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Gong K, Xue C, Feng Z, Pan R, Wang M, Chen S, Chen Y, Guan Y, Dai L, Zhang S, Jiang L, Li L, Wang B, Yin Z, Ma L, Iwakiri Y, Tang J, Liao C, Chen H, Duan Y. Intestinal Nogo-B reduces GLP1 levels by binding to proglucagon on the endoplasmic reticulum to inhibit PCSK1 cleavage. Nat Commun 2024; 15:6845. [PMID: 39122737 PMCID: PMC11315690 DOI: 10.1038/s41467-024-51352-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 08/02/2024] [Indexed: 08/12/2024] Open
Abstract
Glucagon-like peptide 1 (GLP1), which is mainly processed and cleaved from proglucagon in enteroendocrine cells (EECs) of the intestinal tract, acts on the GLP1 receptor in pancreatic cells to stimulate insulin secretion and to inhibit glucagon secretion. However, GLP1 processing is not fully understood. Here, we show that reticulon 4B (Nogo-B), an endoplasmic reticulum (ER)-resident protein, interacts with the major proglucagon fragment of proglucagon to retain proglucagon on the ER, thereby inhibiting PCSK1-mediated cleavage of proglucagon in the Golgi. Intestinal Nogo-B knockout in male type 2 diabetes mellitus (T2DM) mice increases GLP1 and insulin levels and decreases glucagon levels, thereby alleviating pancreatic injury and insulin resistance. Finally, we identify aberrantly elevated Nogo-B expression and inhibited proglucagon cleavage in EECs from diabetic patients. Our study reveals the subcellular regulatory processes involving Nogo-B during GLP1 production and suggests intestinal Nogo-B as a potential therapeutic target for T2DM.
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Affiliation(s)
- Ke Gong
- Division of Life Sciences and Medicine, Department of Cardiology, the First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, Anhui, China
- Department of Physiology, Faculty of Basic Medical Sciences, Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, Hubei, China
- Key Laboratory of Metabolism and Regulation for Major Diseases of Anhui Higher Education Institutes, Hefei University of Technology, Hefei, Anhui, China
| | - Chao Xue
- College of Life Sciences, Key Laboratory of Bioactive Materials of Ministry of Education, Nankai University, Tianjin, China
| | - Zian Feng
- Division of Life Sciences and Medicine, Department of Cardiology, the First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, Anhui, China
| | - Ruru Pan
- Division of Life Sciences and Medicine, Department of Cardiology, the First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, Anhui, China
| | - Mengyao Wang
- Key Laboratory of Metabolism and Regulation for Major Diseases of Anhui Higher Education Institutes, Hefei University of Technology, Hefei, Anhui, China
| | - Shasha Chen
- Key Laboratory of Metabolism and Regulation for Major Diseases of Anhui Higher Education Institutes, Hefei University of Technology, Hefei, Anhui, China
| | - Yuanli Chen
- Key Laboratory of Metabolism and Regulation for Major Diseases of Anhui Higher Education Institutes, Hefei University of Technology, Hefei, Anhui, China
| | - Yudong Guan
- Department of Geriatrics, and Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Lingyun Dai
- Department of Geriatrics, and Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Shuang Zhang
- Key Laboratory of Metabolism and Regulation for Major Diseases of Anhui Higher Education Institutes, Hefei University of Technology, Hefei, Anhui, China
| | - Liwei Jiang
- Laboratory of Immunoengineering, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, China
| | - Ling Li
- Laboratory of Immunoengineering, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, China
| | - Bei Wang
- Department of Pathology, China-Japan Friendship Hospital, Beijing, China
| | - Zequn Yin
- Division of Life Sciences and Medicine, Department of Cardiology, the First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, Anhui, China
| | - Likun Ma
- Division of Life Sciences and Medicine, Department of Cardiology, the First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, Anhui, China
| | - Yasuko Iwakiri
- Section of Digestive Diseases, Yale University School of Medicine, New Haven, CT, USA
| | - Junming Tang
- Department of Physiology, Faculty of Basic Medical Sciences, Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, Hubei, China
| | - Chenzhong Liao
- Key Laboratory of Metabolism and Regulation for Major Diseases of Anhui Higher Education Institutes, Hefei University of Technology, Hefei, Anhui, China
| | - Houzao Chen
- Department of Biochemistry & Molecular Biology, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yajun Duan
- Division of Life Sciences and Medicine, Department of Cardiology, the First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, Anhui, China.
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2
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Chen Q, Wu M, Tang Q, Yan P, Zhu L. Age-Related Alterations in Immune Function and Inflammation: Focus on Ischemic Stroke. Aging Dis 2024; 15:1046-1074. [PMID: 37728582 PMCID: PMC11081165 DOI: 10.14336/ad.2023.0721-1] [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: 05/03/2023] [Accepted: 07/21/2023] [Indexed: 09/21/2023] Open
Abstract
The aging of the global population poses significant scientific challenges. Moreover, the biological process of aging is the most significant risk factor for most chronic illnesses; therefore, understanding the molecular and cellular mechanisms underlying these aging-related challenges is crucial for extending the healthy lifespan of older individuals. Preventing brain aging remains a priority public health goal, and integrative and comprehensive aging analyses have revealed that immunosenescence is a potential cause of age-related brain damage and disease (e.g., stroke). Importantly, the neuroinflammatory and immune systems present two-way contact and thus can affect each other. Emerging evidence supports the numerous effects of immunosenescence- and inflammation-mediated immunity in neurologically injured brains. In this study, we briefly outline how aging alters the pathophysiology and transcriptional amplitude in patients who experienced stroke and then discuss how the immune system and its cellular components and molecular mechanisms are affected by age after stroke. Finally, we highlight emerging interventions with the potential to slow down or reduce aging and prevent stroke onset.
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Affiliation(s)
- Qiuxin Chen
- The First Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin 150000, China
| | - Minmin Wu
- Heilongjiang University of Chinese Medicine, Harbin 150000, China
| | - Qiang Tang
- The Second Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin 150000, China
| | - Peiyu Yan
- Faculty of Chinese Medicine, Macau University of Science and Technology, Macau 999078, China
- State Key Laboratory of Quality Research in Chinese Medicines, Macau University of Science and Technology, Macau 999078, China
| | - Luwen Zhu
- The Second Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin 150000, China
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3
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Savić R, Yang J, Koplev S, An MC, Patel PL, O'Brien RN, Dubose BN, Dodatko T, Rogatsky E, Sukhavasi K, Ermel R, Ruusalepp A, Houten SM, Kovacic JC, Stewart AF, Yohn CB, Schadt EE, Laberge RM, Björkegren JLM, Tu Z, Argmann C. Integration of transcriptomes of senescent cell models with multi-tissue patient samples reveals reduced COL6A3 as an inducer of senescence. Cell Rep 2023; 42:113371. [PMID: 37938972 PMCID: PMC10955802 DOI: 10.1016/j.celrep.2023.113371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 05/23/2023] [Accepted: 10/17/2023] [Indexed: 11/10/2023] Open
Abstract
Senescent cells are a major contributor to age-dependent cardiovascular tissue dysfunction, but knowledge of their in vivo cell markers and tissue context is lacking. To reveal tissue-relevant senescence biology, we integrate the transcriptomes of 10 experimental senescence cell models with a 224 multi-tissue gene co-expression network based on RNA-seq data of seven tissues biopsies from ∼600 coronary artery disease (CAD) patients. We identify 56 senescence-associated modules, many enriched in CAD GWAS genes and correlated with cardiometabolic traits-which supports universality of senescence gene programs across tissues and in CAD. Cross-tissue network analyses reveal 86 candidate senescence-associated secretory phenotype (SASP) factors, including COL6A3. Experimental knockdown of COL6A3 induces transcriptional changes that overlap the majority of the experimental senescence models, with cell-cycle arrest linked to modulation of DREAM complex-targeted genes. We provide a transcriptomic resource for cellular senescence and identify candidate biomarkers, SASP factors, and potential drivers of senescence in human tissues.
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Affiliation(s)
- Radoslav Savić
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Jialiang Yang
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Simon Koplev
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, UK
| | - Mahru C An
- UNITY Biotechnology, South San Francisco, CA 94080, USA
| | | | | | | | - Tetyana Dodatko
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Eduard Rogatsky
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Katyayani Sukhavasi
- Department of Cardiac Surgery and The Heart Clinic, Tartu University Hospital, Tartu, Estonia
| | - Raili Ermel
- Department of Cardiac Surgery and The Heart Clinic, Tartu University Hospital, Tartu, Estonia
| | - Arno Ruusalepp
- Department of Cardiac Surgery and The Heart Clinic, Tartu University Hospital, Tartu, Estonia; Clinical Gene Networks AB, Stockholm, Sweden
| | - Sander M Houten
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Jason C Kovacic
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA; Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia; St. Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Andrew F Stewart
- Diabetes Obesity Metabolism Institute, The Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Eric E Schadt
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | | | - Johan L M Björkegren
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA; Clinical Gene Networks AB, Stockholm, Sweden; Department of Medicine, Karolinska Institutet, Karolinska Universitetssjukhuset, Huddinge, Sweden
| | - Zhidong Tu
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Carmen Argmann
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA.
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4
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Shin JH, Bozadjieva-Kramer N, Seeley RJ. Reg3γ: current understanding and future therapeutic opportunities in metabolic disease. Exp Mol Med 2023; 55:1672-1677. [PMID: 37524871 PMCID: PMC10474034 DOI: 10.1038/s12276-023-01054-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 05/01/2023] [Indexed: 08/02/2023] Open
Abstract
Regenerating family member gamma, Reg3γ (the mouse homolog of human REG3A), belonging to the antimicrobial peptides (AMPs), functions as a part of the host immune system to maintain spatial segregation between the gut bacteria and the host in the intestine via bactericidal activity. There is emerging evidence that gut manipulations such as bariatric surgery, dietary supplementation or drug treatment to produce metabolic benefits alter the gut microbiome. In addition to changes in a wide range of gut hormones, these gut manipulations also induce the expression of Reg3γ in the intestine. Studies over the past decades have revealed that Reg3γ not only plays a role in the gut lumen but can also contribute to host physiology through interaction with the gut microbiota. Herein, we discuss the current knowledge regarding the biology of Reg3γ, its role in various metabolic functions, and new opportunities for therapeutic strategies to treat metabolic disorders.
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Affiliation(s)
- Jae Hoon Shin
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
| | | | - Randy J Seeley
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA.
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5
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Castranio EL, Hasel P, Haure-Mirande JV, Ramirez Jimenez AV, Hamilton BW, Kim RD, Glabe CG, Wang M, Zhang B, Gandy S, Liddelow SA, Ehrlich ME. Microglial INPP5D limits plaque formation and glial reactivity in the PSAPP mouse model of Alzheimer's disease. Alzheimers Dement 2023; 19:2239-2252. [PMID: 36448627 PMCID: PMC10481344 DOI: 10.1002/alz.12821] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 08/23/2022] [Accepted: 09/13/2022] [Indexed: 12/05/2022]
Abstract
INTRODUCTION The inositol polyphosphate-5-phosphatase D (INPP5D) gene encodes a dual-specificity phosphatase that can dephosphorylate both phospholipids and phosphoproteins. Single nucleotide polymorphisms in INPP5D impact risk for developing late onset sporadic Alzheimer's disease (LOAD). METHODS To assess the consequences of inducible Inpp5d knockdown in microglia of APPKM670/671NL /PSEN1Δexon9 (PSAPP) mice, we injected 3-month-old Inpp5dfl/fl /Cx3cr1CreER/+ and PSAPP/Inpp5dfl/fl /Cx3cr1CreER/+ mice with either tamoxifen (TAM) or corn oil (CO) to induce recombination. RESULTS At age 6 months, we found that the percent area of 6E10+ deposits and plaque-associated microglia in Inpp5d knockdown mice were increased compared to controls. Spatial transcriptomics identified a plaque-specific expression profile that was extensively altered by Inpp5d knockdown. DISCUSSION These results demonstrate that conditional Inpp5d downregulation in the PSAPP mouse increases plaque burden and recruitment of microglia to plaques. Spatial transcriptomics highlighted an extended gene expression signature associated with plaques and identified CST7 (cystatin F) as a novel marker of plaques. HIGHLIGHTS Inpp5d knockdown increases plaque burden and plaque-associated microglia number. Spatial transcriptomics identifies an expanded plaque-specific gene expression profile. Plaque-induced gene expression is altered by Inpp5d knockdown in microglia. Our plaque-associated gene signature overlaps with human Alzheimer's disease gene networks.
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Affiliation(s)
- Emilie L. Castranio
- Department of Neurology, Icahn School of Medicine at Mount
Sinai, New York, New York, USA
| | - Philip Hasel
- Neuroscience Institute, NYU Grossman School of Medicine,
New York, New York, USA
| | | | | | - B. Wade Hamilton
- Department of Neurology, Icahn School of Medicine at Mount
Sinai, New York, New York, USA
| | - Rachel D. Kim
- Neuroscience Institute, NYU Grossman School of Medicine,
New York, New York, USA
| | - Charles G. Glabe
- Department of Molecular Biology and Biochemistry,
University of California, Irvine, Irvine, California, USA
| | - Minghui Wang
- Department of Genetics and Genomic Sciences, Icahn School
of Medicine at Mount Sinai, New York, New York, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School
of Medicine at Mount Sinai, New York, New York, USA
| | - Sam Gandy
- Department of Neurology, Icahn School of Medicine at Mount
Sinai, New York, New York, USA
- Department of Psychiatry and Alzheimer’s Disease
Research Center, Icahn School of Medicine at Mount Sinai, New York, New York,
USA
- James J. Peters VA Medical Center, Bronx, New York,
USA
| | - Shane A. Liddelow
- Neuroscience Institute, NYU Grossman School of Medicine,
New York, New York, USA
- Department of Neuroscience & Physiology, NYU Grossman
School of Medicine, New York, New York, USA
- Department of Ophthalmology, NYU Grossman School of
Medicine, New York, New York, USA
- Parekh Center for Interdisciplinary Neurology, NYU Grossman
School of Medicine, New York, New York, USA
| | - Michelle E. Ehrlich
- Department of Neurology, Icahn School of Medicine at Mount
Sinai, New York, New York, USA
- Department of Genetics and Genomic Sciences, Icahn School
of Medicine at Mount Sinai, New York, New York, USA
- Department of Pediatrics, Icahn School of Medicine at
Mount Sinai, New York, New York, USA
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6
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Lacombe J, Guo K, Bonneau J, Faubert D, Gioanni F, Vivoli A, Muir SM, Hezzaz S, Poitout V, Ferron M. Vitamin K-dependent carboxylation regulates Ca 2+ flux and adaptation to metabolic stress in β cells. Cell Rep 2023; 42:112500. [PMID: 37171959 DOI: 10.1016/j.celrep.2023.112500] [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: 05/08/2022] [Revised: 02/24/2023] [Accepted: 04/26/2023] [Indexed: 05/14/2023] Open
Abstract
Vitamin K is a micronutrient necessary for γ-carboxylation of glutamic acids. This post-translational modification occurs in the endoplasmic reticulum (ER) and affects secreted proteins. Recent clinical studies implicate vitamin K in the pathophysiology of diabetes, but the underlying molecular mechanism remains unknown. Here, we show that mouse β cells lacking γ-carboxylation fail to adapt their insulin secretion in the context of age-related insulin resistance or diet-induced β cell stress. In human islets, γ-carboxylase expression positively correlates with improved insulin secretion in response to glucose. We identify endoplasmic reticulum Gla protein (ERGP) as a γ-carboxylated ER-resident Ca2+-binding protein expressed in β cells. Mechanistically, γ-carboxylation of ERGP protects cells against Ca2+ overfilling by diminishing STIM1 and Orai1 interaction and restraining store-operated Ca2+ entry. These results reveal a critical role of vitamin K-dependent carboxylation in regulation of Ca2+ flux in β cells and in their capacity to adapt to metabolic stress.
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Affiliation(s)
- Julie Lacombe
- Molecular Physiology Research Unit, Institut de Recherches Cliniques de Montréal, Montréal, QC H2W 1R7, Canada.
| | - Kevin Guo
- Molecular Physiology Research Unit, Institut de Recherches Cliniques de Montréal, Montréal, QC H2W 1R7, Canada; Division of Experimental Medicine, McGill University, Montréal, QC H4A 3J1, Canada
| | - Jessica Bonneau
- Molecular Physiology Research Unit, Institut de Recherches Cliniques de Montréal, Montréal, QC H2W 1R7, Canada; Programme de Biologie Moléculaire, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Denis Faubert
- Mass Spectrometry and Proteomics Platform, Institut de Recherches Cliniques de Montréal, Montréal, QC H2W 1R7, Canada
| | - Florian Gioanni
- Molecular Physiology Research Unit, Institut de Recherches Cliniques de Montréal, Montréal, QC H2W 1R7, Canada
| | - Alexis Vivoli
- Montreal Diabetes Research Center, Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC H2X 0A9, Canada
| | - Sarah M Muir
- Molecular Physiology Research Unit, Institut de Recherches Cliniques de Montréal, Montréal, QC H2W 1R7, Canada
| | - Soraya Hezzaz
- Molecular Physiology Research Unit, Institut de Recherches Cliniques de Montréal, Montréal, QC H2W 1R7, Canada
| | - Vincent Poitout
- Montreal Diabetes Research Center, Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC H2X 0A9, Canada; Département de Médecine, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Mathieu Ferron
- Molecular Physiology Research Unit, Institut de Recherches Cliniques de Montréal, Montréal, QC H2W 1R7, Canada; Division of Experimental Medicine, McGill University, Montréal, QC H4A 3J1, Canada; Programme de Biologie Moléculaire, Université de Montréal, Montréal, QC H3T 1J4, Canada; Département de Médecine, Université de Montréal, Montréal, QC H3T 1J4, Canada.
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7
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Forst CV, Zeng L, Wang Q, Zhou X, Vatansever S, Xu P, Song W, Tu Z, Zhang B. Multiscale network analysis identifies potential receptors for SARS-CoV-2 and reveals their tissue-specific and age-dependent expression. FEBS Lett 2023; 597:1384-1402. [PMID: 36951513 PMCID: PMC10294276 DOI: 10.1002/1873-3468.14613] [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: 07/11/2022] [Revised: 02/13/2023] [Accepted: 02/27/2023] [Indexed: 03/24/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has affected tens of millions of individuals and caused hundreds of thousands of deaths worldwide. Here, we present a comprehensive, multiscale network analysis of the transcriptional response to the virus. In particular, we focused on key regulators, cell receptors, and host processes that were hijacked by the virus for its advantage. ACE2-controlled processes involved CD300e (a TYROBP receptor) as a key regulator and the activation of IL-2 pro-inflammatory cytokine signaling. We further investigated the age dependency of such receptors in different tissues. In summary, this study provides novel insights into the gene regulatory organization during the SARS-CoV-2 infection and the tissue-specific, age-dependent expression of the cell receptors involved in COVID-19.
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Affiliation(s)
- Christian V. Forst
- Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount SinaiNew YorkNYUSA
- Mount Sinai Center for Transformative Disease ModelingIcahn School of Medicine at Mount SinaiNew YorkNYUSA
- Icahn Institute for Data Science and Genomic TechnologyIcahn School of Medicine at Mount SinaiNew YorkNYUSA
- Department of MicrobiologyIcahn School of Medicine at Mount SinaiNew YorkNYUSA
| | - Lu Zeng
- Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount SinaiNew YorkNYUSA
| | - Qian Wang
- Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount SinaiNew YorkNYUSA
- Mount Sinai Center for Transformative Disease ModelingIcahn School of Medicine at Mount SinaiNew YorkNYUSA
- Icahn Institute for Data Science and Genomic TechnologyIcahn School of Medicine at Mount SinaiNew YorkNYUSA
| | - Xianxiao Zhou
- Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount SinaiNew YorkNYUSA
- Mount Sinai Center for Transformative Disease ModelingIcahn School of Medicine at Mount SinaiNew YorkNYUSA
- Icahn Institute for Data Science and Genomic TechnologyIcahn School of Medicine at Mount SinaiNew YorkNYUSA
| | - Sezen Vatansever
- Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount SinaiNew YorkNYUSA
- Mount Sinai Center for Transformative Disease ModelingIcahn School of Medicine at Mount SinaiNew YorkNYUSA
- Icahn Institute for Data Science and Genomic TechnologyIcahn School of Medicine at Mount SinaiNew YorkNYUSA
| | - Peng Xu
- Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount SinaiNew YorkNYUSA
- Mount Sinai Center for Transformative Disease ModelingIcahn School of Medicine at Mount SinaiNew YorkNYUSA
- Icahn Institute for Data Science and Genomic TechnologyIcahn School of Medicine at Mount SinaiNew YorkNYUSA
| | - Won‐Min Song
- Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount SinaiNew YorkNYUSA
- Mount Sinai Center for Transformative Disease ModelingIcahn School of Medicine at Mount SinaiNew YorkNYUSA
- Icahn Institute for Data Science and Genomic TechnologyIcahn School of Medicine at Mount SinaiNew YorkNYUSA
| | - Zhidong Tu
- Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount SinaiNew YorkNYUSA
- Icahn Institute for Data Science and Genomic TechnologyIcahn School of Medicine at Mount SinaiNew YorkNYUSA
| | - Bin Zhang
- Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount SinaiNew YorkNYUSA
- Mount Sinai Center for Transformative Disease ModelingIcahn School of Medicine at Mount SinaiNew YorkNYUSA
- Icahn Institute for Data Science and Genomic TechnologyIcahn School of Medicine at Mount SinaiNew YorkNYUSA
- Department of Pharmacological SciencesIcahn School of Medicine at Mount SinaiNew YorkNYUSA
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8
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Hernandez R, Shi J, Liu J, Li X, Wu J, Zhao L, Zhou T, Chen Q, Zhou C. PANDORA-Seq unveils the hidden small noncoding RNA landscape in atherosclerosis of LDL receptor-deficient mice. J Lipid Res 2023; 64:100352. [PMID: 36871792 PMCID: PMC10119612 DOI: 10.1016/j.jlr.2023.100352] [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: 09/02/2022] [Revised: 02/08/2023] [Accepted: 02/25/2023] [Indexed: 03/06/2023] Open
Abstract
Small noncoding RNAs (sncRNAs) play diverse roles in numerous biological processes. While the widely used RNA sequencing (RNA-Seq) method has advanced sncRNA discovery, RNA modifications can interfere with the complementary DNA library construction process, preventing the discovery of highly modified sncRNAs including transfer RNA-derived small RNAs (tsRNAs) and ribosomal RNA-derived small RNAs (rsRNAs) that may have important functions in disease development. To address this technical obstacle, we recently developed a novel PANDORA-Seq (Panoramic RNA Display by Overcoming RNA Modification Aborted Sequencing) method to overcome RNA modification-elicited sequence interferences. To identify novel sncRNAs associated with atherosclerosis development, LDL receptor-deficient (LDLR-/-) mice were fed a low-cholesterol diet or high-cholesterol diet (HCD) for 9 weeks. Total RNAs isolated from the intima were subjected to PANDORA-Seq and traditional RNA-Seq. By overcoming RNA modification-elicited limitations, PANDORA-Seq unveiled an rsRNA/tsRNA-enriched sncRNA landscape in the atherosclerotic intima of LDLR-/- mice, which was strikingly different from that detected by traditional RNA-Seq. While microRNAs were the dominant sncRNAs detected by traditional RNA-Seq, PANDORA-Seq substantially increased the reads of rsRNAs and tsRNAs. PANDORA-Seq also detected 1,383 differentially expressed sncRNAs induced by HCD feeding, including 1,160 rsRNAs and 195 tsRNAs. One of HCD-induced intimal tsRNAs, tsRNA-Arg-CCG, may contribute to atherosclerosis development by regulating the proatherogenic gene expression in endothelial cells. Overall, PANDORA-Seq revealed a hidden rsRNA and tsRNA population associated with atherosclerosis development. These understudied tsRNAs and rsRNAs, which are much more abundant than microRNAs in the atherosclerotic intima of LDLR-/- mice, warrant further investigations.
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Affiliation(s)
- Rebecca Hernandez
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA, USA
| | - Junchao Shi
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA, USA
| | - Jingwei Liu
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA, USA
| | - Xiuchun Li
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA, USA
| | - Jake Wu
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA, USA
| | - Linlin Zhao
- Department of Chemistry, University of California, Riverside, CA, USA
| | - Tong Zhou
- Department of Physiology and Cell Biology, Reno School of Medicine, University of Nevada, Reno, NV, USA
| | - Qi Chen
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA, USA; Molecular Medicine Program, Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Changcheng Zhou
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA, USA.
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9
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Sen'kova AV, Savin IA, Odarenko KV, Salomatina OV, Salakhutdinov NF, Zenkova MA, Markov AV. Protective effect of soloxolone derivatives in carrageenan- and LPS-driven acute inflammation: Pharmacological profiling and their effects on key inflammation-related processes. Biomed Pharmacother 2023; 159:114231. [PMID: 36640672 DOI: 10.1016/j.biopha.2023.114231] [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: 10/17/2022] [Revised: 12/21/2022] [Accepted: 01/08/2023] [Indexed: 01/13/2023] Open
Abstract
The anti-inflammatory potential of three cyanoenone-containing triterpenoids, including soloxolone methyl (SM), soloxolone (S) and its novel derivative bearing at the C-30 amidoxime moiety (SAO), was studied in murine models of acute inflammation. It was found that the compounds effectively suppressed the development of carrageenan-induced paw edema and peritonitis as well as lipopolysaccharide (LPS)-driven acute lung injury (ALI) with therapeutic outcomes comparable with that of the reference drugs indomethacin and dexamethasone. Non-immunogenic carrageenan-stimulated inflammation was more sensitive to the transformation of C-30 of SM compared with immunogenic LPS-induced inflammation: the anti-inflammatory properties of the studied compounds against carrageenan-induced paw edema and peritonitis decreased in the order of SAO > S > > SM, whereas the efficiency of these triterpenoids against LPS-driven ALI was similar (SAO ≈ S ≈ SM). Further studies demonstrated that soloxolone derivatives significantly inhibited a range of immune-related processes, including granulocyte influx and the expression of key pro-inflammatory cytokines and chemokines in the inflamed sites as well as the functional activity of macrophages. Moreover, SM was found to prevent inflammation-associated apoptosis of A549 pneumocytes and effectively inhibited the protease activity of thrombin (IC50 = 10.3 µM) tightly associated with rodent inflammatome. Taken together, our findings demonstrate that soloxolone derivatives can be considered as novel promising anti-inflammatory drug candidates with multi-targeted mechanism of action.
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Affiliation(s)
- Aleksandra V Sen'kova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrent'ev avenue, 8, 630090 Novosibirsk, Russia.
| | - Innokenty A Savin
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, Lavrent'ev avenue, 9, 630090 Novosibirsk, Russia.
| | - Kirill V Odarenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrent'ev avenue, 8, 630090 Novosibirsk, Russia.
| | - Oksana V Salomatina
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, Lavrent'ev avenue, 9, 630090 Novosibirsk, Russia.
| | - Nariman F Salakhutdinov
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, Lavrent'ev avenue, 9, 630090 Novosibirsk, Russia.
| | - Marina A Zenkova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrent'ev avenue, 8, 630090 Novosibirsk, Russia.
| | - Andrey V Markov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrent'ev avenue, 8, 630090 Novosibirsk, Russia.
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10
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Identification of Novel Core Genes Involved in Malignant Transformation of Inflamed Colon Tissue Using a Computational Biology Approach and Verification in Murine Models. Int J Mol Sci 2023; 24:ijms24054311. [PMID: 36901742 PMCID: PMC10001800 DOI: 10.3390/ijms24054311] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 02/18/2023] [Accepted: 02/20/2023] [Indexed: 02/24/2023] Open
Abstract
Inflammatory bowel disease (IBD) is a complex and multifactorial systemic disorder of the gastrointestinal tract and is strongly associated with the development of colorectal cancer. Despite extensive studies of IBD pathogenesis, the molecular mechanism of colitis-driven tumorigenesis is not yet fully understood. In the current animal-based study, we report a comprehensive bioinformatics analysis of multiple transcriptomics datasets from the colon tissue of mice with acute colitis and colitis-associated cancer (CAC). We performed intersection of differentially expressed genes (DEGs), their functional annotation, reconstruction, and topology analysis of gene association networks, which, when combined with the text mining approach, revealed that a set of key overexpressed genes involved in the regulation of colitis (C3, Tyrobp, Mmp3, Mmp9, Timp1) and CAC (Timp1, Adam8, Mmp7, Mmp13) occupied hub positions within explored colitis- and CAC-related regulomes. Further validation of obtained data in murine models of dextran sulfate sodium (DSS)-induced colitis and azoxymethane/DSS-stimulated CAC fully confirmed the association of revealed hub genes with inflammatory and malignant lesions of colon tissue and demonstrated that genes encoding matrix metalloproteinases (acute colitis: Mmp3, Mmp9; CAC: Mmp7, Mmp13) can be used as a novel prognostic signature for colorectal neoplasia in IBD. Finally, using publicly available transcriptomics data, translational bridge interconnecting of listed colitis/CAC-associated core genes with the pathogenesis of ulcerative colitis, Crohn's disease, and colorectal cancer in humans was identified. Taken together, a set of key genes playing a core function in colon inflammation and CAC was revealed, which can serve both as promising molecular markers and therapeutic targets to control IBD and IBD-associated colorectal neoplasia.
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11
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Bui TA, Jickling GC, Winship IR. Neutrophil dynamics and inflammaging in acute ischemic stroke: A transcriptomic review. Front Aging Neurosci 2022; 14:1041333. [PMID: 36620775 PMCID: PMC9813499 DOI: 10.3389/fnagi.2022.1041333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022] Open
Abstract
Stroke is among the leading causes of death and disability worldwide. Restoring blood flow through recanalization is currently the only acute treatment for cerebral ischemia. Unfortunately, many patients that achieve a complete recanalization fail to regain functional independence. Recent studies indicate that activation of peripheral immune cells, particularly neutrophils, may contribute to microcirculatory failure and futile recanalization. Stroke primarily affects the elderly population, and mortality after endovascular therapies is associated with advanced age. Previous analyses of differential gene expression across injury status and age identify ischemic stroke as a complex age-related disease. It also suggests robust interactions between stroke injury, aging, and inflammation on a cellular and molecular level. Understanding such interactions is crucial in developing effective protective treatments. The global stroke burden will continue to increase with a rapidly aging human population. Unfortunately, the mechanisms of age-dependent vulnerability are poorly defined. In this review, we will discuss how neutrophil-specific gene expression patterns may contribute to poor treatment responses in stroke patients. We will also discuss age-related transcriptional changes that may contribute to poor clinical outcomes and greater susceptibility to cerebrovascular diseases.
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Affiliation(s)
- Truong An Bui
- Neuroscience and Mental Health Institute, University of Alberta, Edmonton, AB, Canada
| | - Glen C. Jickling
- Neuroscience and Mental Health Institute, University of Alberta, Edmonton, AB, Canada,Department of Medicine, Division of Neurology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Ian R. Winship
- Neuroscience and Mental Health Institute, University of Alberta, Edmonton, AB, Canada,Neuroscience and Mental Health Institute, University of Alberta, Edmonton, AB, Canada,*Correspondence: Ian R. Winship,
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12
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Katsuki S, K. Jha P, Lupieri A, Nakano T, Passos LS, Rogers MA, Becker-Greene D, Le TD, Decano JL, Ho Lee L, Guimaraes GC, Abdelhamid I, Halu A, Muscoloni A, V. Cannistraci C, Higashi H, Zhang H, Vromman A, Libby P, Keith Ozaki C, Sharma A, Singh SA, Aikawa E, Aikawa M. Proprotein Convertase Subtilisin/Kexin 9 (PCSK9) Promotes Macrophage Activation via LDL Receptor-Independent Mechanisms. Circ Res 2022; 131:873-889. [PMID: 36263780 PMCID: PMC9973449 DOI: 10.1161/circresaha.121.320056] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
BACKGROUND Activated macrophages contribute to the pathogenesis of vascular disease. Vein graft failure is a major clinical problem with limited therapeutic options. PCSK9 (proprotein convertase subtilisin/kexin 9) increases low-density lipoprotein (LDL)-cholesterol levels via LDL receptor (LDLR) degradation. The role of PCSK9 in macrophage activation and vein graft failure is largely unknown, especially through LDLR-independent mechanisms. This study aimed to explore a novel mechanism of macrophage activation and vein graft disease induced by circulating PCSK9 in an LDLR-independent fashion. METHODS We used Ldlr-/- mice to examine the LDLR-independent roles of circulating PCSK9 in experimental vein grafts. Adeno-associated virus (AAV) vector encoding a gain-of-function mutant of PCSK9 (rAAV8/D377Y-mPCSK9) induced hepatic PCSK9 overproduction. To explore novel inflammatory targets of PCSK9, we used systems biology in Ldlr-/- mouse macrophages. RESULTS In Ldlr-/- mice, AAV-PCSK9 increased circulating PCSK9, but did not change serum cholesterol and triglyceride levels. AAV-PCSK9 promoted vein graft lesion development when compared with control AAV. In vivo molecular imaging revealed that AAV-PCSK9 increased macrophage accumulation and matrix metalloproteinase activity associated with decreased fibrillar collagen, a molecular determinant of atherosclerotic plaque stability. AAV-PCSK9 induced mRNA expression of the pro-inflammatory mediators IL-1β (interleukin-1 beta), TNFα (tumor necrosis factor alpha), and MCP-1 (monocyte chemoattractant protein-1) in peritoneal macrophages underpinned by an in vitro analysis of Ldlr-/- mouse macrophages stimulated with endotoxin-free recombinant PCSK9. A combination of unbiased global transcriptomics and new network-based hyperedge entanglement prediction analysis identified the NF-κB (nuclear factor-kappa B) signaling molecules, lectin-like oxidized LOX-1 (LDL receptor-1), and SDC4 (syndecan-4) as potential PCSK9 targets mediating pro-inflammatory responses in macrophages. CONCLUSIONS Circulating PCSK9 induces macrophage activation and vein graft lesion development via LDLR-independent mechanisms. PCSK9 may be a potential target for pharmacologic treatment for this unmet medical need.
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Affiliation(s)
- Shunsuke Katsuki
- The Center for Excellence in Vascular Biology, Cardiovascular Division (S.K., P.K.J., A.L., T.N., L.S.A.P., D.B.-G., T.-D.L., G.C.G., A.V., P.L., E.A., M.A.)
| | - Prabhash K. Jha
- The Center for Excellence in Vascular Biology, Cardiovascular Division (S.K., P.K.J., A.L., T.N., L.S.A.P., D.B.-G., T.-D.L., G.C.G., A.V., P.L., E.A., M.A.)
| | - Adrien Lupieri
- The Center for Excellence in Vascular Biology, Cardiovascular Division (S.K., P.K.J., A.L., T.N., L.S.A.P., D.B.-G., T.-D.L., G.C.G., A.V., P.L., E.A., M.A.)
| | - Toshiaki Nakano
- The Center for Excellence in Vascular Biology, Cardiovascular Division (S.K., P.K.J., A.L., T.N., L.S.A.P., D.B.-G., T.-D.L., G.C.G., A.V., P.L., E.A., M.A.)
| | - Livia S.A. Passos
- The Center for Excellence in Vascular Biology, Cardiovascular Division (S.K., P.K.J., A.L., T.N., L.S.A.P., D.B.-G., T.-D.L., G.C.G., A.V., P.L., E.A., M.A.)
| | - Maximillian A. Rogers
- The Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division (M.A.R., J.L.D., L.H.L., I.A., A.H., H.H., H.Z., A.S., S.A.S., E.A., M.A.)
| | - Dakota Becker-Greene
- The Center for Excellence in Vascular Biology, Cardiovascular Division (S.K., P.K.J., A.L., T.N., L.S.A.P., D.B.-G., T.-D.L., G.C.G., A.V., P.L., E.A., M.A.)
| | - Thanh-Dat Le
- The Center for Excellence in Vascular Biology, Cardiovascular Division (S.K., P.K.J., A.L., T.N., L.S.A.P., D.B.-G., T.-D.L., G.C.G., A.V., P.L., E.A., M.A.)
| | - Julius L. Decano
- The Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division (M.A.R., J.L.D., L.H.L., I.A., A.H., H.H., H.Z., A.S., S.A.S., E.A., M.A.)
| | - Lang Ho Lee
- The Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division (M.A.R., J.L.D., L.H.L., I.A., A.H., H.H., H.Z., A.S., S.A.S., E.A., M.A.)
| | - Gabriel C. Guimaraes
- The Center for Excellence in Vascular Biology, Cardiovascular Division (S.K., P.K.J., A.L., T.N., L.S.A.P., D.B.-G., T.-D.L., G.C.G., A.V., P.L., E.A., M.A.)
| | - Ilyes Abdelhamid
- The Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division (M.A.R., J.L.D., L.H.L., I.A., A.H., H.H., H.Z., A.S., S.A.S., E.A., M.A.)
- Channing Division of Network Medicine (I.A., A.H., A.S., M.A.), Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Arda Halu
- The Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division (M.A.R., J.L.D., L.H.L., I.A., A.H., H.H., H.Z., A.S., S.A.S., E.A., M.A.)
- Channing Division of Network Medicine (I.A., A.H., A.S., M.A.), Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Alessandro Muscoloni
- The Biomedical Cybernetics Group, Biotechnology Center, Center for Molecular and Cellular Bioengineering, Center for Systems Biology Dresden, Cluster of Excellence Physics of Life, Department of Physics, Technical University Dresden, Dresden, Germany (A.M., C.V.C)
- Center for Complex Network Intelligence at the Tsinghua Laboratory of Brain and Intelligence, Department of Bioengineering, Tsinghua University, Beijing, China (A.M., C.V.C.)
| | - Carlo V. Cannistraci
- The Center for Excellence in Vascular Biology, Cardiovascular Division (S.K., P.K.J., A.L., T.N., L.S.A.P., D.B.-G., T.-D.L., G.C.G., A.V., P.L., E.A., M.A.)
- Center for Complex Network Intelligence at the Tsinghua Laboratory of Brain and Intelligence, Department of Bioengineering, Tsinghua University, Beijing, China (A.M., C.V.C.)
| | - Hideyuki Higashi
- The Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division (M.A.R., J.L.D., L.H.L., I.A., A.H., H.H., H.Z., A.S., S.A.S., E.A., M.A.)
| | - Hengmin Zhang
- The Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division (M.A.R., J.L.D., L.H.L., I.A., A.H., H.H., H.Z., A.S., S.A.S., E.A., M.A.)
| | - Amélie Vromman
- The Center for Excellence in Vascular Biology, Cardiovascular Division (S.K., P.K.J., A.L., T.N., L.S.A.P., D.B.-G., T.-D.L., G.C.G., A.V., P.L., E.A., M.A.)
| | - Peter Libby
- The Center for Excellence in Vascular Biology, Cardiovascular Division (S.K., P.K.J., A.L., T.N., L.S.A.P., D.B.-G., T.-D.L., G.C.G., A.V., P.L., E.A., M.A.)
| | - C. Keith Ozaki
- Center for Complex Network Intelligence at the Tsinghua Laboratory of Brain and Intelligence, Department of Bioengineering, Tsinghua University, Beijing, China (A.M., C.V.C.)
| | - Amitabh Sharma
- The Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division (M.A.R., J.L.D., L.H.L., I.A., A.H., H.H., H.Z., A.S., S.A.S., E.A., M.A.)
- Channing Division of Network Medicine (I.A., A.H., A.S., M.A.), Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Sasha A. Singh
- The Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division (M.A.R., J.L.D., L.H.L., I.A., A.H., H.H., H.Z., A.S., S.A.S., E.A., M.A.)
| | - Elena Aikawa
- The Center for Excellence in Vascular Biology, Cardiovascular Division (S.K., P.K.J., A.L., T.N., L.S.A.P., D.B.-G., T.-D.L., G.C.G., A.V., P.L., E.A., M.A.)
- The Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division (M.A.R., J.L.D., L.H.L., I.A., A.H., H.H., H.Z., A.S., S.A.S., E.A., M.A.)
| | - Masanori Aikawa
- The Center for Excellence in Vascular Biology, Cardiovascular Division (S.K., P.K.J., A.L., T.N., L.S.A.P., D.B.-G., T.-D.L., G.C.G., A.V., P.L., E.A., M.A.)
- The Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division (M.A.R., J.L.D., L.H.L., I.A., A.H., H.H., H.Z., A.S., S.A.S., E.A., M.A.)
- Channing Division of Network Medicine (I.A., A.H., A.S., M.A.), Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
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13
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Salahi M, Parsa S, Nourmohammadi D, Razmkhah Z, Salimi O, Rahmani M, Zivary S, Askarzadeh M, Tapak MA, Vaezi A, Sadeghsalehi H, Yaghoobpoor S, Mottahedi M, Garousi S, Deravi N. Immunologic aspects of migraine: A review of literature. Front Neurol 2022; 13:944791. [PMID: 36247795 PMCID: PMC9554313 DOI: 10.3389/fneur.2022.944791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 08/29/2022] [Indexed: 12/02/2022] Open
Abstract
Migraine headaches are highly prevalent, affecting 15% of the population. However, despite many studies to determine this disease's mechanism and efficient management, its pathophysiology has not been fully elucidated. There are suggested hypotheses about the possible mediating role of mast cells, immunoglobulin E, histamine, and cytokines in this disease. A higher incidence of this disease in allergic and asthma patients, reported by several studies, indicates the possible role of brain mast cells located around the brain vessels in this disease. The mast cells are more specifically within the dura and can affect the trigeminal nerve and cervical or sphenopalatine ganglion, triggering the secretion of substances that cause migraine. Neuropeptides such as calcitonin gene-related peptide (CGRP), neurokinin-A, neurotensin (NT), pituitary adenylate-cyclase-activating peptide (PACAP), and substance P (SP) trigger mast cells, and in response, they secrete pro-inflammatory and vasodilatory molecules such as interleukin-6 (IL-6) and vascular endothelial growth factor (VEGF) as a selective result of corticotropin-releasing hormone (CRH) secretion. This stress hormone contributes to migraine or intensifies it. Blocking these pathways using immunologic agents such as CGRP antibody, anti-CGRP receptor antibody, and interleukin-1 beta (IL-1β)/interleukin 1 receptor type 1 (IL-1R1) axis-related agents may be promising as potential prophylactic migraine treatments. This review is going to summarize the immunological aspects of migraine.
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Affiliation(s)
- Mehrnaz Salahi
- Student Research Committee, School of Pharmacy and Pharmaceutical Science, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Sina Parsa
- Student Research Committee, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Delaram Nourmohammadi
- Student Research Committee, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zahra Razmkhah
- Student Research Committee, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Omid Salimi
- Student Research Committee, Faculty of Medicine, Islamic Azad University of Najafabad, Isfahan, Iran
| | | | - Saeid Zivary
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
| | - Monireh Askarzadeh
- Department of Immunology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Amin Tapak
- Student Research Committee, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Ali Vaezi
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Hamidreza Sadeghsalehi
- Department of Neuroscience, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Shirin Yaghoobpoor
- Student Research Committee, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mehran Mottahedi
- Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Setareh Garousi
- Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Niloofar Deravi
- Student Research Committee, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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14
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Bauer S, Eigenmann J, Zhao Y, Fleig J, Hawe JS, Pan C, Bongiovanni D, Wengert S, Ma A, Lusis AJ, Kovacic JC, Björkegren JLM, Maegdefessel L, Schunkert H, von Scheidt M. Identification of the Transcription Factor ATF3 as a Direct and Indirect Regulator of the LDLR. Metabolites 2022; 12:metabo12090840. [PMID: 36144244 PMCID: PMC9504235 DOI: 10.3390/metabo12090840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 08/28/2022] [Accepted: 09/02/2022] [Indexed: 11/16/2022] Open
Abstract
Coronary artery disease (CAD) is a complex, multifactorial disease caused, in particular, by inflammation and cholesterol metabolism. At the molecular level, the role of tissue-specific signaling pathways leading to CAD is still largely unexplored. This study relied on two main resources: (1) genes with impact on atherosclerosis/CAD, and (2) liver-specific transcriptome analyses from human and mouse studies. The transcription factor activating transcription factor 3 (ATF3) was identified as a key regulator of a liver network relevant to atherosclerosis and linked to inflammation and cholesterol metabolism. ATF3 was predicted to be a direct and indirect (via MAF BZIP Transcription Factor F (MAFF)) regulator of low-density lipoprotein receptor (LDLR). Chromatin immunoprecipitation DNA sequencing (ChIP-seq) data from human liver cells revealed an ATF3 binding motif in the promoter regions of MAFF and LDLR. siRNA knockdown of ATF3 in human Hep3B liver cells significantly upregulated LDLR expression (p < 0.01). Inflammation induced by lipopolysaccharide (LPS) stimulation resulted in significant upregulation of ATF3 (p < 0.01) and subsequent downregulation of LDLR (p < 0.001). Liver-specific expression data from human CAD patients undergoing coronary artery bypass grafting (CABG) surgery (STARNET) and mouse models (HMDP) confirmed the regulatory role of ATF3 in the homeostasis of cholesterol metabolism. This study suggests that ATF3 might be a promising treatment candidate for lowering LDL cholesterol and reducing cardiovascular risk.
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Affiliation(s)
- Sabine Bauer
- Department of Cardiology, German Heart Centre Munich, Technical University Munich, 80636 Munich, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, 80802 Munich, Germany
- Correspondence: (S.B.); (M.v.S.); Tel.: +49-(0)89-1218-2367 (S.B.); +49-(0)89-1218-2849 (M.v.S.)
| | - Jana Eigenmann
- Department of Cardiology, German Heart Centre Munich, Technical University Munich, 80636 Munich, Germany
| | - Yuqi Zhao
- Department of Integrative Biology and Physiology, Institute for Quantitative and Computational Biosciences, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Julia Fleig
- Department of Cardiology, German Heart Centre Munich, Technical University Munich, 80636 Munich, Germany
| | - Johann S. Hawe
- Department of Cardiology, German Heart Centre Munich, Technical University Munich, 80636 Munich, Germany
| | - Calvin Pan
- Departments of Medicine, Human Genetics, Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Dario Bongiovanni
- DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, 80802 Munich, Germany
- Division of Cardiology, Cardiocentro Ticino Institute, Ente Ospedaliero Cantonale, 6900 Lugano, Switzerland
| | - Simon Wengert
- Helmholtz Pioneer Campus, Helmholtz Center Munich, 85764 Neuherberg, Germany
- Institute of Computational Biology, Helmholtz Center Munich, 85764 Oberschleißheim, Germany
| | - Angela Ma
- Department of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Aldons J. Lusis
- Departments of Medicine, Human Genetics, Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Jason C. Kovacic
- Victor Chang Cardiac Research Institute, Darlinghurst, Sydney, NSW 2010, Australia
- St. Vincent’s Clinical School, University of New South Wales, Darlinghurst, Sydney, NSW 2010, Australia
- Icahn School of Medicine at Mount Sinai, Cardiovascular Research Institute, New York, NY 10029, USA
| | - Johan L. M. Björkegren
- Department of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Clinical Gene Networks AB, 114 44 Stockholm, Sweden
- Integrated Cardio Metabolic Centre, Karolinska Institutet, Novum, Huddinge, 171 77 Stockholm, Sweden
| | - Lars Maegdefessel
- DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, 80802 Munich, Germany
- Department of Vascular and Endovascular Surgery, Klinikum Rechts der Isar, Technical University Munich, 81675 Munich, Germany
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden
| | - Heribert Schunkert
- Department of Cardiology, German Heart Centre Munich, Technical University Munich, 80636 Munich, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, 80802 Munich, Germany
| | - Moritz von Scheidt
- Department of Cardiology, German Heart Centre Munich, Technical University Munich, 80636 Munich, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, 80802 Munich, Germany
- Correspondence: (S.B.); (M.v.S.); Tel.: +49-(0)89-1218-2367 (S.B.); +49-(0)89-1218-2849 (M.v.S.)
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15
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Rescue of Mitochondrial SIRT3 Ameliorates Ischemia-like Injury in Human Endothelial Cells. Int J Mol Sci 2022; 23:ijms23169118. [PMID: 36012382 PMCID: PMC9409423 DOI: 10.3390/ijms23169118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 11/17/2022] Open
Abstract
Structural and functional alterations of vasculature caused by age-related factors is critically involved in the pathogenesis of ischemic stroke. The longevity genes sirtuins (SIRTs) are extensively investigated in aging-associated pathologies, but their distinct roles in ischemic stroke still remain to be clarified. To address this question, we applied oxygen and glucose deprived/reperfusion (OGD/R) to induce ischemic injury in human endothelial cells (ECs), which are the main component of vasculature in the brain. The results showed that OGD/R led to various damages to ECs, including compromised cell viability, increased LDH release, overproduced ROS, enhanced apoptosis and caspase activity. Meanwhile, the expression of mitochondrial SIRT3 was robustly decreased in ECs after OGD/R treatment. Consistently, rescue of SIRT3 by ectopic expression, but not nuclear SIRT1, in ECs reversed the OGD/R-induced cell damage. Interestingly, some front-line drugs for ischemic stroke, including clopidogrel, aspirin and dl-3-n-butylphthalide (NBP), also rescued SIRT3 and reduced OGD/R-induced endothelial injury, suggesting that the recovery of SIRT3 expression was critical for the protection of these drugs. Moreover, our results demonstrated that 10-hydroxy-NBP (OHNBP), a major metabolite of NBP, showed better blood-brain barrier crossing capability than NBP, but still retained the effects on SIRT3 by NBP. Together, our results suggested that SIRT3 may serve as a potential novel target for treatment of ischemic stroke.
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16
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Wang RR, Qiu X, Pan R, Fu H, Zhang Z, Wang Q, Chen H, Wu QQ, Pan X, Zhou Y, Shan P, Wang S, Guo G, Zheng M, Zhu L, Meng ZX. Dietary intervention preserves β cell function in mice through CTCF-mediated transcriptional reprogramming. J Exp Med 2022; 219:213256. [PMID: 35652891 DOI: 10.1084/jem.20211779] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 04/04/2022] [Accepted: 05/12/2022] [Indexed: 12/12/2022] Open
Abstract
Pancreatic β cell plasticity is the primary determinant of disease progression and remission of type 2 diabetes (T2D). However, the dynamic nature of β cell adaptation remains elusive. Here, we establish a mouse model exhibiting the compensation-to-decompensation adaptation of β cell function in response to increasing duration of high-fat diet (HFD) feeding. Comprehensive islet functional and transcriptome analyses reveal a dynamic orchestration of transcriptional networks featuring temporal alteration of chromatin remodeling. Interestingly, prediabetic dietary intervention completely rescues β cell dysfunction, accompanied by a remarkable reversal of HFD-induced reprogramming of islet chromatin accessibility and transcriptome. Mechanistically, ATAC-based motif analysis identifies CTCF as the top candidate driving dietary intervention-induced preservation of β cell function. CTCF expression is markedly decreased in β cells from obese and diabetic mice and humans. Both dietary intervention and AAV-mediated restoration of CTCF expression ameliorate β cell dysfunction ex vivo and in vivo, through transducing the lipid toxicity and inflammatory signals to transcriptional reprogramming of genes critical for β cell glucose metabolism and stress response.
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Affiliation(s)
- Ruo-Ran Wang
- Department of Pathology and Pathophysiology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Key Laboratory of Disease Proteomics of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Chronic Disease Research Institute, School of Public Health, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xinyuan Qiu
- Department of Pathology and Pathophysiology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Department of Biology and Chemistry, College of Liberal Arts and Sciences, National University of Defense Technology, Changsha, Hunan, China
| | - Ran Pan
- Department of Pathology and Pathophysiology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Key Laboratory of Disease Proteomics of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Chronic Disease Research Institute, School of Public Health, Zhejiang University, Hangzhou, Zhejiang, China
| | - Hongxing Fu
- Department of Hepatobiliary and Pancreatic Surgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Ziyin Zhang
- Department of Pathology and Pathophysiology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Key Laboratory of Disease Proteomics of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Chronic Disease Research Institute, School of Public Health, Zhejiang University, Hangzhou, Zhejiang, China
| | - Qintao Wang
- Department of Pathology and Pathophysiology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Key Laboratory of Disease Proteomics of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Chronic Disease Research Institute, School of Public Health, Zhejiang University, Hangzhou, Zhejiang, China
| | - Haide Chen
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Qing-Qian Wu
- Department of Pathology and Pathophysiology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Key Laboratory of Disease Proteomics of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Chronic Disease Research Institute, School of Public Health, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiaowen Pan
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yanping Zhou
- Department of Pathology and Pathophysiology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Pengfei Shan
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Shusen Wang
- Organ Transplant Center, Tianjin First Central Hospital, Tianjin, China.,NHC Key Laboratory for Critical Care Medicine, Tianjin First Central Hospital, Tianjin, China
| | - Guoji Guo
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Min Zheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Lingyun Zhu
- Department of Biology and Chemistry, College of Liberal Arts and Sciences, National University of Defense Technology, Changsha, Hunan, China
| | - Zhuo-Xian Meng
- Department of Pathology and Pathophysiology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Key Laboratory of Disease Proteomics of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Chronic Disease Research Institute, School of Public Health, Zhejiang University, Hangzhou, Zhejiang, China.,Department of Geriatrics, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
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17
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Horgusluoglu E, Neff R, Song W, Wang M, Wang Q, Arnold M, Krumsiek J, Galindo‐Prieto B, Ming C, Nho K, Kastenmüller G, Han X, Baillie R, Zeng Q, Andrews S, Cheng H, Hao K, Goate A, Bennett DA, Saykin AJ, Kaddurah‐Daouk R, Zhang B. Integrative metabolomics-genomics approach reveals key metabolic pathways and regulators of Alzheimer's disease. Alzheimers Dement 2022; 18:1260-1278. [PMID: 34757660 PMCID: PMC9085975 DOI: 10.1002/alz.12468] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 04/14/2021] [Accepted: 04/17/2021] [Indexed: 12/29/2022]
Abstract
Metabolites, the biochemical products of the cellular process, can be used to measure alterations in biochemical pathways related to the pathogenesis of Alzheimer's disease (AD). However, the relationships between systemic abnormalities in metabolism and the pathogenesis of AD are poorly understood. In this study, we aim to identify AD-specific metabolomic changes and their potential upstream genetic and transcriptional regulators through an integrative systems biology framework for analyzing genetic, transcriptomic, metabolomic, and proteomic data in AD. Metabolite co-expression network analysis of the blood metabolomic data in the Alzheimer's Disease Neuroimaging Initiative (ADNI) shows short-chain acylcarnitines/amino acids and medium/long-chain acylcarnitines are most associated with AD clinical outcomes, including episodic memory scores and disease severity. Integration of the gene expression data in both the blood from the ADNI and the brain from the Accelerating Medicines Partnership Alzheimer's Disease (AMP-AD) program reveals ABCA1 and CPT1A are involved in the regulation of acylcarnitines and amino acids in AD. Gene co-expression network analysis of the AMP-AD brain RNA-seq data suggests the CPT1A- and ABCA1-centered subnetworks are associated with neuronal system and immune response, respectively. Increased ABCA1 gene expression and adiponectin protein, a regulator of ABCA1, correspond to decreased short-chain acylcarnitines and amines in AD in the ADNI. In summary, our integrated analysis of large-scale multiomics data in AD systematically identifies novel metabolites and their potential regulators in AD and the findings pave a way for not only developing sensitive and specific diagnostic biomarkers for AD but also identifying novel molecular mechanisms of AD pathogenesis.
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Affiliation(s)
- Emrin Horgusluoglu
- Department of Genetics and Genomic SciencesMount Sinai Center for Transformative Disease ModelingIcahn School of Medicine at Mount SinaiIcahn Institute of Genomics and Multiscale BiologyNew YorkNew YorkUSA
| | - Ryan Neff
- Department of Genetics and Genomic SciencesMount Sinai Center for Transformative Disease ModelingIcahn School of Medicine at Mount SinaiIcahn Institute of Genomics and Multiscale BiologyNew YorkNew YorkUSA
| | - Won‐Min Song
- Department of Genetics and Genomic SciencesMount Sinai Center for Transformative Disease ModelingIcahn School of Medicine at Mount SinaiIcahn Institute of Genomics and Multiscale BiologyNew YorkNew YorkUSA
| | - Minghui Wang
- Department of Genetics and Genomic SciencesMount Sinai Center for Transformative Disease ModelingIcahn School of Medicine at Mount SinaiIcahn Institute of Genomics and Multiscale BiologyNew YorkNew YorkUSA
| | - Qian Wang
- Department of Genetics and Genomic SciencesMount Sinai Center for Transformative Disease ModelingIcahn School of Medicine at Mount SinaiIcahn Institute of Genomics and Multiscale BiologyNew YorkNew YorkUSA
| | - Matthias Arnold
- Institute of Computational BiologyHelmholtz Zentrum MünchenGerman Research Center for Environmental HealthNeuherbergGermany
- Department of Psychiatry and Behavioral SciencesDuke UniversityDurhamNorth CarolinaUSA
| | - Jan Krumsiek
- Department of Physiology and BiophysicsWeill Cornell MedicineInstitute for Computational BiomedicineEnglander Institute for Precision MedicineNew YorkNew YorkUSA
| | - Beatriz Galindo‐Prieto
- Department of Physiology and BiophysicsWeill Cornell MedicineInstitute for Computational BiomedicineEnglander Institute for Precision MedicineNew YorkNew YorkUSA
- Helen and Robert Appel Alzheimer's Disease Research InstituteBrain and Mind Research InstituteWeill Cornell MedicineNew YorkNew YorkUSA
| | - Chen Ming
- Department of Genetics and Genomic SciencesMount Sinai Center for Transformative Disease ModelingIcahn School of Medicine at Mount SinaiIcahn Institute of Genomics and Multiscale BiologyNew YorkNew YorkUSA
| | - Kwangsik Nho
- Department of Radiology and Imaging Sciences; Indiana Alzheimer Disease CenterIndiana University School of MedicineIndianapolisIndianaUSA
| | - Gabi Kastenmüller
- Institute of Computational BiologyHelmholtz Zentrum MünchenGerman Research Center for Environmental HealthNeuherbergGermany
| | - Xianlin Han
- Barshop Institute for Longevity and Aging StudiesUniversity of Texas Health Science Center at San AntonioSan AntonioTexasUSA
| | | | - Qi Zeng
- Department of Genetics and Genomic SciencesMount Sinai Center for Transformative Disease ModelingIcahn School of Medicine at Mount SinaiIcahn Institute of Genomics and Multiscale BiologyNew YorkNew YorkUSA
| | - Shea Andrews
- Department of NeuroscienceRonald M. Loeb Center for Alzheimer's DiseaseIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Haoxiang Cheng
- Department of Genetics and Genomic SciencesMount Sinai Center for Transformative Disease ModelingIcahn School of Medicine at Mount SinaiIcahn Institute of Genomics and Multiscale BiologyNew YorkNew YorkUSA
| | - Ke Hao
- Department of Genetics and Genomic SciencesMount Sinai Center for Transformative Disease ModelingIcahn School of Medicine at Mount SinaiIcahn Institute of Genomics and Multiscale BiologyNew YorkNew YorkUSA
| | - Alison Goate
- Department of NeuroscienceRonald M. Loeb Center for Alzheimer's DiseaseIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - David A. Bennett
- Rush Alzheimer's Disease CenterRush University Medical CenterChicagoIllinoisUSA
| | - Andrew J. Saykin
- Department of Radiology and Imaging Sciences; Indiana Alzheimer Disease CenterIndiana University School of MedicineIndianapolisIndianaUSA
| | - Rima Kaddurah‐Daouk
- Department of Psychiatry and Behavioral SciencesDuke UniversityDurhamNorth CarolinaUSA
- Duke Institute of Brain SciencesDuke UniversityDurhamNorth CarolinaUSA
- Department of MedicineDuke UniversityDurhamNorth CarolinaUSA
| | - Bin Zhang
- Department of Genetics and Genomic SciencesMount Sinai Center for Transformative Disease ModelingIcahn School of Medicine at Mount SinaiIcahn Institute of Genomics and Multiscale BiologyNew YorkNew YorkUSA
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18
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Gasser E, Sancar G, Downes M, Evans RM. Metabolic Messengers: fibroblast growth factor 1. Nat Metab 2022; 4:663-671. [PMID: 35681108 PMCID: PMC9624216 DOI: 10.1038/s42255-022-00580-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 04/15/2022] [Accepted: 04/27/2022] [Indexed: 11/09/2022]
Abstract
While fibroblast growth factor (FGF) 1 is expressed in multiple tissues, only adipose-derived and brain FGF1 have been implicated in the regulation of metabolism. Adipose FGF1 production is upregulated in response to dietary stress and is essential for adipose tissue plasticity in these conditions. Similarly, in the brain, FGF1 secretion into the ventricular space and the adjacent parenchyma is increased after a hypercaloric challenge induced by either feeding or glucose infusion. Potent anorexigenic properties have been ascribed to both peripheral and centrally injected FGF1. The ability of recombinant FGF1 and variants with reduced mitogenicity to lower glucose, suppress adipose lipolysis and promote insulin sensitization elevates their potential as candidates in the treatment of type 2 diabetes mellitus and associated comorbidities. Here, we provide an overview of the known metabolic functions of endogenous FGF1 and discuss its therapeutic potential, distinguishing between peripherally or centrally administered FGF1.
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Affiliation(s)
- Emanuel Gasser
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Gencer Sancar
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Michael Downes
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Ronald M Evans
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA.
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19
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Sonawane AR, Aikawa E, Aikawa M. Connections for Matters of the Heart: Network Medicine in Cardiovascular Diseases. Front Cardiovasc Med 2022; 9:873582. [PMID: 35665246 PMCID: PMC9160390 DOI: 10.3389/fcvm.2022.873582] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 04/19/2022] [Indexed: 01/18/2023] Open
Abstract
Cardiovascular diseases (CVD) are diverse disorders affecting the heart and vasculature in millions of people worldwide. Like other fields, CVD research has benefitted from the deluge of multiomics biomedical data. Current CVD research focuses on disease etiologies and mechanisms, identifying disease biomarkers, developing appropriate therapies and drugs, and stratifying patients into correct disease endotypes. Systems biology offers an alternative to traditional reductionist approaches and provides impetus for a comprehensive outlook toward diseases. As a focus area, network medicine specifically aids the translational aspect of in silico research. This review discusses the approach of network medicine and its application to CVD research.
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Affiliation(s)
- Abhijeet Rajendra Sonawane
- Center for Interdisciplinary Cardiovascular Sciences, Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
- Center for Excellence in Vascular Biology, Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Elena Aikawa
- Center for Interdisciplinary Cardiovascular Sciences, Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
- Center for Excellence in Vascular Biology, Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Masanori Aikawa
- Center for Interdisciplinary Cardiovascular Sciences, Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
- Center for Excellence in Vascular Biology, Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
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20
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Savin IA, Markov AV, Zenkova MA, Sen’kova AV. Asthma and Post-Asthmatic Fibrosis: A Search for New Promising Molecular Markers of Transition from Acute Inflammation to Pulmonary Fibrosis. Biomedicines 2022; 10:biomedicines10051017. [PMID: 35625754 PMCID: PMC9138542 DOI: 10.3390/biomedicines10051017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/27/2022] [Accepted: 04/27/2022] [Indexed: 12/15/2022] Open
Abstract
Asthma is a heterogeneous pulmonary disorder, the progression and chronization of which leads to airway remodeling and fibrogenesis. To understand the molecular mechanisms of pulmonary fibrosis development, key genes forming the asthma-specific regulome and involved in lung fibrosis formation were revealed using a comprehensive bioinformatics analysis. The bioinformatics data were validated using a murine model of ovalbumin (OVA)-induced asthma and post-asthmatic fibrosis. The performed analysis revealed a range of well-known pro-fibrotic markers (Cat, Ccl2, Ccl4, Ccr2, Col1a1, Cxcl12, Igf1, Muc5ac/Muc5b, Spp1, Timp1) and a set of novel genes (C3, C3ar1, Col4a1, Col4a2, Cyp2e1, Fn1, Thbs1, Tyrobp) mediating fibrotic changes in lungs already at the stage of acute/subacute asthma-driven inflammation. The validation of genes related to non-allergic bleomycin-induced pulmonary fibrosis on asthmatic/fibrotic lungs allowed us to identify new universal genes (Col4a1 and Col4a2) associated with the development of lung fibrosis regardless of its etiology. The similarities revealed in the expression profiles of nodal fibrotic genes between asthma-driven fibrosis in mice and nascent idiopathic pulmonary fibrosis in humans suggest a tight association of identified genes with the early stages of airway remodeling and can be considered as promising predictors and early markers of pulmonary fibrosis.
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21
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Yoo S, Sinha A, Yang D, Altorki NK, Tandon R, Wang W, Chavez D, Lee E, Patel AS, Sato T, Kong R, Ding B, Schadt EE, Watanabe H, Massion PP, Borczuk AC, Zhu J, Powell CA. Integrative network analysis of early-stage lung adenocarcinoma identifies aurora kinase inhibition as interceptor of invasion and progression. Nat Commun 2022; 13:1592. [PMID: 35332150 PMCID: PMC8948234 DOI: 10.1038/s41467-022-29230-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 03/01/2022] [Indexed: 12/15/2022] Open
Abstract
Here we focus on the molecular characterization of clinically significant histological subtypes of early-stage lung adenocarcinoma (esLUAD), which is the most common histological subtype of lung cancer. Within lung adenocarcinoma, histology is heterogeneous and associated with tumor invasion and diverse clinical outcomes. We present a gene signature distinguishing invasive and non-invasive tumors among esLUAD. Using the gene signatures, we estimate an Invasiveness Score that is strongly associated with survival of esLUAD patients in multiple independent cohorts and with the invasiveness phenotype in lung cancer cell lines. Regulatory network analysis identifies aurora kinase as one of master regulators of the gene signature and the perturbation of aurora kinases in vitro and in a murine model of invasive lung adenocarcinoma reduces tumor invasion. Our study reveals aurora kinases as a therapeutic target for treatment of early-stage invasive lung adenocarcinoma.
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Affiliation(s)
- Seungyeul Yoo
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, New York, NY, USA
- Sema4, Stamford, CT, USA
| | - Abhilasha Sinha
- Division of Pulmonary, Critical Care and Sleep Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dawei Yang
- Division of Pulmonary, Critical Care and Sleep Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Nasser K Altorki
- Department of Cardiothoracic Surgery, Weill Cornell Medicine-New York Presbyterian Hospital, New York, NY, USA
| | - Radhika Tandon
- School of Medicine, St. George's University, West Indies, Grenada
| | - Wenhui Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, New York, NY, USA
| | - Deebly Chavez
- Division of Pulmonary, Critical Care and Sleep Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eunjee Lee
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, New York, NY, USA
- Sema4, Stamford, CT, USA
| | - Ayushi S Patel
- Division of Pulmonary, Critical Care and Sleep Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Vileck Institute of Graduate Biomedical Sciences, New York University School of Medicine, New York, NY, USA
| | - Takashi Sato
- Division of Pulmonary, Critical Care and Sleep Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
- Department of Respiratory Medicine, Kitasato University School of Medicine, Sagamihara, Japan
| | - Ranran Kong
- Division of Pulmonary, Critical Care and Sleep Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Thoracic Surgery, The Second Affiliated Hospital of Medical School, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Bisen Ding
- Division of Pulmonary, Critical Care and Sleep Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Key Laboratory of Birth Defects and Related Diseases of Women And Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, New York, NY, USA
- Sema4, Stamford, CT, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hideo Watanabe
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, New York, NY, USA
- Division of Pulmonary, Critical Care and Sleep Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Pierre P Massion
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Alain C Borczuk
- Department of Pathology, Weill Cornell Medicine, New York, NY, USA
| | - Jun Zhu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Icahn Institute for Data Science and Genomic Technology, New York, NY, USA.
- Sema4, Stamford, CT, USA.
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Charles A Powell
- Division of Pulmonary, Critical Care and Sleep Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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22
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Koplev S, Seldin M, Sukhavasi K, Ermel R, Pang S, Zeng L, Bankier S, Di Narzo A, Cheng H, Meda V, Ma A, Talukdar H, Cohain A, Amadori L, Argmann C, Houten SM, Franzén O, Mocci G, Meelu OA, Ishikawa K, Whatling C, Jain A, Jain RK, Gan LM, Giannarelli C, Roussos P, Hao K, Schunkert H, Michoel T, Ruusalepp A, Schadt EE, Kovacic JC, Lusis AJ, Björkegren JLM. A mechanistic framework for cardiometabolic and coronary artery diseases. NATURE CARDIOVASCULAR RESEARCH 2022; 1:85-100. [PMID: 36276926 PMCID: PMC9583458 DOI: 10.1038/s44161-021-00009-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/19/2023]
Abstract
Coronary atherosclerosis results from the delicate interplay of genetic and exogenous risk factors, principally taking place in metabolic organs and the arterial wall. Here we show that 224 gene-regulatory coexpression networks (GRNs) identified by integrating genetic and clinical data from patients with (n = 600) and without (n = 250) coronary artery disease (CAD) with RNA-seq data from seven disease-relevant tissues in the Stockholm-Tartu Atherosclerosis Reverse Network Engineering Task (STARNET) study largely capture this delicate interplay, explaining >54% of CAD heritability. Within 89 cross-tissue GRNs associated with clinical severity of CAD, 374 endocrine factors facilitated inter-organ interactions, primarily along an axis from adipose tissue to the liver (n = 152). This axis was independently replicated in genetically diverse mouse strains and by injection of recombinant forms of adipose endocrine factors (EPDR1, FCN2, FSTL3 and LBP) that markedly altered blood lipid and glucose levels in mice. Altogether, the STARNET database and the associated GRN browser (http://starnet.mssm.edu) provide a multiorgan framework for exploration of the molecular interplay between cardiometabolic disorders and CAD.
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Affiliation(s)
- Simon Koplev
- Department of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marcus Seldin
- Departments of Medicine, Human Genetics and Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Biological Chemistry and Center for Epigenetics and Metabolism, University of California, Irvine, CA, USA
| | - Katyayani Sukhavasi
- Department of Cardiac Surgery and the Heart Clinic, Tartu University Hospital and Department of Cardiology, Institute of Clinical Medicine, Tartu University, Tartu, Estonia
| | - Raili Ermel
- Department of Cardiac Surgery and the Heart Clinic, Tartu University Hospital and Department of Cardiology, Institute of Clinical Medicine, Tartu University, Tartu, Estonia
| | - Shichao Pang
- Deutsches Herzzentrum München, Klinik für Herz- und Kreislauferkrankungen, Technische Universität München, DZHK (German Centre for Cardiovascular Research), Munich Heart Alliance, Munich, Germany
| | - Lingyao Zeng
- Deutsches Herzzentrum München, Klinik für Herz- und Kreislauferkrankungen, Technische Universität München, DZHK (German Centre for Cardiovascular Research), Munich Heart Alliance, Munich, Germany
| | - Sean Bankier
- BHF Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Antonio Di Narzo
- Department of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Haoxiang Cheng
- Department of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Vamsidhar Meda
- Department of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Angela Ma
- Department of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Husain Talukdar
- Department of Medicine, Karolinska Institutet, Karolinska Universitetssjukhuset, Huddinge, Sweden
| | - Ariella Cohain
- Department of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Letizia Amadori
- Department of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- New York University Cardiovascular Research Center, Department of Medicine, Leon H. Charney Division of Cardiology, New York University Grossman School of Medicine, New York University Langone Health, New York, NY, USA
| | - Carmen Argmann
- Department of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sander M. Houten
- Department of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Oscar Franzén
- Department of Medicine, Karolinska Institutet, Karolinska Universitetssjukhuset, Huddinge, Sweden
| | - Giuseppe Mocci
- Department of Medicine, Karolinska Institutet, Karolinska Universitetssjukhuset, Huddinge, Sweden
| | - Omar A. Meelu
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kiyotake Ishikawa
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Carl Whatling
- Translational Science and Experimental Medicine, Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Anamika Jain
- Department of Cardiac Surgery and the Heart Clinic, Tartu University Hospital and Department of Cardiology, Institute of Clinical Medicine, Tartu University, Tartu, Estonia
| | - Rajeev Kumar Jain
- Department of Cardiac Surgery and the Heart Clinic, Tartu University Hospital and Department of Cardiology, Institute of Clinical Medicine, Tartu University, Tartu, Estonia
| | - Li-Ming Gan
- Early Clinical Development, Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Chiara Giannarelli
- Department of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- New York University Cardiovascular Research Center, Department of Medicine, Leon H. Charney Division of Cardiology, New York University Grossman School of Medicine, New York University Langone Health, New York, NY, USA
| | - Panos Roussos
- Department of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Dementia Research, Nathan Kline Institute for Psychiatric Research, Orangeburg, NY, USA
- Mental Illness Research Education and Clinical Center (MIRECC), James J. Peters VA Medical Center, Bronx, NY, USA
| | - Ke Hao
- Department of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Sema4, Stamford, CT, USA
| | - Heribert Schunkert
- Deutsches Herzzentrum München, Klinik für Herz- und Kreislauferkrankungen, Technische Universität München, DZHK (German Centre for Cardiovascular Research), Munich Heart Alliance, Munich, Germany
| | - Tom Michoel
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Arno Ruusalepp
- Department of Cardiac Surgery and the Heart Clinic, Tartu University Hospital and Department of Cardiology, Institute of Clinical Medicine, Tartu University, Tartu, Estonia
- Clinical Gene Networks AB, Stockholm, Sweden
| | - Eric E. Schadt
- Department of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Sema4, Stamford, CT, USA
| | - Jason C. Kovacic
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia
- St Vincent’s Clinical School, University of NSW, Sydney, New South Wales, Australia
| | - Aldon J. Lusis
- Departments of Medicine, Human Genetics and Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Johan L. M. Björkegren
- Department of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Karolinska Institutet, Karolinska Universitetssjukhuset, Huddinge, Sweden
- Clinical Gene Networks AB, Stockholm, Sweden
- Correspondence and requests for materials should be addressed to Johan L. M. Björkegren.
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23
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Sen’kova AV, Savin IA, Brenner EV, Zenkova MA, Markov AV. Core genes involved in the regulation of acute lung injury and their association with COVID-19 and tumor progression: A bioinformatics and experimental study. PLoS One 2021; 16:e0260450. [PMID: 34807957 PMCID: PMC8608348 DOI: 10.1371/journal.pone.0260450] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 11/09/2021] [Indexed: 12/12/2022] Open
Abstract
Acute lung injury (ALI) is a specific form of lung damage caused by different infectious and non-infectious agents, including SARS-CoV-2, leading to severe respiratory and systemic inflammation. To gain deeper insight into the molecular mechanisms behind ALI and to identify core elements of the regulatory network associated with this pathology, key genes involved in the regulation of the acute lung inflammatory response (Il6, Ccl2, Cat, Serpine1, Eln, Timp1, Ptx3, Socs3) were revealed using comprehensive bioinformatics analysis of whole-genome microarray datasets, functional annotation of differentially expressed genes (DEGs), reconstruction of protein-protein interaction networks and text mining. The bioinformatics data were validated using a murine model of LPS-induced ALI; changes in the gene expression patterns were assessed during ALI progression and prevention by anti-inflammatory therapy with dexamethasone and the semisynthetic triterpenoid soloxolone methyl (SM), two agents with different mechanisms of action. Analysis showed that 7 of 8 revealed ALI-related genes were susceptible to LPS challenge (up-regulation: Il6, Ccl2, Cat, Serpine1, Eln, Timp1, Socs3; down-regulation: Cat) and their expression was reversed by the pre-treatment of mice with both anti-inflammatory agents. Furthermore, ALI-associated nodal genes were analysed with respect to SARS-CoV-2 infection and lung cancers. The overlap with DEGs identified in postmortem lung tissues from COVID-19 patients revealed genes (Saa1, Rsad2, Ifi44, Rtp4, Mmp8) that (a) showed a high degree centrality in the COVID-19-related regulatory network, (b) were up-regulated in murine lungs after LPS administration, and (c) were susceptible to anti-inflammatory therapy. Analysis of ALI-associated key genes using The Cancer Genome Atlas showed their correlation with poor survival in patients with lung neoplasias (Ptx3, Timp1, Serpine1, Plaur). Taken together, a number of key genes playing a core function in the regulation of lung inflammation were found, which can serve both as promising therapeutic targets and molecular markers to control lung ailments, including COVID-19-associated ALI.
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Affiliation(s)
- Aleksandra V. Sen’kova
- Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Innokenty A. Savin
- Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Evgenyi V. Brenner
- Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Marina A. Zenkova
- Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Andrey V. Markov
- Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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24
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Molecular Biology Networks and Key Gene Regulators for Inflammatory Biomarkers Shared by Breast Cancer Development: Multi-Omics Systems Analysis. Biomolecules 2021; 11:biom11091379. [PMID: 34572592 PMCID: PMC8469138 DOI: 10.3390/biom11091379] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/10/2021] [Accepted: 09/12/2021] [Indexed: 11/17/2022] Open
Abstract
As key inflammatory biomarkers C-reactive protein (CRP) and interleukin-6 (IL6) play an important role in the pathogenesis of non-inflammatory diseases, including specific cancers, such as breast cancer (BC). Previous genome-wide association studies (GWASs) have neither explained the large proportion of genetic heritability nor provided comprehensive understanding of the underlying regulatory mechanisms. We adopted an integrative genomic network approach by incorporating our previous GWAS data for CRP and IL6 with multi-omics datasets, such as whole-blood expression quantitative loci, molecular biologic pathways, and gene regulatory networks to capture the full range of genetic functionalities associated with CRP/IL6 and tissue-specific key drivers (KDs) in gene subnetworks. We applied another systematic genomics approach for BC development to detect shared gene sets in enriched subnetworks across BC and CRP/IL6. We detected the topmost significant common pathways across CRP/IL6 (e.g., immune regulatory; chemokines and their receptors; interferon γ, JAK-STAT, and ERBB4 signaling), several of which overlapped with BC pathways. Further, in gene–gene interaction networks enriched by those topmost pathways, we identified KDs—both well-established (e.g., JAK1/2/3, STAT3) and novel (e.g., CXCR3, CD3D, CD3G, STAT6)—in a tissue-specific manner, for mechanisms shared in regulating CRP/IL6 and BC risk. Our study may provide robust, comprehensive insights into the mechanisms of CRP/IL6 regulation and highlight potential novel genetic targets as preventive and therapeutic strategies for associated disorders, such as BC.
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25
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Satpathy S, Krug K, Jean Beltran PM, Savage SR, Petralia F, Kumar-Sinha C, Dou Y, Reva B, Kane MH, Avanessian SC, Vasaikar SV, Krek A, Lei JT, Jaehnig EJ, Omelchenko T, Geffen Y, Bergstrom EJ, Stathias V, Christianson KE, Heiman DI, Cieslik MP, Cao S, Song X, Ji J, Liu W, Li K, Wen B, Li Y, Gümüş ZH, Selvan ME, Soundararajan R, Visal TH, Raso MG, Parra ER, Babur Ö, Vats P, Anand S, Schraink T, Cornwell M, Rodrigues FM, Zhu H, Mo CK, Zhang Y, da Veiga Leprevost F, Huang C, Chinnaiyan AM, Wyczalkowski MA, Omenn GS, Newton CJ, Schurer S, Ruggles KV, Fenyö D, Jewell SD, Thiagarajan M, Mesri M, Rodriguez H, Mani SA, Udeshi ND, Getz G, Suh J, Li QK, Hostetter G, Paik PK, Dhanasekaran SM, Govindan R, Ding L, Robles AI, Clauser KR, Nesvizhskii AI, Wang P, Carr SA, Zhang B, Mani DR, Gillette MA. A proteogenomic portrait of lung squamous cell carcinoma. Cell 2021; 184:4348-4371.e40. [PMID: 34358469 PMCID: PMC8475722 DOI: 10.1016/j.cell.2021.07.016] [Citation(s) in RCA: 161] [Impact Index Per Article: 53.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 04/26/2021] [Accepted: 07/12/2021] [Indexed: 02/07/2023]
Abstract
Lung squamous cell carcinoma (LSCC) remains a leading cause of cancer death with few therapeutic options. We characterized the proteogenomic landscape of LSCC, providing a deeper exposition of LSCC biology with potential therapeutic implications. We identify NSD3 as an alternative driver in FGFR1-amplified tumors and low-p63 tumors overexpressing the therapeutic target survivin. SOX2 is considered undruggable, but our analyses provide rationale for exploring chromatin modifiers such as LSD1 and EZH2 to target SOX2-overexpressing tumors. Our data support complex regulation of metabolic pathways by crosstalk between post-translational modifications including ubiquitylation. Numerous immune-related proteogenomic observations suggest directions for further investigation. Proteogenomic dissection of CDKN2A mutations argue for more nuanced assessment of RB1 protein expression and phosphorylation before declaring CDK4/6 inhibition unsuccessful. Finally, triangulation between LSCC, LUAD, and HNSCC identified both unique and common therapeutic vulnerabilities. These observations and proteogenomics data resources may guide research into the biology and treatment of LSCC.
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Affiliation(s)
- Shankha Satpathy
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA.
| | - Karsten Krug
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Pierre M Jean Beltran
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Sara R Savage
- Lester and Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Francesca Petralia
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Yongchao Dou
- Lester and Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Boris Reva
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - M Harry Kane
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Shayan C Avanessian
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Suhas V Vasaikar
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Azra Krek
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jonathan T Lei
- Lester and Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Eric J Jaehnig
- Lester and Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Yifat Geffen
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Erik J Bergstrom
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Vasileios Stathias
- Sylvester Comprehensive Cancer Center and Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Karen E Christianson
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - David I Heiman
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Marcin P Cieslik
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Song Cao
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Xiaoyu Song
- Department of Population Health Science and Policy, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jiayi Ji
- Department of Population Health Science and Policy, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Wenke Liu
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Kai Li
- Lester and Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Bo Wen
- Lester and Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yize Li
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Zeynep H Gümüş
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Myvizhi Esai Selvan
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Rama Soundararajan
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Tanvi H Visal
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Maria G Raso
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Edwin Roger Parra
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Özgün Babur
- Computer Science Department, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Pankaj Vats
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Shankara Anand
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Tobias Schraink
- Institute for Systems Genetics and Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - MacIntosh Cornwell
- Institute for Systems Genetics and Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA
| | | | - Houxiang Zhu
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Chia-Kuei Mo
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Yuping Zhang
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Chen Huang
- Lester and Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Arul M Chinnaiyan
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Gilbert S Omenn
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Stephan Schurer
- Sylvester Comprehensive Cancer Center and Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Kelly V Ruggles
- Institute for Systems Genetics and Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - David Fenyö
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Scott D Jewell
- Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Mathangi Thiagarajan
- Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Mehdi Mesri
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Sendurai A Mani
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Namrata D Udeshi
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Gad Getz
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - James Suh
- Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Qing Kay Li
- Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins Medical Institutions, Baltimore, MD 21224, USA
| | | | - Paul K Paik
- Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | | | - Ramaswamy Govindan
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Li Ding
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Ana I Robles
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Karl R Clauser
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Pei Wang
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Steven A Carr
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA.
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
| | - D R Mani
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA.
| | - Michael A Gillette
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA 02115, USA.
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26
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Blencowe M, Yang X. Found in translation-core network preservation across liver diseases and species. CELL REPORTS MEDICINE 2021; 2:100347. [PMID: 34337563 PMCID: PMC8324489 DOI: 10.1016/j.xcrm.2021.100347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Esmaili et al.1 conducted co-expression network analysis to uncover core homeostatic modules critical to a broad spectrum of liver diseases in mouse and human. Perturbation state of core modules may underlie disease stages across species and serve as therapeutic targets.
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Affiliation(s)
- Montgomery Blencowe
- Department Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, USA
- Molecular, Cellular, and Integrative Physiology Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA, USA
| | - Xia Yang
- Department Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, USA
- Molecular, Cellular, and Integrative Physiology Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA, USA
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, Los Angeles, CA, USA
- Corresponding author
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27
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Kursun O, Yemisci M, van den Maagdenberg AMJM, Karatas H. Migraine and neuroinflammation: the inflammasome perspective. J Headache Pain 2021; 22:55. [PMID: 34112082 PMCID: PMC8192049 DOI: 10.1186/s10194-021-01271-1] [Citation(s) in RCA: 97] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 06/01/2021] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Neuroinflammation has an important role in the pathophysiology of migraine, which is a complex neuro-glio-vascular disorder. The main aim of this review is to highlight findings of cortical spreading depolarization (CSD)-induced neuroinflammatory signaling in brain parenchyma from the inflammasome perspective. In addition, we discuss the limited data of the contribution of inflammasomes to other aspects of migraine pathophysiology, foremost the activation of the trigeminovascular system and thereby the generation of migraine pain. MAIN BODY Inflammasomes are signaling multiprotein complexes and key components of the innate immune system. Their activation causes the production of inflammatory cytokines that can stimulate trigeminal neurons and are thus relevant to the generation of migraine pain. The contribution of inflammasome activation to pain signaling has attracted considerable attention in recent years. Nucleotide-binding domain (NOD)-like receptor family pyrin domain containing 3 (NLRP3) is the best characterized inflammasome and there is emerging evidence of its role in a variety of inflammatory pain conditions, including migraine. In this review, we discuss, from an inflammasome point of view, cortical spreading depolarization (CSD)-induced neuroinflammatory signaling in brain parenchyma, the connection with genetic factors that make the brain vulnerable to CSD, and the relation of the inflammasome with diseases that are co-morbid with migraine, including stroke, epilepsy, and the possible links with COVID-19 infection. CONCLUSION Neuroinflammatory pathways, specifically those involving inflammasome proteins, seem promising candidates as treatment targets, and perhaps even biomarkers, in migraine.
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Affiliation(s)
| | - Muge Yemisci
- Institute of Neurological Sciences and Psychiatry, Hacettepe University, Ankara, Turkey.,Department of Neurology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Arn M J M van den Maagdenberg
- Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands.,Department of Neurology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Hulya Karatas
- Institute of Neurological Sciences and Psychiatry, Hacettepe University, Ankara, Turkey.
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28
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Systems genetics in diversity outbred mice inform BMD GWAS and identify determinants of bone strength. Nat Commun 2021; 12:3408. [PMID: 34099702 PMCID: PMC8184749 DOI: 10.1038/s41467-021-23649-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 05/10/2021] [Indexed: 12/14/2022] Open
Abstract
Genome-wide association studies (GWASs) for osteoporotic traits have identified over 1000 associations; however, their impact has been limited by the difficulties of causal gene identification and a strict focus on bone mineral density (BMD). Here, we use Diversity Outbred (DO) mice to directly address these limitations by performing a systems genetics analysis of 55 complex skeletal phenotypes. We apply a network approach to cortical bone RNA-seq data to discover 66 genes likely to be causal for human BMD GWAS associations, including the genes SERTAD4 and GLT8D2. We also perform GWAS in the DO for a wide-range of bone traits and identify Qsox1 as a gene influencing cortical bone accrual and bone strength. In this work, we advance our understanding of the genetics of osteoporosis and highlight the ability of the mouse to inform human genetics. Osteoporosis GWAS faces two challenges, causal gene discovery and a lack of phenotypic diversity. Here, the authors use the Diversity Outbred mouse population to inform human GWAS using networks and map genetic loci for 55 bone traits, identifying new potential bone strength genes.
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29
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Decoding the Transcriptional Response to Ischemic Stroke in Young and Aged Mouse Brain. Cell Rep 2021; 31:107777. [PMID: 32553170 DOI: 10.1016/j.celrep.2020.107777] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 03/25/2020] [Accepted: 05/26/2020] [Indexed: 12/17/2022] Open
Abstract
Ischemic stroke is a well-recognized disease of aging, yet it is unclear how the age-dependent vulnerability occurs and what are the underlying mechanisms. To address these issues, we perform a comprehensive RNA-seq analysis of aging, ischemic stroke, and their interaction in 3- and 18-month-old mice. We assess differential gene expression across injury status and age, estimate cell type proportion changes, assay the results against a range of transcriptional signatures from the literature, and perform unsupervised co-expression analysis, identifying modules of genes with varying response to injury. We uncover downregulation of axonal and synaptic maintenance genetic program, and increased activation of type I interferon (IFN-I) signaling following stroke in aged mice. Together, these results paint a picture of ischemic stroke as a complex age-related disease and provide insights into interaction of aging and stroke on cellular and molecular level.
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The self in context: brain systems linking mental and physical health. Nat Rev Neurosci 2021; 22:309-322. [PMID: 33790441 PMCID: PMC8447265 DOI: 10.1038/s41583-021-00446-8] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/22/2021] [Indexed: 02/01/2023]
Abstract
Increasing evidence suggests that mental health and physical health are linked by neural systems that jointly regulate somatic physiology and high-level cognition. Key systems include the ventromedial prefrontal cortex and the related default-mode network. These systems help to construct models of the 'self-in-context', compressing information across time and sensory modalities into conceptions of the underlying causes of experience. Self-in-context models endow events with personal meaning and allow predictive control over behaviour and peripheral physiology, including autonomic, neuroendocrine and immune function. They guide learning from experience and the formation of narratives about the self and one's world. Disorders of mental and physical health, especially those with high co-occurrence and convergent alterations in the functionality of the ventromedial prefrontal cortex and the default-mode network, could benefit from interventions focused on understanding and shaping mindsets and beliefs about the self, illness and treatment.
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31
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Jung SY. Multi-Omics Data Analysis Uncovers Molecular Networks and Gene Regulators for Metabolic Biomarkers. Biomolecules 2021; 11:biom11030406. [PMID: 33801830 PMCID: PMC8001935 DOI: 10.3390/biom11030406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/07/2021] [Accepted: 03/07/2021] [Indexed: 12/04/2022] Open
Abstract
The insulin-like growth factors (IGFs)/insulin resistance (IR) axis is the major metabolic hormonal pathway mediating the biologic mechanism of several complex human diseases, including type 2 diabetes (T2DM) and cancers. The genomewide association study (GWAS)-based approach has neither fully characterized the phenotype variation nor provided a comprehensive understanding of the regulatory biologic mechanisms. We applied systematic genomics to integrate our previous GWAS data for IGF-I and IR with multi-omics datasets, e.g., whole-blood expression quantitative loci, molecular pathways, and gene network, to capture the full range of genetic functionalities associated with IGF-I/IR and key drivers (KDs) in gene-regulatory networks. We identified both shared (e.g., T2DM, lipid metabolism, and estimated glomerular filtration signaling) and IR-specific (e.g., mechanistic target of rapamycin, phosphoinositide 3-kinases, and erb-b2 receptor tyrosine kinase 4 signaling) molecular biologic processes of IGF-I/IR axis regulation. Next, by using tissue-specific gene–gene interaction networks, we identified both well-established (e.g., IRS1 and IGF1R) and novel (e.g., AKT1, HRAS, and JAK1) KDs in the IGF-I/IR-associated subnetworks. Our results, if validated in additional genomic studies, may provide robust, comprehensive insights into the mechanisms of IGF-I/IR regulation and highlight potential novel genetic targets as preventive and therapeutic strategies for the associated diseases, e.g., T2DM and cancers.
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Affiliation(s)
- Su Yon Jung
- Translational Sciences Section, Jonsson Comprehensive Cancer Center, School of Nursing, University of California, Los Angeles, Los Angeles, CA 90095, USA
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32
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von Scheidt M, Zhao Y, de Aguiar Vallim TQ, Che N, Wierer M, Seldin MM, Franzén O, Kurt Z, Pang S, Bongiovanni D, Yamamoto M, Edwards PA, Ruusalepp A, Kovacic JC, Mann M, Björkegren JLM, Lusis AJ, Yang X, Schunkert H. Transcription Factor MAFF (MAF Basic Leucine Zipper Transcription Factor F) Regulates an Atherosclerosis Relevant Network Connecting Inflammation and Cholesterol Metabolism. Circulation 2021; 143:1809-1823. [PMID: 33626882 DOI: 10.1161/circulationaha.120.050186] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND Coronary artery disease (CAD) is a multifactorial condition with both genetic and exogenous causes. The contribution of tissue-specific functional networks to the development of atherosclerosis remains largely unclear. The aim of this study was to identify and characterize central regulators and networks leading to atherosclerosis. METHODS Based on several hundred genes known to affect atherosclerosis risk in mouse (as demonstrated in knockout models) and human (as shown by genome-wide association studies), liver gene regulatory networks were modeled. The hierarchical order and regulatory directions of genes within the network were based on Bayesian prediction models, as well as experimental studies including chromatin immunoprecipitation DNA-sequencing, chromatin immunoprecipitation mass spectrometry, overexpression, small interfering RNA knockdown in mouse and human liver cells, and knockout mouse experiments. Bioinformatics and correlation analyses were used to clarify associations between central genes and CAD phenotypes in both human and mouse. RESULTS The transcription factor MAFF (MAF basic leucine zipper transcription factor F) interacted as a key driver of a liver network with 3 human genes at CAD genome-wide association studies loci and 11 atherosclerotic murine genes. Most importantly, expression levels of the low-density lipoprotein receptor (LDLR) gene correlated with MAFF in 600 CAD patients undergoing bypass surgery (STARNET [Stockholm-Tartu Atherosclerosis Reverse Network Engineering Task]) and a hybrid mouse diversity panel involving 105 different inbred mouse strains. Molecular mechanisms of MAFF were tested in noninflammatory conditions and showed positive correlation between MAFF and LDLR in vitro and in vivo. Interestingly, after lipopolysaccharide stimulation (inflammatory conditions), an inverse correlation between MAFF and LDLR in vitro and in vivo was observed. Chromatin immunoprecipitation mass spectrometry revealed that the human CAD genome-wide association studies candidate BACH1 (BTB domain and CNC homolog 1) assists MAFF in the presence of lipopolysaccharide stimulation with respective heterodimers binding at the MAF recognition element of the LDLR promoter to transcriptionally downregulate LDLR expression. CONCLUSIONS The transcription factor MAFF was identified as a novel central regulator of an atherosclerosis/CAD-relevant liver network. MAFF triggered context-specific expression of LDLR and other genes known to affect CAD risk. Our results suggest that MAFF is a missing link between inflammation, lipid and lipoprotein metabolism, and a possible treatment target.
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Affiliation(s)
- Moritz von Scheidt
- Department of Cardiology, Deutsches Herzzentrum München, Technische Universität München, Munich, Germany (M.v.S., S.P., H.S.).,Deutsches Zentrum für Herz- und Kreislauferkrankungen, Partner Site Munich Heart Alliance, Germany (M.v.S., D.B., H.S.)
| | | | - Thomas Q de Aguiar Vallim
- Departments of Medicine (T.Q.d.A.V., N.C., P.A.E., A.J.L.), David Geffen School of Medicine, University of California, Los Angeles.,Biological Chemistry (T.Q.d.A.V., P.A.E.), David Geffen School of Medicine, University of California, Los Angeles
| | - Nam Che
- Departments of Medicine (T.Q.d.A.V., N.C., P.A.E., A.J.L.), David Geffen School of Medicine, University of California, Los Angeles.,Microbiology, Immunology and Molecular Genetics (N.C., A.J.L.), David Geffen School of Medicine, University of California, Los Angeles.,Human Genetics (N.C., A.J.L.), David Geffen School of Medicine, University of California, Los Angeles
| | - Michael Wierer
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany (M.W., M.M.)
| | - Marcus M Seldin
- Department of Biological Chemistry and Center for Epigenetics and Metabolism, University of California, Irvine (M.M.S.)
| | - Oscar Franzén
- Integrated Cardio Metabolic Centre, Karolinska Institutet, Novum, Huddinge, Sweden (O.F., J.L.M.B.)
| | - Zeyneb Kurt
- Department of Computer and Information Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom (Z.K.)
| | - Shichao Pang
- Department of Cardiology, Deutsches Herzzentrum München, Technische Universität München, Munich, Germany (M.v.S., S.P., H.S.)
| | - Dario Bongiovanni
- Deutsches Zentrum für Herz- und Kreislauferkrankungen, Partner Site Munich Heart Alliance, Germany (M.v.S., D.B., H.S.).,Department of Internal Medicine, School of Medicine, University Hospital Rechts der Isar, Technical University of Munich, Germany (D.B.)
| | - Masayuki Yamamoto
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan (M.Y.)
| | - Peter A Edwards
- Departments of Medicine (T.Q.d.A.V., N.C., P.A.E., A.J.L.), David Geffen School of Medicine, University of California, Los Angeles.,Biological Chemistry (T.Q.d.A.V., P.A.E.), David Geffen School of Medicine, University of California, Los Angeles
| | - Arno Ruusalepp
- Department of Cardiac Surgery, Tartu University Hospital, Estonia (A.R.).,Clinical Gene Networks AB, Stockholm, Sweden (A.R., J.L.M.B.)
| | - Jason C Kovacic
- Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York (J.C.K., J.L.M.B.)
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany (M.W., M.M.)
| | - Johan L M Björkegren
- Integrated Cardio Metabolic Centre, Karolinska Institutet, Novum, Huddinge, Sweden (O.F., J.L.M.B.).,Clinical Gene Networks AB, Stockholm, Sweden (A.R., J.L.M.B.).,Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York (J.C.K., J.L.M.B.)
| | - Aldons J Lusis
- Departments of Medicine (T.Q.d.A.V., N.C., P.A.E., A.J.L.), David Geffen School of Medicine, University of California, Los Angeles.,Microbiology, Immunology and Molecular Genetics (N.C., A.J.L.), David Geffen School of Medicine, University of California, Los Angeles.,Human Genetics (N.C., A.J.L.), David Geffen School of Medicine, University of California, Los Angeles
| | - Xia Yang
- Department of Integrative Biology and Physiology, Institute for Quantitative and Computational Biosciences (Y.Z., X.Y.), David Geffen School of Medicine, University of California, Los Angeles
| | - Heribert Schunkert
- Department of Cardiology, Deutsches Herzzentrum München, Technische Universität München, Munich, Germany (M.v.S., S.P., H.S.).,Deutsches Zentrum für Herz- und Kreislauferkrankungen, Partner Site Munich Heart Alliance, Germany (M.v.S., D.B., H.S.)
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Network models of primary melanoma microenvironments identify key melanoma regulators underlying prognosis. Nat Commun 2021; 12:1214. [PMID: 33619278 PMCID: PMC7900178 DOI: 10.1038/s41467-021-21457-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 01/21/2021] [Indexed: 02/08/2023] Open
Abstract
Melanoma is the most lethal skin malignancy, driven by genetic and epigenetic alterations in the complex tumour microenvironment. While large-scale molecular profiling of melanoma has identified molecular signatures associated with melanoma progression, comprehensive systems-level modeling remains elusive. This study builds up predictive gene network models of molecular alterations in primary melanoma by integrating large-scale bulk-based multi-omic and single-cell transcriptomic data. Incorporating clinical, epigenetic, and proteomic data into these networks reveals key subnetworks, cell types, and regulators underlying melanoma progression. Tumors with high immune infiltrates are found to be associated with good prognosis, presumably due to induced CD8+ T-cell cytotoxicity, via MYO1F-mediated M1-polarization of macrophages. Seventeen key drivers of the gene subnetworks associated with poor prognosis, including the transcription factor ZNF180, are tested for their pro-tumorigenic effects in vitro. The anti-tumor effect of silencing ZNF180 is further validated using in vivo xenografts. Experimentally validated targets of ZNF180 are enriched in the ZNF180 centered network and the known pathways such as melanoma cell maintenance and immune cell infiltration. The transcriptional networks and their critical regulators provide insights into the molecular mechanisms of melanomagenesis and pave the way for developing therapeutic strategies for melanoma. While the molecular profiling of melanoma progression has been extensively characterised by large-scale studies, there is still need for the comprehensive integration of such datasets. Here the authors construct predictive gene network models for prognostic and therapeutic purposes.
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Busnelli M, Manzini S, Chiara M, Colombo A, Fontana F, Oleari R, Potì F, Horner D, Bellosta S, Chiesa G. Aortic Gene Expression Profiles Show How ApoA-I Levels Modulate Inflammation, Lysosomal Activity, and Sphingolipid Metabolism in Murine Atherosclerosis. Arterioscler Thromb Vasc Biol 2021; 41:651-667. [PMID: 33327742 PMCID: PMC7837693 DOI: 10.1161/atvbaha.120.315669] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 12/01/2020] [Indexed: 01/16/2023]
Abstract
OBJECTIVE HDL (high-density lipoprotein) particles are known to possess several antiatherogenic properties that include the removal of excess cholesterol from peripheral tissues, the maintenance of endothelial integrity, antioxidant, and anti-inflammatory activities. ApoA-I overexpression in apoE-deficient (EKO) mice has been shown to increase HDL levels and to strongly reduce atherosclerosis development. The aim of the study was to investigate gene expression patterns associated with atherosclerosis development in the aorta of EKO mice and how HDL plasma levels relate to gene expression patterns at different stages of atherosclerosis development and with different dietary treatments. Approach and Results: Eight-week-old EKO mice, EKO mice overexpressing human apoA-I, and wild-type mice as controls were fed either normal laboratory or Western diet for 6 or 22 weeks. Cholesterol distribution among lipoproteins was evaluated, and atherosclerosis of the aorta was quantified. High-throughput sequencing technologies were used to analyze the transcriptome of the aorta of the 3 genotypes in each experimental condition. In addition to the well-known activation of inflammation and immune response, the impairment of sphingolipid metabolism, phagosome-lysosome system, and osteoclast differentiation emerged as relevant players in atherosclerosis development. The reduced atherosclerotic burden in the aorta of EKO mice expressing high levels of apoA-I was accompanied by a reduced activation of immune system markers, as well as reduced perturbation of lysosomal activity and a better regulation of the sphingolipid synthesis pathway. CONCLUSIONS ApoA-I modulates atherosclerosis development in the aorta of EKO mice affecting the expression of pathways additional to those associated with inflammation and immune response.
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Affiliation(s)
- Marco Busnelli
- Department of Pharmacological and Biomolecular Sciences (M.B., S.M., A.C., F.F., R.O., S.B., G.C.), Università degli Studi di Milano, Italy
| | - Stefano Manzini
- Department of Pharmacological and Biomolecular Sciences (M.B., S.M., A.C., F.F., R.O., S.B., G.C.), Università degli Studi di Milano, Italy
| | - Matteo Chiara
- Department of Biosciences (M.C., D.H.), Università degli Studi di Milano, Italy
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Bari, Italy (M.C., D.H.)
| | - Alice Colombo
- Department of Pharmacological and Biomolecular Sciences (M.B., S.M., A.C., F.F., R.O., S.B., G.C.), Università degli Studi di Milano, Italy
| | - Fabrizio Fontana
- Department of Pharmacological and Biomolecular Sciences (M.B., S.M., A.C., F.F., R.O., S.B., G.C.), Università degli Studi di Milano, Italy
| | - Roberto Oleari
- Department of Pharmacological and Biomolecular Sciences (M.B., S.M., A.C., F.F., R.O., S.B., G.C.), Università degli Studi di Milano, Italy
| | - Francesco Potì
- Department of Medicine and Surgery—Unit of Neurosciences, University of Parma, Italy (F.P.)
| | - David Horner
- Department of Biosciences (M.C., D.H.), Università degli Studi di Milano, Italy
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Bari, Italy (M.C., D.H.)
| | - Stefano Bellosta
- Department of Pharmacological and Biomolecular Sciences (M.B., S.M., A.C., F.F., R.O., S.B., G.C.), Università degli Studi di Milano, Italy
| | - Giulia Chiesa
- Department of Pharmacological and Biomolecular Sciences (M.B., S.M., A.C., F.F., R.O., S.B., G.C.), Università degli Studi di Milano, Italy
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Cohain AT, Barrington WT, Jordan DM, Beckmann ND, Argmann CA, Houten SM, Charney AW, Ermel R, Sukhavasi K, Franzen O, Koplev S, Whatling C, Belbin GM, Yang J, Hao K, Kenny EE, Tu Z, Zhu J, Gan LM, Do R, Giannarelli C, Kovacic JC, Ruusalepp A, Lusis AJ, Bjorkegren JLM, Schadt EE. An integrative multiomic network model links lipid metabolism to glucose regulation in coronary artery disease. Nat Commun 2021; 12:547. [PMID: 33483510 PMCID: PMC7822923 DOI: 10.1038/s41467-020-20750-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 12/08/2020] [Indexed: 01/30/2023] Open
Abstract
Elevated plasma cholesterol and type 2 diabetes (T2D) are associated with coronary artery disease (CAD). Individuals treated with cholesterol-lowering statins have increased T2D risk, while individuals with hypercholesterolemia have reduced T2D risk. We explore the relationship between lipid and glucose control by constructing network models from the STARNET study with sequencing data from seven cardiometabolic tissues obtained from CAD patients during coronary artery by-pass grafting surgery. By integrating gene expression, genotype, metabolomic, and clinical data, we identify a glucose and lipid determining (GLD) regulatory network showing inverse relationships with lipid and glucose traits. Master regulators of the GLD network also impact lipid and glucose levels in inverse directions. Experimental inhibition of one of the GLD network master regulators, lanosterol synthase (LSS), in mice confirms the inverse relationships to glucose and lipid levels as predicted by our model and provides mechanistic insights.
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Affiliation(s)
- Ariella T Cohain
- Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - William T Barrington
- Department of Human Genetics/Medicine, David Geffen School of Medicine, University of California Los Angeles (UCLA), Los Angeles, CA, USA
| | - Daniel M Jordan
- Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Noam D Beckmann
- Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Carmen A Argmann
- Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Sander M Houten
- Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Alexander W Charney
- Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Raili Ermel
- Department of Cardiac Surgery, Tartu University Hospital, Tartu, Estonia
| | | | - Oscar Franzen
- Integrated Cardio Metabolic Centre, Department of Medicine, Karolinska Institutet, Karolinska Universitetssjukhuset, Huddinge, Sweden
| | - Simon Koplev
- Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Carl Whatling
- Translational Science, Cardiovascular, Renal and Metabolism, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden
| | - Gillian M Belbin
- Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jialiang Yang
- Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ke Hao
- Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Eimear E Kenny
- Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Zhidong Tu
- Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jun Zhu
- Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Li-Ming Gan
- Early Clinical Development, Cardiovascular, Renal and Metabolism, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden
| | - Ron Do
- Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Chiara Giannarelli
- Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Cardiovascular Research Centre, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jason C Kovacic
- Cardiovascular Research Centre, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Arno Ruusalepp
- Department of Cardiac Surgery, Tartu University Hospital, Tartu, Estonia
| | - Aldons J Lusis
- Department of Human Genetics/Medicine, David Geffen School of Medicine, University of California Los Angeles (UCLA), Los Angeles, CA, USA
| | - Johan L M Bjorkegren
- Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Clinical Gene Networks AB, Stockholm, Sweden.
| | - Eric E Schadt
- Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Sema4, Stamford, CT, USA.
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Blencowe M, Ahn IS, Saleem Z, Luk H, Cely I, Mäkinen VP, Zhao Y, Yang X. Gene networks and pathways for plasma lipid traits via multitissue multiomics systems analysis. J Lipid Res 2021; 62:100019. [PMID: 33561811 PMCID: PMC7873371 DOI: 10.1194/jlr.ra120000713] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 12/04/2020] [Accepted: 12/23/2020] [Indexed: 12/13/2022] Open
Abstract
Genome-wide association studies (GWASs) have implicated ∼380 genetic loci for plasma lipid regulation. However, these loci only explain 17-27% of the trait variance, and a comprehensive understanding of the molecular mechanisms has not been achieved. In this study, we utilized an integrative genomics approach leveraging diverse genomic data from human populations to investigate whether genetic variants associated with various plasma lipid traits, namely, total cholesterol, high and low density lipoprotein cholesterol (HDL and LDL), and triglycerides, from GWASs were concentrated on specific parts of tissue-specific gene regulatory networks. In addition to the expected lipid metabolism pathways, gene subnetworks involved in "interferon signaling," "autoimmune/immune activation," "visual transduction," and "protein catabolism" were significantly associated with all lipid traits. In addition, we detected trait-specific subnetworks, including cadherin-associated subnetworks for LDL; glutathione metabolism for HDL; valine, leucine, and isoleucine biosynthesis for total cholesterol; and insulin signaling and complement pathways for triglyceride. Finally, by using gene-gene relations revealed by tissue-specific gene regulatory networks, we detected both known (e.g., APOH, APOA4, and ABCA1) and novel (e.g., F2 in adipose tissue) key regulator genes in these lipid-associated subnetworks. Knockdown of the F2 gene (coagulation factor II, thrombin) in 3T3-L1 and C3H10T1/2 adipocytes altered gene expression of Abcb11, Apoa5, Apof, Fabp1, Lipc, and Cd36; reduced intracellular adipocyte lipid content; and increased extracellular lipid content, supporting a link between adipose thrombin and lipid regulation. Our results shed light on the complex mechanisms underlying lipid metabolism and highlight potential novel targets for lipid regulation and lipid-associated diseases.
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Affiliation(s)
- Montgomery Blencowe
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, USA; Molecular, Cellular, and Integrative Physiology Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA, USA
| | - In Sook Ahn
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Zara Saleem
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Helen Luk
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ingrid Cely
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ville-Petteri Mäkinen
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, USA; South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Yuqi Zhao
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, USA.
| | - Xia Yang
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, USA; Molecular, Cellular, and Integrative Physiology Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA, USA; Interdepartmental Program of Bioinformatics, University of California, Los Angeles, Los Angeles, CA, USA.
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Zhang Z, Li W, Yang G, Lu X, Qi X, Wang S, Cao C, Zhang P, Ren J, Zhao J, Zhang J, Hong S, Tan Y, Burchfield J, Yu Y, Xu T, Yao X, James D, Feng W, Chen Z. CASK modulates the assembly and function of the Mint1/Munc18-1 complex to regulate insulin secretion. Cell Discov 2020; 6:92. [PMID: 33318489 PMCID: PMC7736295 DOI: 10.1038/s41421-020-00216-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 09/07/2020] [Indexed: 11/09/2022] Open
Abstract
Calcium/calmodulin-dependent protein serine kinase (CASK) is a key player in vesicle transport and release in neurons. However, its precise role, particularly in nonneuronal systems, is incompletely understood. We report that CASK functions as an important regulator of insulin secretion. CASK depletion in mouse islets/β cells substantially reduces insulin secretion and vesicle docking/fusion. CASK forms a ternary complex with Mint1 and Munc18-1, and this event is regulated by glucose stimulation in β cells. The crystal structure of the CASK/Mint1 complex demonstrates that Mint1 exhibits a unique "whip"-like structure that wraps tightly around the CASK-CaMK domain, which contains dual hydrophobic interaction sites. When triggered by CASK binding, Mint1 modulates the assembly of the complex. Further investigation revealed that CASK-Mint1 binding is critical for ternary complex formation, thereby controlling Munc18-1 membrane localization and insulin secretion. Our work illustrates the distinctive molecular basis underlying CASK/Mint1/Munc18-1 complex formation and reveals the importance of the CASK-Mint1-Munc18 signaling axis in insulin secretion.
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Affiliation(s)
- Zhe Zhang
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Wei Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Guang Yang
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China.,Charles Perkins Centre, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Xuefeng Lu
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Xin Qi
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuting Wang
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Can Cao
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Peng Zhang
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Jinqi Ren
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jiaxu Zhao
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Junyi Zhang
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Sheng Hong
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Yan Tan
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - James Burchfield
- Charles Perkins Centre, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Yang Yu
- National Center for Protein Science Shanghai, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Tao Xu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xuebiao Yao
- Anhui Key Laboratory for Cellular Dynamics and Chemical Biology, Hefei National Laboratory for Physical Sciences at Nanoscale, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - David James
- Charles Perkins Centre, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia.,Sydney Medical School, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Wei Feng
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China. .,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Zhengjun Chen
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China. .,School of Life Sciences and Technology, ShanghaiTech University, Shanghai, 201210, China.
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Chen YX, Rong Y, Jiang F, Chen JB, Duan YY, Dong SS, Zhu DL, Chen H, Yang TL, Dai Z, Guo Y. An integrative multi-omics network-based approach identifies key regulators for breast cancer. Comput Struct Biotechnol J 2020; 18:2826-2835. [PMID: 33133424 PMCID: PMC7585874 DOI: 10.1016/j.csbj.2020.10.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 09/13/2020] [Accepted: 10/01/2020] [Indexed: 02/06/2023] Open
Abstract
Although genome-wide association studies (GWASs) have successfully identified thousands of risk variants for human complex diseases, understanding the biological function and molecular mechanisms of the associated SNPs involved in complex diseases is challenging. Here we developed a framework named integrative multi-omics network-based approach (IMNA), aiming to identify potential key genes in regulatory networks by integrating molecular interactions across multiple biological scales, including GWAS signals, gene expression-based signatures, chromatin interactions and protein interactions from the network topology. We applied this approach to breast cancer, and prioritized key genes involved in regulatory networks. We also developed an abnormal gene expression score (AGES) signature based on the gene expression deviation of the top 20 rank-ordered genes in breast cancer. The AGES values are associated with genetic variants, tumor properties and patient survival outcomes. Among the top 20 genes, RNASEH2A was identified as a new candidate gene for breast cancer. Thus, our integrative network-based approach provides a genetic-driven framework to unveil tissue-specific interactions from multiple biological scales and reveal potential key regulatory genes for breast cancer. This approach can also be applied in other complex diseases such as ovarian cancer to unravel underlying mechanisms and help for developing therapeutic targets.
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Affiliation(s)
- Yi-Xiao Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi Province 710049, PR China
| | - Yu Rong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi Province 710049, PR China
| | - Feng Jiang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi Province 710049, PR China
| | - Jia-Bin Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi Province 710049, PR China
| | - Yuan-Yuan Duan
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi Province 710049, PR China
| | - Shan-Shan Dong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi Province 710049, PR China
| | - Dong-Li Zhu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi Province 710049, PR China.,Research Institute of Xi'an Jiaotong University, Zhejiang Province 311215, PR China
| | - Hao Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi Province 710049, PR China
| | - Tie-Lin Yang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi Province 710049, PR China.,Research Institute of Xi'an Jiaotong University, Zhejiang Province 311215, PR China
| | - Zhijun Dai
- Department of Breast Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province 310003, PR China
| | - Yan Guo
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi Province 710049, PR China
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Markov AV, Sen’kova AV, Popadyuk II, Salomatina OV, Logashenko EB, Komarova NI, Ilyina AA, Salakhutdinov NF, Zenkova MA. Novel 3'-Substituted-1',2',4'-Oxadiazole Derivatives of 18βH-Glycyrrhetinic Acid and Their O-Acylated Amidoximes: Synthesis and Evaluation of Antitumor and Anti-Inflammatory Potential In Vitro and In Vivo. Int J Mol Sci 2020; 21:E3511. [PMID: 32429154 PMCID: PMC7279002 DOI: 10.3390/ijms21103511] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 05/10/2020] [Accepted: 05/12/2020] [Indexed: 12/22/2022] Open
Abstract
A series of novel 18βH-glycyrrhetinic acid (GA) derivatives containing 3'-(alkyl/phenyl/pyridin(-2″, -3″, and -4″)-yl)-1',2',4'-oxadiazole moieties at the C-30 position were synthesized by condensation of triterpenoid's carboxyl group with corresponding amidoximes and further cyclization. Screening of the cytotoxicity of novel GA derivatives on a panel of tumor cell lines showed that the 3-acetoxy triterpenoid intermediates-O-acylated amidoxime 3a-h-display better solubility under bioassay conditions and more pronounced cytotoxicity compared to their 1',2',4'-oxadiazole analogs 4f-h (median IC50 = 7.0 and 49.7 µM, respectively). Subsequent replacement of the 3-acetoxy group by the hydroxyl group of pyridin(-2″, 3″, and -4″)-yl-1',2',4'-oxadiazole-bearing GA derivatives produced compounds 5f-h, showing the most pronounced selective toxicity toward tumor cells (median selectivity index (SI) > 12.1). Further detailed analysis of the antitumor activity of hit derivative 5f revealed its marked proapoptotic activity and inhibitory effects on clonogenicity and motility of HeLa cervical carcinoma cells in vitro, and the metastatic growth of B16 melanoma in vivo. Additionally, the comprehensive in silico study revealed intermediate 3d, bearing the tert-butyl moiety in O-acylated amidoxime, as a potent anti-inflammatory candidate, which was able to effectively inhibit inflammatory response induced by IFNγ in macrophages in vitro and carrageenan in murine models in vivo, probably by primary interactions with active sites of MMP9, neutrophil elastase, and thrombin. Taken together, our findings provide a basis for a better understanding of the structure-activity relationship of 1',2',4'-oxadiazole-containing triterpenoids and reveal two hit molecules with pronounced antitumor (5f) and anti-inflammatory (3d) activities.
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Affiliation(s)
- Andrey V. Markov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrent’ev ave., 8, 630090 Novosibirsk, Russia; (A.V.S.); (O.V.S.); (E.B.L.); (A.A.I.); (M.A.Z.)
| | - Aleksandra V. Sen’kova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrent’ev ave., 8, 630090 Novosibirsk, Russia; (A.V.S.); (O.V.S.); (E.B.L.); (A.A.I.); (M.A.Z.)
| | - Irina I. Popadyuk
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, Lavrent’ev ave., 9, 630090 Novosibirsk, Russia; (I.I.P.); (N.I.K.); (N.F.S.)
| | - Oksana V. Salomatina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrent’ev ave., 8, 630090 Novosibirsk, Russia; (A.V.S.); (O.V.S.); (E.B.L.); (A.A.I.); (M.A.Z.)
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, Lavrent’ev ave., 9, 630090 Novosibirsk, Russia; (I.I.P.); (N.I.K.); (N.F.S.)
| | - Evgeniya B. Logashenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrent’ev ave., 8, 630090 Novosibirsk, Russia; (A.V.S.); (O.V.S.); (E.B.L.); (A.A.I.); (M.A.Z.)
| | - Nina I. Komarova
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, Lavrent’ev ave., 9, 630090 Novosibirsk, Russia; (I.I.P.); (N.I.K.); (N.F.S.)
| | - Anna A. Ilyina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrent’ev ave., 8, 630090 Novosibirsk, Russia; (A.V.S.); (O.V.S.); (E.B.L.); (A.A.I.); (M.A.Z.)
| | - Nariman F. Salakhutdinov
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, Lavrent’ev ave., 9, 630090 Novosibirsk, Russia; (I.I.P.); (N.I.K.); (N.F.S.)
| | - Marina A. Zenkova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrent’ev ave., 8, 630090 Novosibirsk, Russia; (A.V.S.); (O.V.S.); (E.B.L.); (A.A.I.); (M.A.Z.)
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40
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Zeng L, Talukdar HA, Koplev S, Giannarelli C, Ivert T, Gan LM, Ruusalepp A, Schadt EE, Kovacic JC, Lusis AJ, Michoel T, Schunkert H, Björkegren JLM. Contribution of Gene Regulatory Networks to Heritability of Coronary Artery Disease. J Am Coll Cardiol 2020; 73:2946-2957. [PMID: 31196451 DOI: 10.1016/j.jacc.2019.03.520] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Revised: 02/27/2019] [Accepted: 03/16/2019] [Indexed: 12/21/2022]
Abstract
BACKGROUND Genetic variants currently known to affect coronary artery disease (CAD) risk explain less than one-quarter of disease heritability. The heritability contribution of gene regulatory networks (GRNs) in CAD, which are modulated by both genetic and environmental factors, is unknown. OBJECTIVES This study sought to determine the heritability contributions of single nucleotide polymorphisms affecting gene expression (eSNPs) in GRNs causally linked to CAD. METHODS Seven vascular and metabolic tissues collected in 2 independent genetics-of-gene-expression studies of patients with CAD were used to identify eSNPs and to infer coexpression networks. To construct GRNs with causal relations to CAD, the prior information of eSNPs in the coexpression networks was used in a Bayesian algorithm. Narrow-sense CAD heritability conferred by the GRNs was calculated from individual-level genotype data from 9 European genome-wide association studies (GWAS) (13,612 cases, 13,758 control cases). RESULTS The authors identified and replicated 28 independent GRNs active in CAD. The genetic variation in these networks contributed to 10.0% of CAD heritability beyond the 22% attributable to risk loci identified by GWAS. GRNs in the atherosclerotic arterial wall (n = 7) and subcutaneous or visceral abdominal fat (n = 9) were most strongly implicated, jointly explaining 8.2% of CAD heritability. In all, these 28 GRNs (each contributing to >0.2% of CAD heritability) comprised 24 to 841 genes, whereof 1 to 28 genes had strong regulatory effects (key disease drivers) and harbored many relevant functions previously associated with CAD. The gene activity in these 28 GRNs also displayed strong associations with genetic and phenotypic cardiometabolic disease variations both in humans and mice, indicative of their pivotal roles as mediators of gene-environmental interactions in CAD. CONCLUSIONS GRNs capture a major portion of genetic variance and contribute to heritability beyond that of genetic loci currently known to affect CAD risk. These networks provide a framework to identify novel risk genes/pathways and study molecular interactions within and across disease-relevant tissues leading to CAD.
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Affiliation(s)
- Lingyao Zeng
- Deutsches Herzzentrum München, Klinik für Herz- und Kreislauferkrankungen, Technische Universität München, DZHK (German Centre for Cardiovascular Research), Munich Heart Alliance, Munich, Germany
| | - Husain A Talukdar
- Integrated Cardio Metabolic Centre, Department of Medicine, Karolinska Institutet, Karolinska Universitetssjukhuset, Huddinge, Sweden
| | - Simon Koplev
- Department of Genetics & Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Chiara Giannarelli
- Department of Genetics & Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York; Cardiovascular Research Centre, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Torbjörn Ivert
- Department of Thoracic Surgery, Karolinska University Hospital and Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Li-Ming Gan
- Cardiovascular, Renal and Metabolism Translational Medicines Unit, Early Clinical Development, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden
| | - Arno Ruusalepp
- Department of Cardiac Surgery, Tartu University Hospital, Tartu, Estonia; Clinical Gene Networks AB, Stockholm, Sweden
| | - Eric E Schadt
- Department of Genetics & Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jason C Kovacic
- Cardiovascular Research Centre, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Aldons J Lusis
- Departments of Medicine, Cardiology, Human Genetics, Microbiology, Immunology & Molecular Genetics, University of California-Los Angeles, Los Angeles, California
| | - Tom Michoel
- Clinical Gene Networks AB, Stockholm, Sweden; Division of Genetics and Genomics, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Heribert Schunkert
- Deutsches Herzzentrum München, Klinik für Herz- und Kreislauferkrankungen, Technische Universität München, DZHK (German Centre for Cardiovascular Research), Munich Heart Alliance, Munich, Germany.
| | - Johan L M Björkegren
- Deutsches Herzzentrum München, Klinik für Herz- und Kreislauferkrankungen, Technische Universität München, DZHK (German Centre for Cardiovascular Research), Munich Heart Alliance, Munich, Germany; Integrated Cardio Metabolic Centre, Department of Medicine, Karolinska Institutet, Karolinska Universitetssjukhuset, Huddinge, Sweden; Department of Genetics & Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York; Clinical Gene Networks AB, Stockholm, Sweden.
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41
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Dehghani A, Karatas H. Mouse Models of Familial Hemiplegic Migraine for Studying Migraine Pathophysiology. Curr Neuropharmacol 2020; 17:961-973. [PMID: 31092180 PMCID: PMC7052833 DOI: 10.2174/1570159x17666190513085013] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 02/08/2019] [Accepted: 04/23/2019] [Indexed: 12/14/2022] Open
Abstract
Migraine, an extremely disabling neurological disorder, has a strong genetic component. Since monogenic mi-graines (resulting from mutations or changes in a single gene) may help researchers discover migraine pathophysiology, transgenic mice models harboring gene mutations identified in Familial Hemiplegic Migraine (FHM) patients have been gen-erated. Studies in these FHM mutant mice models have shed light on the mechanisms of migraine and may aid in the identifi-cation of novel targets for treatment. More specifically, the studies shed light on how gene mutations, hormones, and other factors impact the pathophysiology of migraine. The models may also be of relevance to researchers outside the field of mi-graine as some of their aspects are relevant to pain in general. Additionally, because of the comorbidities associated with mi-graine, they share similarities with the mutant mouse models of epilepsy, stroke, and perhaps depression. Here, we review the experimental data obtained from these mutant mice and focus on how they can be used to investigate the pathophysiology of migraine, including synaptic plasticity, neuroinflammation, metabolite alterations, and molecular and behavioral mecha-nisms of pain.
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Affiliation(s)
- Anisa Dehghani
- Institute of Neurological Sciences and Psychiatry, Faculty of Medicine, Hacettepe University, Ankara 06100, Turkey
| | - Hulya Karatas
- Institute of Neurological Sciences and Psychiatry, Faculty of Medicine, Hacettepe University, Ankara 06100, Turkey
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42
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Corso M, García de la Torre VS. Biomolecular approaches to understanding metal tolerance and hyperaccumulation in plants. Metallomics 2020; 12:840-859. [DOI: 10.1039/d0mt00043d] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Trace metal elements are essential for plant growth but become toxic at high concentrations, while some non-essential elements, such as Cd and As, show toxicity even in traces.
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Affiliation(s)
- Massimiliano Corso
- Institut Jean-Pierre Bourgin
- Université Paris-Saclay
- INRAE
- AgroParisTech
- 78000 Versailles
| | - Vanesa S. García de la Torre
- Molecular Genetics and Physiology of Plants
- Faculty of Biology and Biotechnology
- Ruhr University Bochum
- 44801 Bochum
- Germany
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43
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Chen L, Yao Y, Jin C, Wu S, Liu Q, Li J, Ma Y, Xu Y, Zhong Y. Integrative genomic analysis identified common regulatory networks underlying the correlation between coronary artery disease and plasma lipid levels. BMC Cardiovasc Disord 2019; 19:310. [PMID: 31870308 PMCID: PMC6927120 DOI: 10.1186/s12872-019-01271-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 11/21/2019] [Indexed: 12/15/2022] Open
Abstract
Background Coronary artery disease (CAD) and plasma lipid levels are highly correlated, indicating the presence of common pathways between them. Nevertheless, the molecular pathways underlying the pathogenic comorbidities for both traits remain poorly studied. We sought to identify common pathways and key driver genes by performing a comprehensive integrative analysis based on multi-omic datasets. Methods By performing a pathway-based analysis of GWAS summary data, we identified that lipoprotein metabolism process-related pathways were significantly associated with CAD risk. Based on LD score regression analysis of CAD-related SNPs, significant heritability enrichments were observed in the cardiovascular and digestive system, as well as in liver and gastrointestinal tissues, which are the main regulators for lipid level. Results We found there existed significant genetic correlation between CAD and other lipid metabolism related traits (the smallest P value < 1 × 10− 16). A total of 13 genes (e.g., LPA, APOC1, APOE and SLC22A3) was found to be overlapped between CAD and plasma lipid levels. By using the data-driven approach that integrated transcriptome information, we discovered co-expression modules associated prominently with both CAD and plasma lipids. With the detailed topology information on gene-gene regulatory relationship, we illustrated that the identified hub genes played important roles in the pathogenesis of CAD and plasma lipid turbulence. Conclusion Together, we identified the shared molecular mechanisms underlying the correlation between CAD and plasma lipid levels.
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Affiliation(s)
- Liuying Chen
- Zhejiang Chinese Medical University, Hangzhou, China
| | - Yinghao Yao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University School of Medicine, Hangzhou, China
| | | | - Shen Wu
- Department of Cardiology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qiang Liu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University School of Medicine, Hangzhou, China
| | - Jingjing Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University School of Medicine, Hangzhou, China
| | - Yunlong Ma
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University School of Medicine, Hangzhou, China
| | - Yizhou Xu
- Zhejiang Chinese Medical University, Hangzhou, China.,Department of Cardiology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yigang Zhong
- Department of Cardiology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China.
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Chevrier N. Decoding the Body Language of Immunity: Tackling the Immune System at the Organism Level. ACTA ACUST UNITED AC 2019; 18:19-26. [PMID: 32490290 DOI: 10.1016/j.coisb.2019.10.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The immune system is a dynamic mesh of molecules, cells and tissues spanning the entire organism. Despite a wealth of knowledge about the components of the immune system, little is known about the general rules governing the organismal circuitry of immunity. Deciphering the immune system at the scale of the whole organism is crucial to understanding fundamental problems in immunobiology and physiology, and to manipulate immunity for maintaining health and preventing disease. Here I discuss the emerging principles of inter-organ communications during immune responses by focusing on three common themes that are the regulation of the (i) composition, (ii) condition and (iii) coordination of communicating organs by molecular and cellular factors. Based on these common principles, I emphasize fundamental gaps in our knowledge of organismal immune processes and the outlook to tackle immunity at the scale of the whole organism.
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Affiliation(s)
- Nicolas Chevrier
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL 60637, USA
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45
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Zhou M, Shao J, Wu CY, Shu L, Dong W, Liu Y, Chen M, Wynn RM, Wang J, Wang J, Gui WJ, Qi X, Lusis AJ, Li Z, Wang W, Ning G, Yang X, Chuang DT, Wang Y, Sun H. Targeting BCAA Catabolism to Treat Obesity-Associated Insulin Resistance. Diabetes 2019; 68:1730-1746. [PMID: 31167878 PMCID: PMC6702639 DOI: 10.2337/db18-0927] [Citation(s) in RCA: 179] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Accepted: 05/29/2019] [Indexed: 12/12/2022]
Abstract
Recent studies implicate a strong association between elevated plasma branched-chain amino acids (BCAAs) and insulin resistance (IR). However, a causal relationship and whether interrupted BCAA homeostasis can serve as a therapeutic target for diabetes remain to be established experimentally. In this study, unbiased integrative pathway analyses identified a unique genetic link between obesity-associated IR and BCAA catabolic gene expression at the pathway level in human and mouse populations. In genetically obese (ob/ob) mice, rate-limiting branched-chain α-keto acid (BCKA) dehydrogenase deficiency (i.e., BCAA and BCKA accumulation), a metabolic feature, accompanied the systemic suppression of BCAA catabolic genes. Restoring BCAA catabolic flux with a pharmacological inhibitor of BCKA dehydrogenase kinase (BCKDK) ( a suppressor of BCKA dehydrogenase) reduced the abundance of BCAA and BCKA and markedly attenuated IR in ob/ob mice. Similar outcomes were achieved by reducing protein (and thus BCAA) intake, whereas increasing BCAA intake did the opposite; this corroborates the pathogenic roles of BCAAs and BCKAs in IR in ob/ob mice. Like BCAAs, BCKAs also suppressed insulin signaling via activation of mammalian target of rapamycin complex 1. Finally, the small-molecule BCKDK inhibitor significantly attenuated IR in high-fat diet-induced obese mice. Collectively, these data demonstrate a pivotal causal role of a BCAA catabolic defect and elevated abundance of BCAAs and BCKAs in obesity-associated IR and provide proof-of-concept evidence for the therapeutic validity of manipulating BCAA metabolism for treating diabetes.
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Affiliation(s)
- Meiyi Zhou
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jing Shao
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Cheng-Yang Wu
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX
| | - Le Shu
- Department of Integrative Biology and Physiology, University of California at Los Angeles, Los Angeles, CA
| | - Weibing Dong
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yunxia Liu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mengping Chen
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - R Max Wynn
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX
| | - Jiqiu Wang
- Department of Endocrinology and Metabolism, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ji Wang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wen-Jun Gui
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX
| | - Xiangbing Qi
- Chemistry Center, National Institute of Biological Science, Beijing, China
| | - Aldons J Lusis
- Departments of Medicine, Microbiology, and Human Genetics, University of California at Los Angeles, Los Angeles, CA
| | - Zhaoping Li
- Department of Clinical Nutrition, University of California at Los Angeles, Los Angeles, CA
| | - Weiqing Wang
- Department of Endocrinology and Metabolism, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Guang Ning
- Department of Endocrinology and Metabolism, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xia Yang
- Department of Integrative Biology and Physiology, University of California at Los Angeles, Los Angeles, CA
| | - David T Chuang
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX
| | - Yibin Wang
- Departments of Anesthesiology, Medicine, and Physiology, University of California at Los Angeles, Los Angeles, CA
| | - Haipeng Sun
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Departments of Anesthesiology, Medicine, and Physiology, University of California at Los Angeles, Los Angeles, CA
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46
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Melouane A, Ghanemi A, Yoshioka M, St-Amand J. Functional genomics applications and therapeutic implications in sarcopenia. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2019; 781:175-185. [PMID: 31416575 DOI: 10.1016/j.mrrev.2019.04.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 03/14/2019] [Accepted: 04/17/2019] [Indexed: 12/11/2022]
Abstract
The human genome contains around 20,000-25,000 genes coding for 30,000 proteins. Some proteins and genes represent therapeutic targets for human diseases. RNA and protein expression profiling tools allow the study of the molecular basis of aging and drug discovery validation. Throughout the life, there is an age-related and disease-related muscle decline. Sarcopenia is defined as a loss of muscle mass and a decrease in functional properties such as muscle strength and physical performance. Yet, there is still no consensus on the evaluation methods of sarcopenia prognosis. The main challenge of this complex biological phenomena is its multifactorial etiology. Thus, functional genomics methods attempt to shape the related scientific approaches via an innovative in-depth view on sarcopenia. Gene and drug high throughput screening combined with functional genomics allow the generation and the interpretation of a large amount of data related to sarcopenia and therapeutic progress. This review focuses on the application of selected functional genomics techniques such as RNA interference, RNA silencing, proteomics, transgenic mice, metabolomics, genomics, and epigenomics to better understand sarcopenia mechanisms.
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Affiliation(s)
- Aicha Melouane
- CREMI, CHU de Québec Research Center, Quebec, Quebec, G1V 4G2, Canada; Department of Molecular Medicine, Faculty of Medicine, Laval University, Quebec, Quebec, G1V 4G2, Canada
| | - Abdelaziz Ghanemi
- CREMI, CHU de Québec Research Center, Quebec, Quebec, G1V 4G2, Canada; Department of Molecular Medicine, Faculty of Medicine, Laval University, Quebec, Quebec, G1V 4G2, Canada
| | - Mayumi Yoshioka
- CREMI, CHU de Québec Research Center, Quebec, Quebec, G1V 4G2, Canada
| | - Jonny St-Amand
- CREMI, CHU de Québec Research Center, Quebec, Quebec, G1V 4G2, Canada; Department of Molecular Medicine, Faculty of Medicine, Laval University, Quebec, Quebec, G1V 4G2, Canada.
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47
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Allostatic load and ageing: linking the microbiome and nutrition with age-related health. Biochem Soc Trans 2019; 47:1165-1172. [PMID: 31416886 DOI: 10.1042/bst20190110] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/17/2019] [Accepted: 07/23/2019] [Indexed: 12/14/2022]
Abstract
Ageing is a process of decline in physiological function and capability over time. It is an anticipated major burden on societal health-care costs due to an increasingly aged global population. Accelerated biological ageing is a feature of age-related morbidities, which also appear to share common underpinning features, including low-grade persistent inflammation, phosphate toxicity, diminished Nrf2 activity, a depleted metabolic capability, depressed mitochondrial biogenesis and a low diversity gut microbiome.Social, psychological, lifestyle and nutritional risk factors can all influence the trajectory of age-related health, as part of an individual's exposome, which reflects the interplay between the genome and the environment. This is manifest as allostatic (over)load reflecting the burden of lifestyle/disease at both a physiological and molecular level. In particular, age-related genomic methylation levels and inflammatory status reflect exposome differences. These features may be mediated by changes in microbial diversity. This can drive the generation of pro-inflammatory factors, such as TMAO, implicated in the 'diseasome' of ageing. Additionally, it can be influenced by the 'foodome', via nutritional differences affecting the availability of methyl donors required for maintenance of the epigenome and by the provision of nutritionally derived Nrf2 agonists. Both these factors influence age-related physiological resilience and health. This offers novel insights into possible interventions to improve health span, including a rage of emerging senotherapies and simple modifications of the nutritional and environmental exposome. In essence, the emerging strategy is to treat ageing processes common to the diseasome of ageing itself and thus preempt the development or progression of a range of age-related morbidities.
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Zhao Y, Blencowe M, Shi X, Shu L, Levian C, Ahn IS, Kim SK, Huan T, Levy D, Yang X. Integrative Genomics Analysis Unravels Tissue-Specific Pathways, Networks, and Key Regulators of Blood Pressure Regulation. Front Cardiovasc Med 2019; 6:21. [PMID: 30931314 PMCID: PMC6423920 DOI: 10.3389/fcvm.2019.00021] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 02/18/2019] [Indexed: 01/23/2023] Open
Abstract
Blood pressure (BP) is a highly heritable trait and a major cardiovascular disease risk factor. Genome wide association studies (GWAS) have implicated a number of susceptibility loci for systolic (SBP) and diastolic (DBP) blood pressure. However, a large portion of the heritability cannot be explained by the top GWAS loci and a comprehensive understanding of the underlying molecular mechanisms is still lacking. Here, we utilized an integrative genomics approach that leveraged multiple genetic and genomic datasets including (a) GWAS for SBP and DBP from the International Consortium for Blood Pressure (ICBP), (b) expression quantitative trait loci (eQTLs) from genetics of gene expression studies of human tissues related to BP, (c) knowledge-driven biological pathways, and (d) data-driven tissue-specific regulatory gene networks. Integration of these multidimensional datasets revealed tens of pathways and gene subnetworks in vascular tissues, liver, adipose, blood, and brain functionally associated with DBP and SBP. Diverse processes such as platelet production, insulin secretion/signaling, protein catabolism, cell adhesion and junction, immune and inflammation, and cardiac/smooth muscle contraction, were shared between DBP and SBP. Furthermore, "Wnt signaling" and "mammalian target of rapamycin (mTOR) signaling" pathways were found to be unique to SBP, while "cytokine network", and "tryptophan catabolism" to DBP. Incorporation of gene regulatory networks in our analysis informed on key regulator genes that orchestrate tissue-specific subnetworks of genes whose variants together explain ~20% of BP heritability. Our results shed light on the complex mechanisms underlying BP regulation and highlight potential novel targets and pathways for hypertension and cardiovascular diseases.
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Affiliation(s)
- Yuqi Zhao
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Montgomery Blencowe
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Xingyi Shi
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Le Shu
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Candace Levian
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, United States
| | - In Sook Ahn
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Stuart K. Kim
- Department of Genetics, Department of Developmental Biology, Stanford University Medical Center, Stanford, CA, United States
| | - Tianxiao Huan
- The National Heart Lung and Blood Institute's Framingham Heart Study, Framingham, MA, United States
- The Population Sciences Branch and the Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, MD, United States
| | - Daniel Levy
- The National Heart Lung and Blood Institute's Framingham Heart Study, Framingham, MA, United States
- The Population Sciences Branch and the Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, MD, United States
| | - Xia Yang
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, United States
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Kajiwara Y, Wang E, Wang M, Sin WC, Brennand KJ, Schadt E, Naus CC, Buxbaum J, Zhang B. GJA1 (connexin43) is a key regulator of Alzheimer's disease pathogenesis. Acta Neuropathol Commun 2018; 6:144. [PMID: 30577786 PMCID: PMC6303945 DOI: 10.1186/s40478-018-0642-x] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 12/01/2018] [Indexed: 12/02/2022] Open
Abstract
GJA1 (connexin43) has been predicted as the top key driver of an astrocyte enriched subnetwork associated with Alzheimer's disease (AD). In this study, we comprehensively examined GJA1 expression across 29 transcriptomic and proteomic datasets from post-mortem AD and normal control brains. We demonstrated that GJA1 was strongly associated with AD amyloid and tau pathologies and cognitive functions. RNA sequencing analysis of Gja1-/- astrocytes validated that Gja1 regulated the subnetwork identified in AD, and many genes involved in Aβ metabolism. Astrocytes lacking Gja1 showed reduced Apoe protein levels as well as impaired Aβ phagocytosis. Consistent with this, wildtype neurons co-cultured with Gja1-/- astrocytes contained higher levels of Aβ species than those with wildtype astrocytes. Moreover, Gja1-/- astrocytes was more neuroprotective under Aβ stress. Our results underscore the importance of GJA1 in AD pathogenesis and its potential for further investigation as a promising pharmacological target in AD.
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Affiliation(s)
- Yuji Kajiwara
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Current address: Denali Therapeutics,, South San Francisco,, CA, 94080, USA
| | - Erming Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Minghui Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Wun Chey Sin
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Kristen J Brennand
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Eric Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Christian C Naus
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Joseph Buxbaum
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Mount Sinai Center for Transformative Disease Modeling, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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50
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Kurt Z, Barrere-Cain R, LaGuardia J, Mehrabian M, Pan C, Hui ST, Norheim F, Zhou Z, Hasin Y, Lusis AJ, Yang X. Tissue-specific pathways and networks underlying sexual dimorphism in non-alcoholic fatty liver disease. Biol Sex Differ 2018; 9:46. [PMID: 30343673 PMCID: PMC6196429 DOI: 10.1186/s13293-018-0205-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 10/03/2018] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Non-alcoholic fatty liver disease (NAFLD) encompasses benign steatosis and more severe conditions such as non-alcoholic steatohepatitis (NASH), cirrhosis, and liver cancer. This chronic liver disease has a poorly understood etiology and demonstrates sexual dimorphisms. We aim to examine the molecular mechanisms underlying sexual dimorphisms in NAFLD pathogenesis through a comprehensive multi-omics study. We integrated genomics (DNA variations), transcriptomics of liver and adipose tissue, and phenotypic data of NAFLD derived from female mice of ~ 100 strains included in the hybrid mouse diversity panel (HMDP) and compared the NAFLD molecular pathways and gene networks between sexes. RESULTS We identified both shared and sex-specific biological processes for NAFLD. Adaptive immunity, branched chain amino acid metabolism, oxidative phosphorylation, and cell cycle/apoptosis were shared between sexes. Among the sex-specific pathways were vitamins and cofactors metabolism and ion channel transport for females, and phospholipid, lysophospholipid, and phosphatidylinositol metabolism and insulin signaling for males. Additionally, numerous lipid and insulin-related pathways and inflammatory processes in the adipose and liver tissue appeared to show more prominent association with NAFLD in male HMDP. Using data-driven network modeling, we identified plausible sex-specific and tissue-specific regulatory genes as well as those that are shared between sexes. These key regulators orchestrate the NAFLD pathways in a sex- and tissue-specific manner. Gonadectomy experiments support that sex hormones may partially underlie the sexually dimorphic genes and pathways involved in NAFLD. CONCLUSIONS Our multi-omics integrative study reveals sex- and tissue-specific genes, processes, and networks underlying sexual dimorphism in NAFLD and may facilitate sex-specific precision medicine.
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Affiliation(s)
- Zeyneb Kurt
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA USA
| | - Rio Barrere-Cain
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA USA
| | - Jonnby LaGuardia
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA USA
| | - Margarete Mehrabian
- Department of Medicine/Division of Cardiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA USA
| | - Calvin Pan
- Department of Medicine/Division of Cardiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA USA
| | - Simon T Hui
- Department of Medicine/Division of Cardiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA USA
| | - Frode Norheim
- Department of Medicine/Division of Cardiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA USA
| | - Zhiqiang Zhou
- Department of Medicine/Division of Cardiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA USA
| | - Yehudit Hasin
- Department of Medicine/Division of Cardiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA USA
| | - Aldons J Lusis
- Department of Medicine/Division of Cardiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA USA
| | - Xia Yang
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA USA
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