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Skelly DA, Graham JP, Cheng M, Furuta M, Walter A, Stoklasek TA, Yang H, Stearns TM, Poirion O, Zhang JG, Grassmann JDS, Luo D, Flynn WF, Courtois ET, Chang CH, Serreze DV, Menghi F, Reinholdt LG, Liu ET. Mapping the genetic landscape establishing a tumor immune microenvironment favorable for anti-PD-1 response in mice and humans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.11.603136. [PMID: 39071392 PMCID: PMC11275897 DOI: 10.1101/2024.07.11.603136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Identifying host genetic factors modulating immune checkpoint inhibitor (ICI) efficacy has been experimentally challenging because of variations in both host and tumor genomes, differences in the microbiome, and patient life exposures. Utilizing the Collaborative Cross (CC) multi-parent mouse genetic resource population, we developed an approach that fixes the tumor genomic configuration while varying host genetics. With this approach, we discovered that response to anti-PD-1 (aPD1) immunotherapy was significantly heritable in four distinct murine tumor models (H2 between 0.18-0.40). For the MC38 colorectal carcinoma system (H2 = 0.40), we mapped four significant ICI response quantitative trait loci (QTL) localized to mouse chromosomes (mChr) 5, 9, 15 and 17, and identified significant epistatic interactions between specific QTL pairs. Differentially expressed genes within these QTL were highly enriched for immune genes and pathways mediating allograft rejection and graft vs host disease. Using a cross species analytical approach, we found a core network of 48 genes within the four QTLs that showed significant prognostic value for overall survival in aPD1 treated human cohorts that outperformed all other existing validated immunotherapy biomarkers, especially in human tumors of the previously defined immune subtype 4. Functional blockade of two top candidate immune targets within the 48 gene network, GM-CSF and high affinity IL-2/IL-15 signaling, completely abrogated the MC38 tumor transcriptional response to aPD1 therapy in vivo. Thus, we have established a powerful cross species in vivo platform capable of uncovering host genetic factors that establish the tumor immune microenvironment configuration propitious for ICI response.
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Affiliation(s)
- Daniel A. Skelly
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, USA
| | - John P. Graham
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, USA
| | | | - Mayuko Furuta
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Andrew Walter
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, USA
| | | | | | | | - Olivier Poirion
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Ji-Gang Zhang
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, USA
| | | | - Diane Luo
- Single Cell Biology Lab, The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - William F. Flynn
- Single Cell Biology Lab, The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Elise T. Courtois
- Single Cell Biology Lab, The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- OB/Gyn Department, UConn Health, Farmington, CT, USA
| | - Chih-Hao Chang
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, USA
| | - David V. Serreze
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, USA
| | - Francesca Menghi
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Edison T. Liu
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
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2
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Nemkov T, Stephenson D, Earley EJ, Keele GR, Hay A, Key A, Haiman ZB, Erickson C, Dzieciatkowska M, Reisz JA, Moore A, Stone M, Deng X, Kleinman S, Spitalnik SL, Hod EA, Hudson KE, Hansen KC, Palsson BO, Churchill GA, Roubinian N, Norris PJ, Busch MP, Zimring JC, Page GP, D'Alessandro A. Biological and genetic determinants of glycolysis: Phosphofructokinase isoforms boost energy status of stored red blood cells and transfusion outcomes. Cell Metab 2024:S1550-4131(24)00232-8. [PMID: 38964323 DOI: 10.1016/j.cmet.2024.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 01/04/2024] [Accepted: 06/07/2024] [Indexed: 07/06/2024]
Abstract
Mature red blood cells (RBCs) lack mitochondria and thus exclusively rely on glycolysis to generate adenosine triphosphate (ATP) during aging in vivo or storage in blood banks. Here, we leveraged 13,029 volunteers from the Recipient Epidemiology and Donor Evaluation Study to identify associations between end-of-storage levels of glycolytic metabolites and donor age, sex, and ancestry-specific genetic polymorphisms in regions encoding phosphofructokinase 1, platelet (detected in mature RBCs); hexokinase 1 (HK1); and ADP-ribosyl cyclase 1 and 2 (CD38/BST1). Gene-metabolite associations were validated in fresh and stored RBCs from 525 Diversity Outbred mice and via multi-omics characterization of 1,929 samples from 643 human RBC units during storage. ATP and hypoxanthine (HYPX) levels-and the genetic traits linked to them-were associated with hemolysis in vitro and in vivo, both in healthy autologous transfusion recipients and in 5,816 critically ill patients receiving heterologous transfusions, suggesting their potential as markers to improve transfusion outcomes.
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Affiliation(s)
- Travis Nemkov
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver - Anschutz Medical Campus, Aurora, CO, USA; Omix Technologies Inc., Aurora, CO, USA
| | - Daniel Stephenson
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver - Anschutz Medical Campus, Aurora, CO, USA
| | | | | | - Ariel Hay
- Department of Pathology, University of Virginia, Charlottesville, VA, USA
| | - Alicia Key
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver - Anschutz Medical Campus, Aurora, CO, USA
| | - Zachary B Haiman
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Christopher Erickson
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver - Anschutz Medical Campus, Aurora, CO, USA
| | - Monika Dzieciatkowska
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver - Anschutz Medical Campus, Aurora, CO, USA
| | - Julie A Reisz
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver - Anschutz Medical Campus, Aurora, CO, USA
| | | | - Mars Stone
- Vitalant Research Institute, San Francisco, CA, USA; Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Xutao Deng
- Vitalant Research Institute, San Francisco, CA, USA; Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | | | - Steven L Spitalnik
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Eldad A Hod
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Krystalyn E Hudson
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Kirk C Hansen
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver - Anschutz Medical Campus, Aurora, CO, USA; Omix Technologies Inc., Aurora, CO, USA
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | | | - Nareg Roubinian
- Vitalant Research Institute, San Francisco, CA, USA; Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA; Kaiser Permanente Northern California Division of Research, Oakland, CA, USA
| | - Philip J Norris
- Vitalant Research Institute, San Francisco, CA, USA; Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Michael P Busch
- Vitalant Research Institute, San Francisco, CA, USA; Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - James C Zimring
- Department of Pathology, University of Virginia, Charlottesville, VA, USA
| | | | - Angelo D'Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver - Anschutz Medical Campus, Aurora, CO, USA; Omix Technologies Inc., Aurora, CO, USA.
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3
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Nemkov T, Key A, Stephenson D, Earley EJ, Keele GR, Hay A, Amireault P, Casimir M, Dussiot M, Dzieciatkowska M, Reisz JA, Deng X, Stone M, Kleinman S, Spitalnik SL, Hansen KC, Norris PJ, Churchill GA, Busch MP, Roubinian N, Page GP, Zimring JC, Arduini A, D’Alessandro A. Genetic regulation of carnitine metabolism controls lipid damage repair and aging RBC hemolysis in vivo and in vitro. Blood 2024; 143:2517-2533. [PMID: 38513237 PMCID: PMC11208298 DOI: 10.1182/blood.2024023983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 02/22/2024] [Accepted: 03/13/2024] [Indexed: 03/23/2024] Open
Abstract
ABSTRACT Recent large-scale multiomics studies suggest that genetic factors influence the chemical individuality of donated blood. To examine this concept, we performed metabolomics analyses of 643 blood units from volunteers who donated units of packed red blood cells (RBCs) on 2 separate occasions. These analyses identified carnitine metabolism as the most reproducible pathway across multiple donations from the same donor. We also measured l-carnitine and acyl-carnitines in 13 091 packed RBC units from donors in the Recipient Epidemiology and Donor Evaluation study. Genome-wide association studies against 879 000 polymorphisms identified critical genetic factors contributing to interdonor heterogeneity in end-of-storage carnitine levels, including common nonsynonymous polymorphisms in genes encoding carnitine transporters (SLC22A16, SLC22A5, and SLC16A9); carnitine synthesis (FLVCR1 and MTDH) and metabolism (CPT1A, CPT2, CRAT, and ACSS2), and carnitine-dependent repair of lipids oxidized by ALOX5. Significant associations between genetic polymorphisms on SLC22 transporters and carnitine pools in stored RBCs were validated in 525 Diversity Outbred mice. Donors carrying 2 alleles of the rs12210538 SLC22A16 single-nucleotide polymorphism exhibited the lowest l-carnitine levels, significant elevations of in vitro hemolysis, and the highest degree of vesiculation, accompanied by increases in lipid peroxidation markers. Separation of RBCs by age, via in vivo biotinylation in mice, and Percoll density gradients of human RBCs, showed age-dependent depletions of l-carnitine and acyl-carnitine pools, accompanied by progressive failure of the reacylation process after chemically induced membrane lipid damage. Supplementation of stored murine RBCs with l-carnitine boosted posttransfusion recovery, suggesting this could represent a viable strategy to improve RBC storage quality.
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Affiliation(s)
- Travis Nemkov
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO
- Omix Technologies Inc, Aurora, CO
| | - Alicia Key
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO
| | - Daniel Stephenson
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO
| | - Eric J. Earley
- Genomics and Translational Research Center, RTI International, Research Triangle Park, NC
| | - Gregory R. Keele
- Genomics and Translational Research Center, RTI International, Research Triangle Park, NC
- The Jackson Laboratory, Bar Harbor, ME
| | - Ariel Hay
- Department of Pathology, University of Virginia, Charlottesville, VA
| | - Pascal Amireault
- Université Paris Cité et Université des Antilles, INSERM, Biologie Intégrée du Globule Rouge, Paris, France
- Université Paris Cité, Institut Imagine, Laboratory of Cellular and Molecular Mechanisms of Hematological Disorders and Therapeutic Implications, INSERM, Paris, France
| | - Madeleine Casimir
- Université Paris Cité et Université des Antilles, INSERM, Biologie Intégrée du Globule Rouge, Paris, France
- Université Paris Cité, Institut Imagine, Laboratory of Cellular and Molecular Mechanisms of Hematological Disorders and Therapeutic Implications, INSERM, Paris, France
| | - Michaël Dussiot
- Université Paris Cité et Université des Antilles, INSERM, Biologie Intégrée du Globule Rouge, Paris, France
- Université Paris Cité, Institut Imagine, Laboratory of Cellular and Molecular Mechanisms of Hematological Disorders and Therapeutic Implications, INSERM, Paris, France
| | - Monika Dzieciatkowska
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO
| | - Julie A. Reisz
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO
| | - Xutao Deng
- Vitalant Research Institute, San Francisco, CA
| | - Mars Stone
- Vitalant Research Institute, San Francisco, CA
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA
| | - Steve Kleinman
- The University of British Columbia, Victoria, BC, Canada
| | | | - Kirk C. Hansen
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO
| | - Philip J. Norris
- Vitalant Research Institute, San Francisco, CA
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA
| | | | - Michael P. Busch
- Vitalant Research Institute, San Francisco, CA
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA
| | - Nareg Roubinian
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA
- Kaiser Permanente Northern California Division of Research, Oakland, CA
| | - Grier P. Page
- Genomics and Translational Research Center, RTI International, Research Triangle Park, NC
| | - James C. Zimring
- Department of Pathology, University of Virginia, Charlottesville, VA
| | - Arduino Arduini
- Department of Research and Development, CoreQuest Sagl, Lugano, Switzerland
| | - Angelo D’Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO
- Omix Technologies Inc, Aurora, CO
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4
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Nemkov T, Stephenson D, Earley EJ, Keele GR, Hay A, Key A, Haiman Z, Erickson C, Dzieciatkowska M, Reisz JA, Moore A, Stone M, Deng X, Kleinman S, Spitalnik SL, Hod EA, Hudson KE, Hansen KC, Palsson BO, Churchill GA, Roubinian N, Norris PJ, Busch MP, Zimring JC, Page GP, D'Alessandro A. Biological and Genetic Determinants of Glycolysis: Phosphofructokinase Isoforms Boost Energy Status of Stored Red Blood Cells and Transfusion Outcomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.11.557250. [PMID: 38260479 PMCID: PMC10802247 DOI: 10.1101/2023.09.11.557250] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Mature red blood cells (RBCs) lack mitochondria, and thus exclusively rely on glycolysis to generate adenosine triphosphate (ATP) during aging in vivo or storage in the blood bank. Here we leveraged 13,029 volunteers from the Recipient Epidemiology and Donor Evaluation Study to identify an association between end-of-storage levels of glycolytic metabolites and donor age, sex, and ancestry-specific genetic polymorphisms in regions encoding phosphofructokinase 1, platelet (detected in mature RBCs), hexokinase 1, ADP-ribosyl cyclase 1 and 2 (CD38/BST1). Gene-metabolite associations were validated in fresh and stored RBCs from 525 Diversity Outbred mice, and via multi-omics characterization of 1,929 samples from 643 human RBC units during storage. ATP and hypoxanthine levels - and the genetic traits linked to them - were associated with hemolysis in vitro and in vivo, both in healthy autologous transfusion recipients and in 5,816 critically ill patients receiving heterologous transfusions, suggesting their potential as markers to improve transfusion outcomes. eTOC and Highlights Highlights Blood donor age and sex affect glycolysis in stored RBCs from 13,029 volunteers;Ancestry, genetic polymorphisms in PFKP, HK1, CD38/BST1 influence RBC glycolysis;Modeled PFKP effects relate to preventing loss of the total AXP pool in stored RBCs;ATP and hypoxanthine are biomarkers of hemolysis in vitro and in vivo.
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5
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D'Alessandro A, Keele GR, Hay A, Nemkov T, Earley EJ, Stephenson D, Vincent M, Deng X, Stone M, Dzieciatkowska M, Hansen KC, Kleinman S, Spitalnik SL, Roubinian NH, Norris PJ, Busch MP, Page GP, Stockwell BR, Churchill GA, Zimring JC. Ferroptosis regulates hemolysis in stored murine and human red blood cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.11.598512. [PMID: 38915523 PMCID: PMC11195277 DOI: 10.1101/2024.06.11.598512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Red blood cell (RBC) metabolism regulates hemolysis during aging in vivo and in the blood bank. Here, we leveraged a diversity outbred mouse population to map the genetic drivers of fresh/stored RBC metabolism and extravascular hemolysis upon storage and transfusion in 350 mice. We identify the ferrireductase Steap3 as a critical regulator of a ferroptosis-like process of lipid peroxidation. Steap3 polymorphisms were associated with RBC iron content, in vitro hemolysis, and in vivo extravascular hemolysis both in mice and 13,091 blood donors from the Recipient Epidemiology and Donor evaluation Study. Using metabolite Quantitative Trait Loci analyses, we identified a network of gene products (FADS1/2, EPHX2 and LPCAT3) - enriched in donors of African descent - associated with oxylipin metabolism in stored human RBCs and related to Steap3 or its transcriptional regulator, the tumor protein TP53. Genetic variants were associated with lower in vivo hemolysis in thousands of single-unit transfusion recipients. Highlights Steap3 regulates lipid peroxidation and extravascular hemolysis in 350 diversity outbred miceSteap3 SNPs are linked to RBC iron, hemolysis, vesiculation in 13,091 blood donorsmQTL analyses of oxylipins identified ferroptosis-related gene products FADS1/2, EPHX2, LPCAT3Ferroptosis markers are linked to hemoglobin increments in transfusion recipients. Graphical abstract
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6
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Christians JK, Reue K. The role of gonadal hormones and sex chromosomes in sex-dependent effects of early nutrition on metabolic health. Front Endocrinol (Lausanne) 2023; 14:1304050. [PMID: 38189044 PMCID: PMC10770830 DOI: 10.3389/fendo.2023.1304050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 12/11/2023] [Indexed: 01/09/2024] Open
Abstract
Early-life conditions such as prenatal nutrition can have long-term effects on metabolic health, and these effects may differ between males and females. Understanding the biological mechanisms underlying sex differences in the response to early-life environment will improve interventions, but few such mechanisms have been identified, and there is no overall framework for understanding sex differences. Biological sex differences may be due to chromosomal sex, gonadal sex, or interactions between the two. This review describes approaches to distinguish between the roles of chromosomal and gonadal sex, and summarizes findings regarding sex differences in metabolism. The Four Core Genotypes (FCG) mouse model allows dissociation of the sex chromosome genotype from gonadal type, whereas the XY* mouse model can be used to distinguish effects of X chromosome dosage vs the presence of the Y chromosome. Gonadectomy can be used to distinguish between organizational (permanent) and activational (reversible) effects of sex hormones. Baseline sex differences in a variety of metabolic traits are influenced by both activational and organizational effects of gonadal hormones, as well as sex chromosome complement. Thus far, these approaches have not been widely applied to examine sex-dependent effects of prenatal conditions, although a number of studies have found activational effects of estradiol to be protective against the development of hypertension following early-life adversity. Genes that escape X chromosome inactivation (XCI), such as Kdm5c, contribute to baseline sex-differences in metabolism, while Ogt, another XCI escapee, leads to sex-dependent responses to prenatal maternal stress. Genome-wide approaches to the study of sex differences include mapping genetic loci influencing metabolic traits in a sex-dependent manner. Seeking enrichment for binding sites of hormone receptors among genes showing sexually-dimorphic expression can elucidate the relative roles of hormones. Using the approaches described herein to identify mechanisms underlying sex-dependent effects of early nutrition on metabolic health may enable the identification of fundamental mechanisms and potential interventions.
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Affiliation(s)
- Julian K. Christians
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC, Canada
- Centre for Cell Biology, Development and Disease, Simon Fraser University, Burnaby, BC, Canada
- British Columbia Children’s Hospital Research Institute, Vancouver, BC, Canada
- Women’s Health Research Institute, BC Women’s Hospital and Health Centre, Vancouver, BC, Canada
| | - Karen Reue
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
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7
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O'Connor C, Keele GR, Martin W, Stodola T, Gatti D, Hoffman BR, Korstanje R, Churchill GA, Reinholdt LG. Cell morphology QTL reveal gene by environment interactions in a genetically diverse cell population. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.18.567597. [PMID: 38014303 PMCID: PMC10680806 DOI: 10.1101/2023.11.18.567597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Genetically heterogenous cell lines from laboratory mice are promising tools for population-based screening as they offer power for genetic mapping, and potentially, predictive value for in vivo experimentation in genetically matched individuals. To explore this further, we derived a panel of fibroblast lines from a genetic reference population of laboratory mice (the Diversity Outbred, DO). We then used high-content imaging to capture hundreds of cell morphology traits in cells exposed to the oxidative stress-inducing arsenic metabolite monomethylarsonous acid (MMAIII). We employed dose-response modeling to capture latent parameters of response and we then used these parameters to identify several hundred cell morphology quantitative trait loci (cmQTL). Response cmQTL encompass genes with established associations with cellular responses to arsenic exposure, including Abcc4 and Txnrd1, as well as novel gene candidates like Xrcc2. Moreover, baseline trait cmQTL highlight the influence of natural variation on fundamental aspects of nuclear morphology. We show that the natural variants influencing response include both coding and non-coding variation, and that cmQTL haplotypes can be used to predict response in orthogonal cell lines. Our study sheds light on the major molecular initiating events of oxidative stress that are under genetic regulation, including the NRF2-mediated antioxidant response, cellular detoxification pathways, DNA damage repair response, and cell death trajectories.
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Affiliation(s)
- Callan O'Connor
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
- Graduate School of Biomedical Sciences, Tufts University, Boston, MA 02111, USA
| | - Gregory R Keele
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
- RTI International, RTP, NC 27709, USA
| | | | | | - Daniel Gatti
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | | | | | | | - Laura G Reinholdt
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
- Graduate School of Biomedical Sciences, Tufts University, Boston, MA 02111, USA
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8
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Allayee H, Farber CR, Seldin MM, Williams EG, James DE, Lusis AJ. Systems genetics approaches for understanding complex traits with relevance for human disease. eLife 2023; 12:e91004. [PMID: 37962168 PMCID: PMC10645424 DOI: 10.7554/elife.91004] [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: 07/14/2023] [Accepted: 10/16/2023] [Indexed: 11/15/2023] Open
Abstract
Quantitative traits are often complex because of the contribution of many loci, with further complexity added by environmental factors. In medical research, systems genetics is a powerful approach for the study of complex traits, as it integrates intermediate phenotypes, such as RNA, protein, and metabolite levels, to understand molecular and physiological phenotypes linking discrete DNA sequence variation to complex clinical and physiological traits. The primary purpose of this review is to describe some of the resources and tools of systems genetics in humans and rodent models, so that researchers in many areas of biology and medicine can make use of the data.
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Affiliation(s)
- Hooman Allayee
- Departments of Population & Public Health Sciences, University of Southern CaliforniaLos AngelesUnited States
- Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern CaliforniaLos AngelesUnited States
| | - Charles R Farber
- Center for Public Health Genomics, University of Virginia School of MedicineCharlottesvilleUnited States
- Departments of Biochemistry & Molecular Genetics, University of Virginia School of MedicineCharlottesvilleUnited States
- Public Health Sciences, University of Virginia School of MedicineCharlottesvilleUnited States
| | - Marcus M Seldin
- Department of Biological Chemistry, University of California, IrvineIrvineUnited States
| | - Evan Graehl Williams
- Luxembourg Centre for Systems Biomedicine, University of LuxembourgLuxembourgLuxembourg
| | - David E James
- School of Life and Environmental Sciences, University of SydneyCamperdownAustralia
- Faculty of Medicine and Health, University of SydneyCamperdownAustralia
- Charles Perkins Centre, University of SydneyCamperdownAustralia
| | - Aldons J Lusis
- Departments of Human Genetics, University of California, Los AngelesLos AngelesUnited States
- Medicine, University of California, Los AngelesLos AngelesUnited States
- Microbiology, Immunology, & Molecular Genetics, David Geffen School of Medicine of UCLALos AngelesUnited States
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9
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Shaikh SR, Bazinet RP. Heterogeneity in the response to n-3 polyunsaturated fatty acids. Curr Opin Clin Nutr Metab Care 2023; 26:284-287. [PMID: 36943155 PMCID: PMC10794042 DOI: 10.1097/mco.0000000000000930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
PURPOSE OF REVIEW A central goal in the study of long chain n-3 polyunsaturated fatty acids (PUFA) is to translate findings from the basic sciences to the population level to improve human health and prevent chronic diseases. A tenet of this vision is to think in terms of precision medicine and nutrition, that is, stratification of individuals into differing groups that will have different needs across the lifespan for n-3 PUFAs. Therefore, there is a critical need to identify the sources of heterogeneity in the human population in the dietary response to n-3 PUFA intervention. RECENT FINDINGS We briefly review key sources of heterogeneity in the response to intake of long chain n-3 PUFAs. These include background diet, host genome, composition of the gut microbiome, and sex. We also discuss the need to integrate data from newer rodent models (e.g. population-based approaches), multi -omics, and analyses of big data using machine learning and data-driven cluster analyses. SUMMARY Accounting for vast heterogeneity in the human population, particularly with the use of big data integrated with preclinical evidence, will drive the next generation of precision nutrition studies and randomized clinical trials with long-chain n-3 PUFAs.
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Affiliation(s)
- Saame Raza Shaikh
- Department of Nutrition, Gillings School of Global Public Health & School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - Richard P Bazinet
- Department of Nutritional Sciences, Faculty of Medicine, University of Toronto, Toronto, Canada
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10
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Jurrjens AW, Seldin MM, Giles C, Meikle PJ, Drew BG, Calkin AC. The potential of integrating human and mouse discovery platforms to advance our understanding of cardiometabolic diseases. eLife 2023; 12:e86139. [PMID: 37000167 PMCID: PMC10065800 DOI: 10.7554/elife.86139] [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: 01/16/2023] [Accepted: 03/15/2023] [Indexed: 04/01/2023] Open
Abstract
Cardiometabolic diseases encompass a range of interrelated conditions that arise from underlying metabolic perturbations precipitated by genetic, environmental, and lifestyle factors. While obesity, dyslipidaemia, smoking, and insulin resistance are major risk factors for cardiometabolic diseases, individuals still present in the absence of such traditional risk factors, making it difficult to determine those at greatest risk of disease. Thus, it is crucial to elucidate the genetic, environmental, and molecular underpinnings to better understand, diagnose, and treat cardiometabolic diseases. Much of this information can be garnered using systems genetics, which takes population-based approaches to investigate how genetic variance contributes to complex traits. Despite the important advances made by human genome-wide association studies (GWAS) in this space, corroboration of these findings has been hampered by limitations including the inability to control environmental influence, limited access to pertinent metabolic tissues, and often, poor classification of diseases or phenotypes. A complementary approach to human GWAS is the utilisation of model systems such as genetically diverse mouse panels to study natural genetic and phenotypic variation in a controlled environment. Here, we review mouse genetic reference panels and the opportunities they provide for the study of cardiometabolic diseases and related traits. We discuss how the post-GWAS era has prompted a shift in focus from discovery of novel genetic variants to understanding gene function. Finally, we highlight key advantages and challenges of integrating complementary genetic and multi-omics data from human and mouse populations to advance biological discovery.
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Affiliation(s)
- Aaron W Jurrjens
- Baker Heart and Diabetes Institute, Melbourne, Australia
- Central Clinical School, Monash University, Melbourne, Australia
| | - Marcus M Seldin
- Department of Biological Chemistry and Center for Epigenetics and Metabolism, University of California, Irvine, Irvine, United States
| | - Corey Giles
- Baker Heart and Diabetes Institute, Melbourne, Australia
- Baker Department of Cardiometabolic Health, University of Melbourne, Melbourne, Australia
- Baker Department of Cardiovascular Research Translation and Implementation, La Trobe University, Bundoora, Australia
| | - Peter J Meikle
- Baker Heart and Diabetes Institute, Melbourne, Australia
- Central Clinical School, Monash University, Melbourne, Australia
- Baker Department of Cardiometabolic Health, University of Melbourne, Melbourne, Australia
- Baker Department of Cardiovascular Research Translation and Implementation, La Trobe University, Bundoora, Australia
| | - Brian G Drew
- Baker Heart and Diabetes Institute, Melbourne, Australia
- Central Clinical School, Monash University, Melbourne, Australia
- Baker Department of Cardiometabolic Health, University of Melbourne, Melbourne, Australia
| | - Anna C Calkin
- Baker Heart and Diabetes Institute, Melbourne, Australia
- Central Clinical School, Monash University, Melbourne, Australia
- Baker Department of Cardiometabolic Health, University of Melbourne, Melbourne, Australia
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11
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Zhang T, Keele GR, Gyuricza IG, Vincent M, Brunton C, Bell TA, Hock P, Shaw GD, Munger SC, de Villena FPM, Ferris MT, Paulo JA, Gygi SP, Churchill GA. Multi-omics analysis identifies drivers of protein phosphorylation. Genome Biol 2023; 24:52. [PMID: 36944993 PMCID: PMC10031968 DOI: 10.1186/s13059-023-02892-2] [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: 06/17/2022] [Accepted: 03/09/2023] [Indexed: 03/23/2023] Open
Abstract
BACKGROUND Phosphorylation of proteins is a key step in the regulation of many cellular processes including activation of enzymes and signaling cascades. The abundance of a phosphorylated peptide (phosphopeptide) is determined by the abundance of its parent protein and the proportion of target sites that are phosphorylated. RESULTS We quantified phosphopeptides, proteins, and transcripts in heart, liver, and kidney tissue samples of mice from 58 strains of the Collaborative Cross strain panel. We mapped ~700 phosphorylation quantitative trait loci (phQTL) across the three tissues and applied genetic mediation analysis to identify causal drivers of phosphorylation. We identified kinases, phosphatases, cytokines, and other factors, including both known and potentially novel interactions between target proteins and genes that regulate site-specific phosphorylation. Our analysis highlights multiple targets of pyruvate dehydrogenase kinase 1 (PDK1), a regulator of mitochondrial function that shows reduced activity in the NZO/HILtJ mouse, a polygenic model of obesity and type 2 diabetes. CONCLUSIONS Together, this integrative multi-omics analysis in genetically diverse CC strains provides a powerful tool to identify regulators of protein phosphorylation. The data generated in this study provides a resource for further exploration.
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Affiliation(s)
- Tian Zhang
- Harvard Medical School, Boston, MA, 02115, USA
| | | | | | | | | | - Timothy A Bell
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Pablo Hock
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Ginger D Shaw
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | | | - Fernando Pardo-Manuel de Villena
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Martin T Ferris
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
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