOI: 10.1158/1078-0432.ccr-22-1936] [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: 06/19/2022] [Revised: 10/12/2022] [Accepted: 01/10/2023] [Indexed: 02/24/2023]
Abstract
PURPOSE Patients with resected localized clear-cell renal cell carcinoma (ccRCC) remain at variable risk of recurrence. Incorporation of biomarkers may refine risk prediction and inform adjuvant treatment decisions. We explored the role of tumor genomics in this setting, leveraging the largest cohort to date of localized ccRCC tissues subjected to targeted gene sequencing. EXPERIMENTAL DESIGN The somatic mutation status of 12 genes was determined in 943 ccRCC cases from a multinational cohort of patients, and associations to outcomes were examined in a Discovery (n = 469) and Validation (n = 474) framework. RESULTS Tumors containing a von-Hippel Lindau (VHL) mutation alone were associated with significantly improved outcomes in comparison with tumors containing a VHL plus additional mutations. Within the Discovery cohort, those with VHL+0, VHL+1, VHL+2, and VHL+≥3 tumors had disease-free survival (DFS) rates of 90.8%, 80.1%, 68.2%, and 50.7% respectively, at 5 years. This trend was replicated in the Validation cohort. Notably, these genomically defined groups were independent of tumor mutational burden. Amongst patients eligible for adjuvant therapy, those with a VHL+0 tumor (29%) had a 5-year DFS rate of 79.3% and could, therefore, potentially be spared further treatment. Conversely, patients with VHL+2 and VHL+≥3 tumors (32%) had equivalent DFS rates of 45.6% and 35.3%, respectively, and should be prioritized for adjuvant therapy. CONCLUSIONS Genomic characterization of ccRCC identified biologically distinct groups of patients with divergent relapse rates. These groups account for the ∼80% of cases with VHL mutations and could be used to personalize adjuvant treatment discussions with patients as well as inform future adjuvant trial design.
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Affiliation(s)
- Naveen S. Vasudev
- Leeds Institute of Medical Research at St James's, University of Leeds, St James's University Hospital, Leeds, United Kingdom
| | - Ghislaine Scelo
- World Health Organisation (WHO), International Agency for Research on Cancer (IARC), The Genomic Epidemiology Branch, Lyon, France
| | - Kate I. Glennon
- Victor Philip Dahdaleh Institute of Genomic Medicine at McGill University, Montreal, Québec, Canada
- Department of Human Genetics, McGill University, Montreal, Québec, Canada
| | - Michelle Wilson
- Leeds Institute of Medical Research at St James's, University of Leeds, St James's University Hospital, Leeds, United Kingdom
| | - Louis Letourneau
- Victor Philip Dahdaleh Institute of Genomic Medicine at McGill University, Montreal, Québec, Canada
| | - Robert Eveleigh
- Victor Philip Dahdaleh Institute of Genomic Medicine at McGill University, Montreal, Québec, Canada
| | - Nazanin Nourbehesht
- Victor Philip Dahdaleh Institute of Genomic Medicine at McGill University, Montreal, Québec, Canada
- Department of Human Genetics, McGill University, Montreal, Québec, Canada
| | - Madeleine Arseneault
- Victor Philip Dahdaleh Institute of Genomic Medicine at McGill University, Montreal, Québec, Canada
| | - Antoine Paccard
- Victor Philip Dahdaleh Institute of Genomic Medicine at McGill University, Montreal, Québec, Canada
| | - Lars Egevad
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Juris Viksna
- Institute of Mathematics and Computer Science, University of Latvia, Riga, Latvia
| | - Edgars Celms
- Institute of Mathematics and Computer Science, University of Latvia, Riga, Latvia
| | - Sharon M. Jackson
- Leeds Institute of Medical Research at St James's, University of Leeds, St James's University Hospital, Leeds, United Kingdom
| | - Behnoush Abedi-Ardekani
- World Health Organisation (WHO), International Agency for Research on Cancer (IARC), The Genomic Epidemiology Branch, Lyon, France
| | - Anne Y. Warren
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Hills Road, Cambridge, United Kingdom
| | - Peter J. Selby
- Leeds Institute of Medical Research at St James's, University of Leeds, St James's University Hospital, Leeds, United Kingdom
| | - Sebastian Trainor
- Leeds Institute of Medical Research at St James's, University of Leeds, St James's University Hospital, Leeds, United Kingdom
| | - Michael Kimuli
- Pyrah Department of Urology, Leeds Teaching Hospitals NHS Trust, Lincoln Wing, St James's University Hospital, Leeds, United Kingdom
| | - Jon Cartledge
- Pyrah Department of Urology, Leeds Teaching Hospitals NHS Trust, Lincoln Wing, St James's University Hospital, Leeds, United Kingdom
| | - Naeem Soomro
- Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | | | - Poulam M. Patel
- Division of Cancer & Stem Cells, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Magdalena B. Wozniak
- World Health Organisation (WHO), International Agency for Research on Cancer (IARC), The Genomic Epidemiology Branch, Lyon, France
| | - Ivana Holcatova
- Charles University in Prague, First Faculty of Medicine, Institute of Hygiene and Epidemiology, Prague, Czech Republic
| | | | - Vladimir Janout
- Faculty of Health Sciences, Palacky University, Olomouc, Czech Republic
| | - Estelle Chanudet
- World Health Organisation (WHO), International Agency for Research on Cancer (IARC), The Genomic Epidemiology Branch, Lyon, France
| | - David Zaridze
- N.N. Blokhin National Medical Research Centre of Oncology, Moscow, Russian Federation
| | - Anush Moukeria
- N.N. Blokhin National Medical Research Centre of Oncology, Moscow, Russian Federation
| | - Oxana Shangina
- N.N. Blokhin National Medical Research Centre of Oncology, Moscow, Russian Federation
| | - Lenka Foretova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Marie Navratilova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Dana Mates
- National Institute of Public Health, Bucuresti, Romania
| | - Viorel Jinga
- Carol Davila University of Medicine and Pharmacy, Prof. Dr. Th. Burghele Clinical Hospital, Bucharest, Romania
| | - Ljiljana Bogdanovic
- Institute of Pathology, School of Medicine Belgrade, University of Belgrade, Belgrade, Serbia
| | - Bozidar Kovacevic
- Institute of Pathology and Forensic Medicine, Military Medical Academy, Belgrade, Serbia
| | - Anne Cambon-Thomsen
- Institut National de la Santé et de la Recherche Médicale (INSERM) and Université Toulouse III Paul Sabatier (UPS), Toulouse, France
| | - Guillaume Bourque
- Victor Philip Dahdaleh Institute of Genomic Medicine at McGill University, Montreal, Québec, Canada
- Department of Human Genetics, McGill University, Montreal, Québec, Canada
| | - Alvis Brazma
- European Bioinformatics Institute, European Molecular Biology Laboratory, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Jörg Tost
- Centre National de Recherche en Génomique Humaine, CEA - Institut de Biologie Francois Jacob, University Paris Saclay, Evry, France
| | - Paul Brennan
- World Health Organisation (WHO), International Agency for Research on Cancer (IARC), The Genomic Epidemiology Branch, Lyon, France
| | - Mark Lathrop
- Victor Philip Dahdaleh Institute of Genomic Medicine at McGill University, Montreal, Québec, Canada
- Department of Human Genetics, McGill University, Montreal, Québec, Canada
| | - Yasser Riazalhosseini
- Victor Philip Dahdaleh Institute of Genomic Medicine at McGill University, Montreal, Québec, Canada
- Department of Human Genetics, McGill University, Montreal, Québec, Canada
| | - Rosamonde E. Banks
- Leeds Institute of Medical Research at St James's, University of Leeds, St James's University Hospital, Leeds, United Kingdom
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35
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Khazaei S, Chen CCL, Andrade AF, Kabir N, Azarafshar P, Morcos SM, França JA, Lopes M, Lund PJ, Danieau G, Worme S, Adnani L, Nzirorera N, Chen X, Yogarajah G, Russo C, Zeinieh M, Wong CJ, Bryant L, Hébert S, Tong B, Sihota TS, Faury D, Puligandla E, Jawhar W, Sandy V, Cowan M, Nakada EM, Jerome-Majewska LA, Ellezam B, Gomes CC, Denecke J, Lessel D, McDonald MT, Pizoli CE, Taylor K, Cocanougher BT, Bhoj EJ, Gingras AC, Garcia BA, Lu C, Campos EI, Kleinman CL, Garzia L, Jabado N. Single substitution in H3.3G34 alters DNMT3A recruitment to cause progressive neurodegeneration. Cell 2023; 186:1162-1178.e20. [PMID: 36931244 PMCID: PMC10112048 DOI: 10.1016/j.cell.2023.02.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 11/04/2022] [Accepted: 02/16/2023] [Indexed: 03/18/2023]
Abstract
Germline histone H3.3 amino acid substitutions, including H3.3G34R/V, cause severe neurodevelopmental syndromes. To understand how these mutations impact brain development, we generated H3.3G34R/V/W knock-in mice and identified strikingly distinct developmental defects for each mutation. H3.3G34R-mutants exhibited progressive microcephaly and neurodegeneration, with abnormal accumulation of disease-associated microglia and concurrent neuronal depletion. G34R severely decreased H3K36me2 on the mutant H3.3 tail, impairing recruitment of DNA methyltransferase DNMT3A and its redistribution on chromatin. These changes were concurrent with sustained expression of complement and other innate immune genes possibly through loss of non-CG (CH) methylation and silencing of neuronal gene promoters through aberrant CG methylation. Complement expression in G34R brains may lead to neuroinflammation possibly accounting for progressive neurodegeneration. Our study reveals that H3.3G34-substitutions have differential impact on the epigenome, which underlie the diverse phenotypes observed, and uncovers potential roles for H3K36me2 and DNMT3A-dependent CH-methylation in modulating synaptic pruning and neuroinflammation in post-natal brains.
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Affiliation(s)
- Sima Khazaei
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
| | - Carol C L Chen
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
| | | | - Nisha Kabir
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
| | - Pariya Azarafshar
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
| | - Shahir M Morcos
- Genetics & Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Josiane Alves França
- Department of Pathology, Biological Sciences Institute, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Mariana Lopes
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Peder J Lund
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Geoffroy Danieau
- Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada; Division of Orthopedic Surgery, Faculty of Surgery, McGill University, Montreal, QC H3G 1A4, Canada
| | - Samantha Worme
- Lady Davis Research Institute, Jewish General Hospital, Montreal, QC H3T 1E2, Canada
| | - Lata Adnani
- Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Nadine Nzirorera
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
| | - Xiao Chen
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA; Marine College, Shandong University, Weihai 264209, China
| | - Gayathri Yogarajah
- Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada; Department of Biochemistry and Molecular Medicine, Université de Montreal, Research Center of the CHU Sainte-Justine, Montreal, QC H3T 1C5, Canada
| | - Caterina Russo
- Department of Pediatrics, McGill University, and The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Michele Zeinieh
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
| | - Cassandra J Wong
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada
| | - Laura Bryant
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Steven Hébert
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; Lady Davis Research Institute, Jewish General Hospital, Montreal, QC H3T 1E2, Canada
| | - Bethany Tong
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Canada
| | - Tianna S Sihota
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
| | - Damien Faury
- Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Evan Puligandla
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Wajih Jawhar
- Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada; Child Health and Human Development, The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada; Division of Experimental Medicine, Department of Medicine, McGill University, Montreal, QC H4A 3J1, Canada
| | - Veronica Sandy
- Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Mitra Cowan
- McGill Integrated Core for Animal Modeling (MICAM), McGill University, Montreal, QC, Canada
| | - Emily M Nakada
- Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Loydie A Jerome-Majewska
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; Department of Pediatrics, McGill University, and The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada; Department of Anatomy and Cell Biology, McGill University, Montreal, QC, Canada
| | - Benjamin Ellezam
- Department of Pathology, Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montréal, QC H3T 1C5, Canada
| | - Carolina Cavalieri Gomes
- Department of Pathology, Biological Sciences Institute, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Jonas Denecke
- Department of Pediatrics, University Medical Center Eppendorf, Hamburg, Germany
| | - Davor Lessel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; Institute of Human Genetics, University Hospital of the Paracelsus Medical University Salzburg, Salzburg, Austria
| | - Marie T McDonald
- Division of Medical Genetics, Duke University Hospital, Durham, NC, USA
| | - Carolyn E Pizoli
- Division of Pediatric Neurology, Duke University Hospital, Durham, NC, USA
| | - Kathryn Taylor
- Division of Medical Genetics, Duke University Hospital, Durham, NC, USA
| | | | | | - Anne-Claude Gingras
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada
| | - Benjamin A Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Chao Lu
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Eric I Campos
- Genetics & Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Claudia L Kleinman
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; Lady Davis Research Institute, Jewish General Hospital, Montreal, QC H3T 1E2, Canada
| | - Livia Garzia
- Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada; Division of Orthopedic Surgery, Faculty of Surgery, McGill University, Montreal, QC H3G 1A4, Canada
| | - Nada Jabado
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada; Department of Pediatrics, McGill University, and The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada; Division of Experimental Medicine, Department of Medicine, McGill University, Montreal, QC H4A 3J1, Canada.
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Neumann H, Jeronimo C, Lucier JF, Pasquier E, Robert F, Wellinger RJ, Gaudreau L. The Histone Variant H2A.Z C-Terminal Domain Has Locus-Specific Differential Effects on H2A.Z Occupancy and Nucleosome Localization. Microbiol Spectr 2023; 11:e0255022. [PMID: 36815792 PMCID: PMC10100702 DOI: 10.1128/spectrum.02550-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 01/05/2023] [Indexed: 02/24/2023] Open
Abstract
The incorporation of histone variant H2A.Z into nucleosomes creates specialized chromatin domains that regulate DNA-templated processes, such as gene transcription. In Saccharomyces cerevisiae, the diverging H2A.Z C terminus is thought to provide the H2A.Z exclusive functions. To elucidate the roles of this H2A.Z C terminus genome-wide, we used derivatives in which the C terminus was replaced with the corresponding region of H2A (ZA protein), or the H2A region plus a transcriptional activating peptide (ZA-rII'), with the intent of regenerating the H2A.Z-dependent regulation globally. The distribution of these H2A.Z derivatives indicates that the H2A.Z C-terminal region is crucial for both maintaining the occupation level of H2A.Z and the proper positioning of targeted nucleosomes. Interestingly, the specific contribution on incorporation efficiency versus nucleosome positioning varies enormously depending on the locus analyzed. Specifically, the role of H2A.Z in global transcription regulation relies on its C-terminal region. Remarkably, however, this mostly involves genes without a H2A.Z nucleosome in the promoter. Lastly, we demonstrate that the main chaperone complex which deposits H2A.Z to gene regulatory region (SWR1-C) is necessary to localize all H2A.Z derivatives at their specific loci, indicating that the differential association of these derivatives is not due to impaired interaction with SWR1-C. IMPORTANCE We provide evidence that the Saccharomyces cerevisiae C-terminal region of histone variant H2A.Z can mediate its special function in performing gene regulation by interacting with effector proteins and chaperones. These functional interactions allow H2A.Z not only to incorporate to very specific gene regulatory regions, but also to facilitate the gene expression process. To achieve this, we used a chimeric protein which lacks the native H2A.Z C-terminal region but contains an acidic activating region, a module that is known to interact with components of chromatin-remodeling entities and/or transcription modulators. We reasoned that because this activating region can fulfill the role of the H2A.Z C-terminal region, at least in part, the role of the latter would be to interact with these activating region targets.
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Affiliation(s)
- Hannah Neumann
- Department of Biology, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Celia Jeronimo
- Montreal Clinical Research Institute, Montréal, Quebec, Canada
| | - Jean-François Lucier
- Department of Biology, Université de Sherbrooke, Sherbrooke, Quebec, Canada
- Center for Computational Science, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Emeline Pasquier
- Department of Microbiology and Infectious Diseases, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - François Robert
- Montreal Clinical Research Institute, Montréal, Quebec, Canada
- Department of Medicine, Université de Montréal, Montréal, Quebec, Canada
| | - Raymund J. Wellinger
- Department of Microbiology and Infectious Diseases, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Luc Gaudreau
- Department of Biology, Université de Sherbrooke, Sherbrooke, Quebec, Canada
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Casimir L, Zimmer S, Racine-Brassard F, Jacques PÉ, Maréchal A. The mutational impact of Illudin S on human cells. DNA Repair (Amst) 2023; 122:103433. [PMID: 36566616 DOI: 10.1016/j.dnarep.2022.103433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 12/03/2022] [Accepted: 12/07/2022] [Indexed: 12/15/2022]
Abstract
Illudin S (ILS) is a fungal sesquiterpene secondary metabolite with potent genotoxic and cytotoxic properties. Early genetic studies and more recent genome-wide CRISPR screens showed that Illudin-induced lesions are preferentially repaired by transcription-coupled nucleotide excision repair (TC-NER) with some contribution from post-replication repair pathways. In line with these results, Irofulven, a semi-synthetic ILS analog was recently shown to be particularly effective on cell lines and patient-derived xenografts with impaired NER (e.g. ERCC2/3 mutations), raising hope that ILS-derived molecules may soon enter the clinic. Despite the therapeutic potential of ILS and its analogs, we still lack a global understanding of their mutagenic potential. Here, we characterize the mutational signatures associated with chronic exposure to ILS in human cells. ILS treatment rapidly stalls DNA replication and transcription, leading to the activation of the replication stress response and the accumulation of DNA damage. Novel single and double base substitution signatures as well as a characteristic indel signature indicate that ILS treatment preferentially alkylates purine residues and induces oxidative stress, confirming prior in vitro data. Many mutation contexts exhibit a strong transcriptional strand bias, highlighting the contribution of TC-NER to the repair of ILS lesions. Finally, collateral mutations are also observed in response to ILS, suggesting a contribution of translesion synthesis pathways to ILS tolerance. Accordingly, ILS treatment led to the rapid recruitment of the Y-family DNA polymerase kappa onto chromatin, supporting its preferential use for ILS lesion bypass. Altogether, our work provides the first global assessment of the genomic impact of ILS, demonstrating the contribution of multiple DNA repair pathways to ILS resistance and mutagenicity.
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Affiliation(s)
- Lisa Casimir
- Département de Biologie, Université de Sherbrooke, Sherbrooke, QC, Canada J1K 2R1; Institut de Recherche sur le Cancer de l'Université de Sherbrooke (IRCUS), Sherbrooke, QC, Canada J1E 4K8
| | - Samuel Zimmer
- Département de Biologie, Université de Sherbrooke, Sherbrooke, QC, Canada J1K 2R1; Institut de Recherche sur le Cancer de l'Université de Sherbrooke (IRCUS), Sherbrooke, QC, Canada J1E 4K8
| | - Félix Racine-Brassard
- Département de Biologie, Université de Sherbrooke, Sherbrooke, QC, Canada J1K 2R1; Institut de Recherche sur le Cancer de l'Université de Sherbrooke (IRCUS), Sherbrooke, QC, Canada J1E 4K8
| | - Pierre-Étienne Jacques
- Département de Biologie, Université de Sherbrooke, Sherbrooke, QC, Canada J1K 2R1; Institut de Recherche sur le Cancer de l'Université de Sherbrooke (IRCUS), Sherbrooke, QC, Canada J1E 4K8; Centre de recherche du Centre hospitalier universitaire de Sherbrooke (CRCHUS), Sherbrooke, QC, Canada J1H 5N3.
| | - Alexandre Maréchal
- Département de Biologie, Université de Sherbrooke, Sherbrooke, QC, Canada J1K 2R1; Institut de Recherche sur le Cancer de l'Université de Sherbrooke (IRCUS), Sherbrooke, QC, Canada J1E 4K8; Centre de recherche du Centre hospitalier universitaire de Sherbrooke (CRCHUS), Sherbrooke, QC, Canada J1H 5N3.
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Earley ZM, Lisicka W, Sifakis JJ, Aguirre-Gamboa R, Kowalczyk A, Barlow JT, Shaw DG, Discepolo V, Tan IL, Gona S, Ernest JD, Matzinger P, Barreiro LB, Morgun A, Bendelac A, Ismagilov RF, Shulzhenko N, Riesenfeld SJ, Jabri B. GATA4 controls regionalization of tissue immunity and commensal-driven immunopathology. Immunity 2023; 56:43-57.e10. [PMID: 36630917 PMCID: PMC10262782 DOI: 10.1016/j.immuni.2022.12.009] [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: 09/15/2022] [Revised: 11/16/2022] [Accepted: 12/12/2022] [Indexed: 01/12/2023]
Abstract
There is growing recognition that regionalization of bacterial colonization and immunity along the intestinal tract has an important role in health and disease. Yet, the mechanisms underlying intestinal regionalization and its dysregulation in disease are not well understood. This study found that regional epithelial expression of the transcription factor GATA4 controls bacterial colonization and inflammatory tissue immunity in the proximal small intestine by regulating retinol metabolism and luminal IgA. Furthermore, in mice without jejunal GATA4 expression, the commensal segmented filamentous bacteria promoted pathogenic inflammatory immune responses that disrupted barrier function and increased mortality upon Citrobacter rodentium infection. In celiac disease patients, low GATA4 expression was associated with metabolic alterations, mucosal Actinobacillus, and increased IL-17 immunity. Taken together, these results reveal broad impacts of GATA4-regulated intestinal regionalization on bacterial colonization and tissue immunity, highlighting an elaborate interdependence of intestinal metabolism, immunity, and microbiota in homeostasis and disease.
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Affiliation(s)
- Zachary M Earley
- Committee on Immunology, University of Chicago, Chicago, IL, USA; Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Wioletta Lisicka
- Committee on Immunology, University of Chicago, Chicago, IL, USA; Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Joseph J Sifakis
- Department of Chemistry, University of Chicago, Chicago, IL, USA
| | | | - Anita Kowalczyk
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Jacob T Barlow
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Dustin G Shaw
- Committee on Immunology, University of Chicago, Chicago, IL, USA; Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Valentina Discepolo
- Department of Medical Translational Sciences and European Laboratory for the Investigation of Food Induced Diseases, University of Federico II, Naples, Italy
| | - Ineke L Tan
- Department of Gastroenterology and Hepatology, University of Groningen and University of Medical Center Groningen, Groningen, the Netherlands
| | - Saideep Gona
- Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Jordan D Ernest
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Polly Matzinger
- Ghost Lab, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Luis B Barreiro
- Committee on Immunology, University of Chicago, Chicago, IL, USA; Department of Medicine, University of Chicago, Chicago, IL, USA; Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Andrey Morgun
- College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | - Albert Bendelac
- Committee on Immunology, University of Chicago, Chicago, IL, USA; Department of Pathology, University of Chicago, Chicago, IL, USA
| | - Rustem F Ismagilov
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA; Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Natalia Shulzhenko
- Department of Biomedical Sciences, Oregon State University, Corvallis, OR, USA
| | - Samantha J Riesenfeld
- Committee on Immunology, University of Chicago, Chicago, IL, USA; Department of Medicine, University of Chicago, Chicago, IL, USA; Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA; Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA.
| | - Bana Jabri
- Committee on Immunology, University of Chicago, Chicago, IL, USA; Department of Medicine, University of Chicago, Chicago, IL, USA; Department of Pathology, University of Chicago, Chicago, IL, USA; Department of Pediatrics, University of Chicago, Chicago, IL, USA.
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Schreiber L, Fortin N, Mazza A, Maynard C, Wasserscheid J, Tremblay J, Lee K, Greer CW. An experimental oil spill at a tidal freshwater wetland along the St. Lawrence River re-visited after 21 years. ENVIRONMENTAL RESEARCH 2023; 216:114456. [PMID: 36181891 DOI: 10.1016/j.envres.2022.114456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 09/21/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
In 1999, a tidal wetland located along the St. Lawrence River close to Ste. Croix de Lotbinière (Quebec, Eastern Canada) was the site of an experimental oil spill. Test plots were established and subjected to an experimental crude oil spill to evaluate natural attenuation, nutrient amendment and vegetation cropping as countermeasures. In 2020, this study re-visited the test plots to investigate residual oil and habitat recovery. Only concentrations of mid-chain length n-alkanes (C10-C36), but not of polycyclic aromatic hydrocarbons (PAHs), were significantly above detection limit, and were detected in both test plot and control sediments. Hydrocarbon, total organic carbon, nitrogen and phosphate contents did not differ significantly between test plot and control sediments. Microbial analyses did not detect significant differences in microbial load, microbial diversity or microbial community composition between test plot and control sediments. Key genes for the aerobic and anaerobic degradation of n-alkanes as well as for the aerobic degradation of PAHs were detected in all sediment samples. Associated gene abundances did not differ significantly between test plot and control sediments. This study shows that oil-exposed test plot sediments of the Ste. Croix wetland can be considered completely recovered after 21 years irrespective of the performed countermeasure.
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Affiliation(s)
- Lars Schreiber
- Energy, Mining and Environment Research Center, National Research Council Canada, 6100 Royalmount Ave, Montreal, QC, H4P 2R2, Canada.
| | - Nathalie Fortin
- Energy, Mining and Environment Research Center, National Research Council Canada, 6100 Royalmount Ave, Montreal, QC, H4P 2R2, Canada
| | - Alberto Mazza
- Energy, Mining and Environment Research Center, National Research Council Canada, 6100 Royalmount Ave, Montreal, QC, H4P 2R2, Canada
| | - Christine Maynard
- Energy, Mining and Environment Research Center, National Research Council Canada, 6100 Royalmount Ave, Montreal, QC, H4P 2R2, Canada
| | - Jessica Wasserscheid
- Energy, Mining and Environment Research Center, National Research Council Canada, 6100 Royalmount Ave, Montreal, QC, H4P 2R2, Canada
| | - Julien Tremblay
- Energy, Mining and Environment Research Center, National Research Council Canada, 6100 Royalmount Ave, Montreal, QC, H4P 2R2, Canada
| | - Kenneth Lee
- Fisheries and Oceans Canada, Ecosystem Science, Ottawa, ON, K1A 0E6, Canada
| | - Charles W Greer
- Energy, Mining and Environment Research Center, National Research Council Canada, 6100 Royalmount Ave, Montreal, QC, H4P 2R2, Canada; Department of Natural Resource Sciences, McGill University, 21111 Lakeshore Rd, Ste-Anne-de-Bellevue, QC, H9X 3V9, Canada
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40
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Identification of R-Spondin Gene Signature Predictive of Metastatic Progression in BRAFV 600E-Positive Papillary Thyroid Cancer. Cells 2022; 12:cells12010139. [PMID: 36611933 PMCID: PMC9818556 DOI: 10.3390/cells12010139] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/19/2022] [Accepted: 12/22/2022] [Indexed: 12/31/2022] Open
Abstract
Papillary thyroid carcinoma (PTC) is the most common malignancy of the thyroid gland and early stages are curable. However, a subset of PTCs shows an unusually aggressive phenotype with extensive lymph node metastasis and higher incidence of locoregional recurrence. In this study, we investigated a large cohort of PTC cases with an unusual aggressive phenotype using a high-throughput RNA sequencing (RNA-Seq) to identify differentially regulated genes associated with metastatic PTC. All metastatic PTC with mutated BRAF (V600E) but not BRAF wild-type expressed an up-regulation of R-Spondin Protein 4 (RSPO4) concomitant with an upregulation of genes involved in focal adhesion and cell-extracellular matrix signaling. Further immunohistochemistry validation confirmed the upregulation of these target genes in metastatic PTC cases. Preclinical studies using established PTC cell lines support that RSPO4 overexpression is associated with BRAF V600E mutation and is a critical upstream event that promote activation of kinases of focal adhesion signaling known to drive cancer cell locomotion and invasion. This finding opens up the potential of co-targeting B-Raf, RSPO and focal adhesion proteins as a pharmacological approach for aggressive BRAF V600E PTC.
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41
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Hooker JC, Nissan N, Luckert D, Charette M, Zapata G, Lefebvre F, Mohr RM, Daba KA, Warkentin TD, Hadinezhad M, Barlow B, Hou A, Golshani A, Cober ER, Samanfar B. A Multi-Year, Multi-Cultivar Approach to Differential Expression Analysis of High- and Low-Protein Soybean ( Glycine max). Int J Mol Sci 2022; 24:ijms24010222. [PMID: 36613666 PMCID: PMC9820483 DOI: 10.3390/ijms24010222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 12/12/2022] [Accepted: 12/15/2022] [Indexed: 12/25/2022] Open
Abstract
Soybean (Glycine max (L.) Merr.) is among the most valuable crops based on its nutritious seed protein and oil. Protein quality, evaluated as the ratio of glycinin (11S) to β-conglycinin (7S), can play a role in food and feed quality. To help uncover the underlying differences between high and low protein soybean varieties, we performed differential expression analysis on high and low total protein soybean varieties and high and low 11S soybean varieties grown in four locations across Eastern and Western Canada over three years (2018-2020). Simultaneously, ten individual differential expression datasets for high vs. low total protein soybeans and ten individual differential expression datasets for high vs. low 11S soybeans were assessed, for a total of 20 datasets. The top 15 most upregulated and the 15 most downregulated genes were extracted from each differential expression dataset and cross-examination was conducted to create shortlists of the most consistently differentially expressed genes. Shortlisted genes were assessed for gene ontology to gain a global appreciation of the commonly differentially expressed genes. Genes with roles in the lipid metabolic pathway and carbohydrate metabolic pathway were differentially expressed in high total protein and high 11S soybeans in comparison to their low total protein and low 11S counterparts. Expression differences were consistent between East and West locations with the exception of one, Glyma.03G054100. These data are important for uncovering the genes and biological pathways responsible for the difference in seed protein between high and low total protein or 11S cultivars.
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Affiliation(s)
- Julia C. Hooker
- Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON K1A 0C6, Canada
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, 1125 Colonel By Dr., Ottawa, ON K1S 5B6, Canada
| | - Nour Nissan
- Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON K1A 0C6, Canada
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, 1125 Colonel By Dr., Ottawa, ON K1S 5B6, Canada
| | - Doris Luckert
- Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON K1A 0C6, Canada
| | - Martin Charette
- Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON K1A 0C6, Canada
| | - Gerardo Zapata
- Canadian Centre for Computational Genomics, 740 Dr. Penfield Ave, Montréal, QC H3A 0G1, Canada
| | - François Lefebvre
- Canadian Centre for Computational Genomics, 740 Dr. Penfield Ave, Montréal, QC H3A 0G1, Canada
| | - Ramona M. Mohr
- Agriculture and Agri-Food Canada, 2701 Grand Valley Road, Brandon, MB R7A 5Y3, Canada
| | - Ketema A. Daba
- Crop Development Centre, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
| | - Thomas D. Warkentin
- Crop Development Centre, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
| | - Mehri Hadinezhad
- Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON K1A 0C6, Canada
| | - Brent Barlow
- Crop Development Centre, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
| | - Anfu Hou
- Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada
| | - Ashkan Golshani
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, 1125 Colonel By Dr., Ottawa, ON K1S 5B6, Canada
| | - Elroy R. Cober
- Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON K1A 0C6, Canada
| | - Bahram Samanfar
- Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON K1A 0C6, Canada
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, 1125 Colonel By Dr., Ottawa, ON K1S 5B6, Canada
- Correspondence:
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K27M in canonical and noncanonical H3 variants occurs in distinct oligodendroglial cell lineages in brain midline gliomas. Nat Genet 2022; 54:1865-1880. [PMID: 36471070 PMCID: PMC9742294 DOI: 10.1038/s41588-022-01205-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 09/16/2022] [Indexed: 12/12/2022]
Abstract
Canonical (H3.1/H3.2) and noncanonical (H3.3) histone 3 K27M-mutant gliomas have unique spatiotemporal distributions, partner alterations and molecular profiles. The contribution of the cell of origin to these differences has been challenging to uncouple from the oncogenic reprogramming induced by the mutation. Here, we perform an integrated analysis of 116 tumors, including single-cell transcriptome and chromatin accessibility, 3D chromatin architecture and epigenomic profiles, and show that K27M-mutant gliomas faithfully maintain chromatin configuration at developmental genes consistent with anatomically distinct oligodendrocyte precursor cells (OPCs). H3.3K27M thalamic gliomas map to prosomere 2-derived lineages. In turn, H3.1K27M ACVR1-mutant pontine gliomas uniformly mirror early ventral NKX6-1+/SHH-dependent brainstem OPCs, whereas H3.3K27M gliomas frequently resemble dorsal PAX3+/BMP-dependent progenitors. Our data suggest a context-specific vulnerability in H3.1K27M-mutant SHH-dependent ventral OPCs, which rely on acquisition of ACVR1 mutations to drive aberrant BMP signaling required for oncogenesis. The unifying action of K27M mutations is to restrict H3K27me3 at PRC2 landing sites, whereas other epigenetic changes are mainly contingent on the cell of origin chromatin state and cycling rate.
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Tremblay J, Schreiber L, Greer CW. High-resolution shotgun metagenomics: the more data, the better? Brief Bioinform 2022; 23:6780270. [PMID: 36352504 DOI: 10.1093/bib/bbac443] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 09/01/2022] [Accepted: 09/13/2022] [Indexed: 11/11/2022] Open
Abstract
In shotgun metagenomics (SM), the state-of-the-art bioinformatic workflows are referred to as high-resolution shotgun metagenomics (HRSM) and require intensive computing and disk storage resources. While the increase in data output of the latest iteration of high-throughput DNA sequencing systems can allow for unprecedented sequencing depth at a minimal cost, adjustments in HRSM workflows will be needed to properly process these ever-increasing sequence datasets. One potential adaptation is to generate so-called shallow SM datasets that contain fewer sequencing data per sample as compared with the more classic high coverage sequencing. While shallow sequencing is a promising avenue for SM data analysis, detailed benchmarks using real-data are lacking. In this case study, we took four public SM datasets, one massive and the others moderate in size and subsampled each dataset at various levels to mimic shallow sequencing datasets of various sequencing depths. Our results suggest that shallow SM sequencing is a viable avenue to obtain sound results regarding microbial community structures and that high-depth sequencing does not bring additional elements for ecological interpretation. More specifically, results obtained by subsampling as little as 0.5 M sequencing clusters per sample were similar to the results obtained with the largest subsampled dataset for human gut and agricultural soil datasets. For an Antarctic dataset, which contained only a few samples, 4 M sequencing clusters per sample was found to generate comparable results to the full dataset. One area where ultra-deep sequencing and maximizing the usage of all data was undeniably beneficial was in the generation of metagenome-assembled genomes.
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Affiliation(s)
- Julien Tremblay
- Energy Mining and Environment Research Centre, National Research Council Canada, Montreal, QC, Canada H4P-2R2
| | - Lars Schreiber
- Energy Mining and Environment Research Centre, National Research Council Canada, Montreal, QC, Canada H4P-2R2
| | - Charles W Greer
- Energy Mining and Environment Research Centre, National Research Council Canada, Montreal, QC, Canada H4P-2R2
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Ferreira-Neto JRC, de Araújo FC, de Oliveira Silva RL, de Melo NF, Pandolfi V, Frosi G, de Lima Morais DA, da Silva MD, Rivas R, Santos MG, de Tarso Aidar S, Morgante CV, Benko-Iseppon AM. Dehydration response in Stylosanthes scabra: Transcriptional, biochemical, and physiological modulations. PHYSIOLOGIA PLANTARUM 2022; 174:e13821. [PMID: 36345266 DOI: 10.1111/ppl.13821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/22/2022] [Accepted: 11/01/2022] [Indexed: 06/16/2023]
Abstract
Stylosanthes scabra, popularly known as stylo, is native to the Brazilian Caatinga semiarid region and stands out as a drought-tolerant shrub forage crop. This work provides information about the plant response during the first 48 h of water deficit, followed by a rehydration treatment. Besides root transcriptomics data, 13 physiological or biochemical parameters were scrutinized. Additionally, RNA-Seq annotated transcripts not associated with the "Viridiplantae" clade were taxonomically categorized. It was found that S. scabra quickly perceives and recovers from the oscillations of the imposed water regime. Physiologically, mechanisms that minimize evapotranspiration or protect the photosynthetic apparatus stood out. Biochemically, it was found that the root tissue invests in synthesizing compounds that can act as osmolytes (proline and sugars), emphasizing the importance of osmoregulation to water deficit acclimation. Consistently, transcriptome and qPCR analyses showed that a set of enriched biological processes with upregulated (UR) transcripts were involved in protective functions against reactive oxygen species or encoding enzymes of important metabolic pathways, which might contribute to S. scabra response to water deficit. Additionally, several UR kinases and transcription factors were identified. Finally, in an innovative approach, some naturally occurring microbial groups (such as Schizosaccharomyces, Bradyrhizobium, etc.) were identified in the S. scabra roots. This study reveals insights into the physiological, biochemical, and molecular mechanisms underlying the S. scabra response to water deficit and provides candidate genes that may be useful in developing drought-tolerant crop varieties through biotechnological applications.
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Affiliation(s)
- José Ribamar Costa Ferreira-Neto
- Laboratório de Genética e Biotecnologia Vegetal, Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | - Flávia Czekalski de Araújo
- Laboratório de Genética e Biotecnologia Vegetal, Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | - Roberta Lane de Oliveira Silva
- Laboratório de Genética e Biotecnologia Vegetal, Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | | | - Valesca Pandolfi
- Laboratório de Genética e Biotecnologia Vegetal, Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | - Gabriella Frosi
- Départament de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | | | - Manassés Daniel da Silva
- Laboratório de Genética Molecular, Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | - Rebeca Rivas
- Laboratório de Genética Molecular, Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | - Mauro Guida Santos
- Laboratório de Fisiologia Vegetal, Departamento de Botânica, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | - Saulo de Tarso Aidar
- Empresa Brasileira de Pesquisa Agropecuária (SEMIÁRIDO), Petrolina, Pernambuco, Brazil
| | | | - Ana Maria Benko-Iseppon
- Laboratório de Genética e Biotecnologia Vegetal, Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
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45
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Derderian S, Vesval Q, Wissing MD, Hamel L, Côté N, Vanhuyse M, Ferrario C, Bladou F, Aprikian A, Chevalier S. Liquid biopsy-based targeted gene screening highlights tumor cell subtypes in patients with advanced prostate cancer. Clin Transl Sci 2022; 15:2597-2612. [PMID: 36172886 PMCID: PMC9652435 DOI: 10.1111/cts.13372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 06/23/2022] [Accepted: 07/08/2022] [Indexed: 01/25/2023] Open
Abstract
Prostate cancer (PCa) clinical heterogeneity underscores tumor heterogeneity, which may be best defined by cell subtypes. To test if cell subtypes contributing to progression can be assessed noninvasively, we investigated whether 14 genes representing luminal, neuroendocrine, and stem cells are detectable in whole blood RNA of patients with advanced PCa. For each gene, reverse transcription quantitative polymerase chain reaction assays were first validated using RNA from PCa cell lines, and their traceability in blood was assessed in cell spiking experiments. These were next tested in blood RNA of 40 advanced PCa cases and 40 healthy controls. Expression in controls, which was low or negative, was used to define stringent thresholds for gene overexpression in patients to account for normal variation in white blood cells. Thirty-five of 40 patients overexpressed at least one gene. Patients with more genes overexpressed had a higher risk of death (hazard ratio 1.42, range 1.12-1.77). Progression on androgen receptor inhibitors was associated with overexpression of stem (odds ratio [OR] 7.74, range 1.68-35.61) and neuroendocrine (OR 13.10, range 1.24-142.34) genes, while luminal genes were associated with taxanes (OR 2.7, range 1.07-6.82). Analyses in PCa transcriptomic datasets revealed that this gene panel was most prominent in metastases of advanced disease, with diversity among patients. Collectively, these findings support the contribution of the prostate cell subtypes to disease progression. Cell-subtype specific genes are traceable in blood RNA of patients with advanced PCa and are associated with clinically relevant end points. This opens the door to minimally invasive liquid biopsies for better management of this deadly disease.
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Affiliation(s)
- Seta Derderian
- Urologic Oncology Research Group, Cancer Research ProgramResearch Institute (RI)‐McGill University Health Center (MUHC)MontrealCanada,Department of Surgery (Urology Division)MUHC and McGill UniversityMontrealCanada
| | - Quentin Vesval
- Urologic Oncology Research Group, Cancer Research ProgramResearch Institute (RI)‐McGill University Health Center (MUHC)MontrealCanada,Department of UrologyCentre Hospitalier Régional et Universitaire (CHRU) de RennesRennesFrance
| | - Michel D. Wissing
- Urologic Oncology Research Group, Cancer Research ProgramResearch Institute (RI)‐McGill University Health Center (MUHC)MontrealCanada,Department of OncologyMUHC and McGill UniversityMontrealCanada
| | - Lucie Hamel
- Urologic Oncology Research Group, Cancer Research ProgramResearch Institute (RI)‐McGill University Health Center (MUHC)MontrealCanada
| | - Nathalie Côté
- Urologic Oncology Research Group, Cancer Research ProgramResearch Institute (RI)‐McGill University Health Center (MUHC)MontrealCanada
| | - Marie Vanhuyse
- Department of OncologyMUHC and McGill UniversityMontrealCanada
| | - Cristiano Ferrario
- Department of OncologyJewish General Hospital (JGH) and McGill UniversityMontrealCanada
| | - Franck Bladou
- Department of UrologyCentre Hospitalier Universitaire de BordeauxBordeauxFrance
| | - Armen Aprikian
- Urologic Oncology Research Group, Cancer Research ProgramResearch Institute (RI)‐McGill University Health Center (MUHC)MontrealCanada,Department of Surgery (Urology Division)MUHC and McGill UniversityMontrealCanada,Department of OncologyMUHC and McGill UniversityMontrealCanada
| | - Simone Chevalier
- Urologic Oncology Research Group, Cancer Research ProgramResearch Institute (RI)‐McGill University Health Center (MUHC)MontrealCanada,Department of Surgery (Urology Division)MUHC and McGill UniversityMontrealCanada,Department of OncologyMUHC and McGill UniversityMontrealCanada,Department of MedicineMcGill UniversityMontrealCanada
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46
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Transcriptome Analysis of Duck and Chicken Brains Infected with Aquatic Bird Bornavirus-1 (ABBV-1). Viruses 2022; 14:v14102211. [PMID: 36298766 PMCID: PMC9611670 DOI: 10.3390/v14102211] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 10/02/2022] [Accepted: 10/06/2022] [Indexed: 12/21/2022] Open
Abstract
Aquatic bird bornavirus 1 (ABBV-1) is a neurotropic virus that infects waterfowls, resulting in persistent infection. Experimental infection showed that both Muscovy ducks and chickens support persistent ABBV-1 infection in the central nervous system (CNS), up to 12 weeks post-infection (wpi), without the development of clinical disease. The aim of the present study was to describe the transcriptomic profiles in the brains of experimentally infected Muscovy ducks and chickens infected with ABBV-1 at 4 and 12 wpi. Transcribed RNA was sequenced by next-generation sequencing and analyzed by principal component analysis (PCA) and differential gene expression. The functional annotation of differentially expressed genes was evaluated by gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. The PCA showed that the infected ducks sampled at both 4 and 12 wpi clustered separately from the controls, while only the samples from the chickens at 12 wpi, but not at 4 wpi, formed a separate cluster. In the ducks, more genes were differentially expressed at 4 wpi than 12 wpi, and the majority of the highly differentially expressed genes (DEG) were upregulated. On the other hand, the infected chickens had fewer DEGs at 4 wpi than at 12 wpi, and the majority of those with high numbers of DEGs were downregulated at 4 wpi and upregulated at 12 wpi. The functional annotation showed that the most enriched GO terms were immune-associated in both species; however, the terms associated with the innate immune response were predominantly enriched in the ducks, whereas the chickens had enrichment of both the innate and adaptive immune response. Immune-associated pathways were also enriched according to the KEGG pathway analysis in both species. Overall, the transcriptomic analysis of the duck and chicken brains showed that the main biological responses to ABBV-1 infection were immune-associated and corresponded with the levels of inflammation in the CNS.
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Hooker JC, Nissan N, Luckert D, Zapata G, Hou A, Mohr RM, Glenn AJ, Barlow B, Daba KA, Warkentin TD, Lefebvre F, Golshani A, Cober ER, Samanfar B. GmSWEET29 and Paralog GmSWEET34 Are Differentially Expressed between Soybeans Grown in Eastern and Western Canada. PLANTS 2022; 11:plants11182337. [PMID: 36145738 PMCID: PMC9502396 DOI: 10.3390/plants11182337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 08/31/2022] [Accepted: 09/01/2022] [Indexed: 11/16/2022]
Abstract
Over the past two decades soybeans grown in western Canada have persistently had lower seed protein than those grown in eastern Canada. To understand the discrepancy in seed protein content between eastern- and western-grown soybeans, RNA-seq and differential expression analysis have been investigated. Ten soybean genotypes, ranging from low to high in seed protein content, were grown in four locations across eastern (Ottawa) and western (Morden, Brandon, and Saskatoon) Canada. Differential expression analysis revealed 34 differentially expressed genes encoding Glycine max Sugars Will Eventually be Exported Transporters (GmSWEETs), including paralogs GmSWEET29 and GmSWEET34 (AtSWEET2 homologs) that were consistently upregulated across all ten genotypes in each of the western locations over three years. GmSWEET29 and GmSWEET34 are likely candidates underlying the lower seed protein content of western soybeans. GmSWEET20 (AtSWEET12 homolog) was downregulated in the western locations and may also play a role in lower seed protein content. These findings are valuable for improving soybean agriculture in western growing regions, establishing more strategic and efficient agricultural practices.
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Affiliation(s)
- Julia C. Hooker
- Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Nour Nissan
- Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Doris Luckert
- Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
| | - Gerardo Zapata
- Canadian Centre for Computational Genomics, Montréal, QC H3A 0G1, Canada
| | - Anfu Hou
- Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada
| | - Ramona M. Mohr
- Agriculture and Agri-Food Canada, Brandon, MB R7A 5Y3, Canada
| | - Aaron J. Glenn
- Agriculture and Agri-Food Canada, Brandon, MB R7A 5Y3, Canada
| | - Brent Barlow
- Crop Development Centre, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
| | - Ketema A. Daba
- Crop Development Centre, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
| | - Thomas D. Warkentin
- Crop Development Centre, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
| | - François Lefebvre
- Canadian Centre for Computational Genomics, Montréal, QC H3A 0G1, Canada
| | - Ashkan Golshani
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Elroy R. Cober
- Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
| | - Bahram Samanfar
- Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
- Correspondence:
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48
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Rabinovich-Nikitin I, Blant A, Dhingra R, Kirshenbaum LA, Czubryt MP. NF-κB p65 Attenuates Cardiomyocyte PGC-1α Expression in Hypoxia. Cells 2022; 11:cells11142193. [PMID: 35883637 PMCID: PMC9322255 DOI: 10.3390/cells11142193] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 07/11/2022] [Accepted: 07/11/2022] [Indexed: 01/27/2023] Open
Abstract
Hypoxia exerts broad effects on cardiomyocyte function and viability, ranging from altered metabolism and mitochondrial physiology to apoptotic or necrotic cell death. The transcriptional coactivator peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1α) is a key regulator of cardiomyocyte metabolism and mitochondrial function and is down-regulated in hypoxia; however, the underlying mechanism is incompletely resolved. Using primary rat cardiomyocytes coupled with electrophoretic mobility shift and luciferase assays, we report that hypoxia impaired mitochondrial energetics and resulted in an increase in nuclear localization of the Nuclear Factor-κB (NF-κB) p65 subunit, and the association of p65 with the PGC-1α proximal promoter. Tumor necrosis factor α (TNFα), an activator of NF-κB signaling, similarly reduced PGC-1α expression and p65 binding to the PGC-1α promoter in a dose-dependent manner, and TNFα-mediated down-regulation of PGC-1α expression could be reversed by the NF-κB inhibitor parthenolide. RNA-seq analysis revealed that cardiomyocytes isolated from p65 knockout mice exhibited alterations in genes associated with chromatin remodeling. Decreased PGC-1α promoter transactivation by p65 could be partially reversed by the histone deacetylase inhibitor trichostatin A. These results implicate NF-κB signaling, and specifically p65, as a potent inhibitor of PGC-1α expression in cardiac myocyte hypoxia.
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Affiliation(s)
- Inna Rabinovich-Nikitin
- Institute of Cardiovascular Sciences, St. Boniface Hospital Albrechtsen Research Centre, Winnipeg, MB R2H 2A6, Canada; (I.R.-N.); (R.D.)
- Department of Physiology and Pathophysiology, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Alexandra Blant
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0J9, Canada;
| | - Rimpy Dhingra
- Institute of Cardiovascular Sciences, St. Boniface Hospital Albrechtsen Research Centre, Winnipeg, MB R2H 2A6, Canada; (I.R.-N.); (R.D.)
- Department of Physiology and Pathophysiology, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Lorrie A. Kirshenbaum
- Institute of Cardiovascular Sciences, St. Boniface Hospital Albrechtsen Research Centre, Winnipeg, MB R2H 2A6, Canada; (I.R.-N.); (R.D.)
- Department of Physiology and Pathophysiology, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
- Correspondence: (L.A.K.); (M.P.C.); Tel.: +1-204-235-3661 (L.A.K.); +1-204-235-3719 (M.P.C.)
| | - Michael P. Czubryt
- Institute of Cardiovascular Sciences, St. Boniface Hospital Albrechtsen Research Centre, Winnipeg, MB R2H 2A6, Canada; (I.R.-N.); (R.D.)
- Department of Physiology and Pathophysiology, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
- Correspondence: (L.A.K.); (M.P.C.); Tel.: +1-204-235-3661 (L.A.K.); +1-204-235-3719 (M.P.C.)
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Anilkumar Sithara A, Maripuri D, Moorthy K, Amirtha Ganesh S, Philip P, Banerjee S, Sudhakar M, Raman K. iCOMIC: a graphical interface-driven bioinformatics pipeline for analyzing cancer omics data. NAR Genom Bioinform 2022; 4:lqac053. [PMID: 35899080 PMCID: PMC9310080 DOI: 10.1093/nargab/lqac053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 06/17/2022] [Accepted: 07/04/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
Despite the tremendous increase in omics data generated by modern sequencing technologies, their analysis can be tricky and often requires substantial expertise in bioinformatics. To address this concern, we have developed a user-friendly pipeline to analyze (cancer) genomic data that takes in raw sequencing data (FASTQ format) as input and outputs insightful statistics. Our iCOMIC toolkit pipeline featuring many independent workflows is embedded in the popular Snakemake workflow management system. It can analyze whole-genome and transcriptome data and is characterized by a user-friendly GUI that offers several advantages, including minimal execution steps and eliminating the need for complex command-line arguments. Notably, we have integrated algorithms developed in-house to predict pathogenicity among cancer-causing mutations and differentiate between tumor suppressor genes and oncogenes from somatic mutation data. We benchmarked our tool against Genome In A Bottle benchmark dataset (NA12878) and got the highest F1 score of 0.971 and 0.988 for indels and SNPs, respectively, using the BWA MEM—GATK HC DNA-Seq pipeline. Similarly, we achieved a correlation coefficient of r = 0.85 using the HISAT2-StringTie-ballgown and STAR-StringTie-ballgown RNA-Seq pipelines on the human monocyte dataset (SRP082682). Overall, our tool enables easy analyses of omics datasets, significantly ameliorating complex data analysis pipelines.
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Affiliation(s)
- Anjana Anilkumar Sithara
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras , Chennai 600036, India
- Centre for Integrative Biology and Systems mEdicine , IIT Madras, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI) , IIT Madras, India
| | - Devi Priyanka Maripuri
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras , Chennai 600036, India
- Centre for Integrative Biology and Systems mEdicine , IIT Madras, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI) , IIT Madras, India
| | - Keerthika Moorthy
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras , Chennai 600036, India
- Centre for Integrative Biology and Systems mEdicine , IIT Madras, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI) , IIT Madras, India
| | - Sai Sruthi Amirtha Ganesh
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras , Chennai 600036, India
- Centre for Integrative Biology and Systems mEdicine , IIT Madras, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI) , IIT Madras, India
| | - Philge Philip
- Centre for Integrative Biology and Systems mEdicine , IIT Madras, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI) , IIT Madras, India
| | - Shayantan Banerjee
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras , Chennai 600036, India
- Centre for Integrative Biology and Systems mEdicine , IIT Madras, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI) , IIT Madras, India
| | - Malvika Sudhakar
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras , Chennai 600036, India
- Centre for Integrative Biology and Systems mEdicine , IIT Madras, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI) , IIT Madras, India
| | - Karthik Raman
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras , Chennai 600036, India
- Centre for Integrative Biology and Systems mEdicine , IIT Madras, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI) , IIT Madras, India
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50
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Lao L, Bourdeau I, Gagliardi L, He X, Shi W, Hao B, Tan M, Hu Y, Peng J, Coulombe B, Torpy DJ, Scott HS, Lacroix A, Luo H, Wu J. ARMC5 is part of an RPB1-specific ubiquitin ligase implicated in adrenal hyperplasia. Nucleic Acids Res 2022; 50:6343-6367. [PMID: 35687106 PMCID: PMC9226510 DOI: 10.1093/nar/gkac483] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 05/19/2022] [Accepted: 05/24/2022] [Indexed: 12/13/2022] Open
Abstract
ARMC5 is implicated in several pathological conditions, but its function remains unknown. We have previously identified CUL3 and RPB1 (the largest subunit of RNA polymerase II (Pol II) as potential ARMC5-interacting proteins. Here, we show that ARMC5, CUL3 and RBX1 form an active E3 ligase complex specific for RPB1. ARMC5, CUL3, and RBX1 formed an active E3 specific for RPB1. Armc5 deletion caused a significant reduction in RPB1 ubiquitination and an increase in an accumulation of RPB1, and hence an enlarged Pol II pool in normal tissues and organs. The compromised RPB1 degradation did not cause generalized Pol II stalling nor depressed transcription in the adrenal glands but did result in dysregulation of a subset of genes, with most upregulated. We found RPB1 to be highly expressed in the adrenal nodules from patients with primary bilateral macronodular adrenal hyperplasia (PBMAH) harboring germline ARMC5 mutations. Mutant ARMC5 had altered binding with RPB1. In summary, we discovered that wildtype ARMC5 was part of a novel RPB1-specific E3. ARMC5 mutations resulted in an enlarged Pol II pool, which dysregulated a subset of effector genes. Such an enlarged Pol II pool and gene dysregulation was correlated to adrenal hyperplasia in humans and KO mice.
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Affiliation(s)
- Linjiang Lao
- Centre de recherché, Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec H2X 0A9, Canada
| | - Isabelle Bourdeau
- Centre de recherché, Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec H2X 0A9, Canada.,Endocrinology Division, Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec H2X 0A9, Canada
| | - Lucia Gagliardi
- Adelaide Medical School, University of Adelaide, Adelaide, SA5000, Australia.,Endocrine and Metabolic Unit, Royal Adelaide Hospital, Adelaide, SA5000, Australia.,Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA5006, Australia.,Endocrine and Diabetes Unit, Queen Elizabeth Hospital, Adelaide, SA5011, Australia
| | - Xiao He
- Centre de recherché, Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec H2X 0A9, Canada
| | - Wei Shi
- Centre de recherché, Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec H2X 0A9, Canada
| | - Bingbing Hao
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Minjia Tan
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Yan Hu
- Centre de recherché, Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec H2X 0A9, Canada
| | - Junzheng Peng
- Centre de recherché, Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec H2X 0A9, Canada
| | - Benoit Coulombe
- Department of Translational Proteomics, Institut de Recherches Cliniques de Montréal, Montréal, Québec, Canada.,Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, Quebec, Canada
| | - David J Torpy
- Adelaide Medical School, University of Adelaide, Adelaide, SA5000, Australia.,Endocrine and Metabolic Unit, Royal Adelaide Hospital, Adelaide, SA5000, Australia
| | - Hamish S Scott
- Adelaide Medical School, University of Adelaide, Adelaide, SA5000, Australia.,Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA5006, Australia.,Centre for Cancer Biology, an alliance between SA Pathology and the University of South Australia, Adelaide, SA5001, Australia.,UniSA Clinical and Health Sciences, University of South Australia, Adelaide, SA5001, Australia
| | - Andre Lacroix
- Centre de recherché, Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec H2X 0A9, Canada.,Endocrinology Division, Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec H2X 0A9, Canada
| | - Hongyu Luo
- Centre de recherché, Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec H2X 0A9, Canada
| | - Jiangping Wu
- Centre de recherché, Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec H2X 0A9, Canada.,Nephrology Division, Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec H2X 0A9, Canada
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