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Wright KM, Deighan AG, Di Francesco A, Freund A, Jojic V, Churchill GA, Raj A. Age and diet shape the genetic architecture of body weight in diversity outbred mice. eLife 2022; 11:64329. [PMID: 35838135 PMCID: PMC9286741 DOI: 10.7554/elife.64329] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 05/20/2022] [Indexed: 12/26/2022] Open
Abstract
Understanding how genetic variation shapes a complex trait relies on accurately quantifying both the additive genetic and genotype–environment interaction effects in an age-dependent manner. We used a linear mixed model to quantify diet-dependent genetic contributions to body weight measured through adulthood in diversity outbred female mice under five diets. We observed that heritability of body weight declined with age under all diets, except the 40% calorie restriction diet. We identified 14 loci with age-dependent associations and 19 loci with age- and diet-dependent associations, with many diet-dependent loci previously linked to neurological function and behavior in mice or humans. We found their allelic effects to be dynamic with respect to genomic background, age, and diet, identifying several loci where distinct alleles affect body weight at different ages. These results enable us to more fully understand and predict the effectiveness of dietary intervention on overall health throughout age in distinct genetic backgrounds. Body weight is one trait influenced by genes, age and environmental factors. Both internal and external environmental pressures are known to affect genetic variation over time. However, it is largely unknown how all factors – including age – interact to shape metabolism and bodyweight. Wright et al. set out to quantify the interactions between genes and diet in ageing mice and found that the effect of genetics on mouse body weight changes with age. In the experiments, Wright et al. weighed 960 female mice with diverse genetic backgrounds, starting at two months of age into adulthood. The animals were randomized to different diets at six months of age. Some mice had unlimited food access, others received 20% or 40% less calories than a typical mouse diet, and some fasted one or two days per week. Variations in their genetic background explained about 80% of differences in mice’s weight, but the influence of genetics relative to non-genetic factors decreased as they aged. Mice on the 40% calorie restriction diet were an exception to this rule and genetics accounted for 80% of their weight throughout adulthood, likely due to reduced influence from diet and reduced interactions between diet and genes. Several genes involved in metabolism, neurological function, or behavior, were associated with mouse weight. The experiments highlight the importance of considering interactions between genetics, environment, and age in determining complex traits like body weight. The results and the approaches used by Wright et al. may help other scientists learn more about how the genetic predisposition to disease changes with environmental stimuli and age.
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Affiliation(s)
- Kevin M Wright
- Calico Life Sciences LLC, South San Francisco, United States
| | | | | | - Adam Freund
- Calico Life Sciences LLC, South San Francisco, United States
| | - Vladimir Jojic
- Calico Life Sciences LLC, South San Francisco, United States
| | | | - Anil Raj
- Calico Life Sciences LLC, South San Francisco, United States
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2
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McCaffrey EF, Donato M, Keren L, Chen Z, Delmastro A, Fitzpatrick MB, Gupta S, Greenwald NF, Baranski A, Graf W, Kumar R, Bosse M, Fullaway CC, Ramdial PK, Forgó E, Jojic V, Van Valen D, Mehra S, Khader SA, Bendall SC, van de Rijn M, Kalman D, Kaushal D, Hunter RL, Banaei N, Steyn AJC, Khatri P, Angelo M. Author Correction: The immunoregulatory landscape of human tuberculosis granulomas. Nat Immunol 2022; 23:814. [PMID: 35277696 PMCID: PMC9098386 DOI: 10.1038/s41590-022-01178-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Erin F McCaffrey
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Michele Donato
- Department of Medicine, Division of Biomedical Informatics Research, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Leeat Keren
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Zhenghao Chen
- Calico Life Sciences LLC, South San Francisco, CA, USA
| | - Alea Delmastro
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Sanjana Gupta
- Department of Medicine, Division of Biomedical Informatics Research, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Noah F Greenwald
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Alex Baranski
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - William Graf
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena, CA, USA
| | - Rashmi Kumar
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Marc Bosse
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Pratista K Ramdial
- Africa Health Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Erna Forgó
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - David Van Valen
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena, CA, USA
| | - Smriti Mehra
- Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Shabaana A Khader
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Sean C Bendall
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Matt van de Rijn
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Daniel Kalman
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Deepak Kaushal
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Robert L Hunter
- Department of Pathology and Laboratory Medicine, University of Texas Health Sciences Center at Houston, Houston, TX, USA
| | - Niaz Banaei
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Division of Infectious Diseases & Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Adrie J C Steyn
- Africa Health Research Institute, University of KwaZulu-Natal, Durban, South Africa
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Purvesh Khatri
- Department of Medicine, Division of Biomedical Informatics Research, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael Angelo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
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3
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Chen Z, Raj A, Prateek GV, Di Francesco A, Liu J, Keyes BE, Kolumam G, Jojic V, Freund A. Automated, high-dimensional evaluation of physiological aging and resilience in outbred mice. eLife 2022; 11:e72664. [PMID: 35404230 PMCID: PMC9000950 DOI: 10.7554/elife.72664] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 03/29/2022] [Indexed: 02/06/2023] Open
Abstract
Behavior and physiology are essential readouts in many studies but have not benefited from the high-dimensional data revolution that has transformed molecular and cellular phenotyping. To address this, we developed an approach that combines commercially available automated phenotyping hardware with a systems biology analysis pipeline to generate a high-dimensional readout of mouse behavior/physiology, as well as intuitive and health-relevant summary statistics (resilience and biological age). We used this platform to longitudinally evaluate aging in hundreds of outbred mice across an age range from 3 months to 3.4 years. In contrast to the assumption that aging can only be measured at the limits of animal ability via challenge-based tasks, we observed widespread physiological and behavioral aging starting in early life. Using network connectivity analysis, we found that organism-level resilience exhibited an accelerating decline with age that was distinct from the trajectory of individual phenotypes. We developed a method, Combined Aging and Survival Prediction of Aging Rate (CASPAR), for jointly predicting chronological age and survival time and showed that the resulting model is able to predict both variables simultaneously, a behavior that is not captured by separate age and mortality prediction models. This study provides a uniquely high-resolution view of physiological aging in mice and demonstrates that systems-level analysis of physiology provides insights not captured by individual phenotypes. The approach described here allows aging, and other processes that affect behavior and physiology, to be studied with improved throughput, resolution, and phenotypic scope.
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Affiliation(s)
- Zhenghao Chen
- Calico Life Sciences LLC, South San FranciscoSouth San FranciscoUnited States
| | - Anil Raj
- Calico Life Sciences LLC, South San FranciscoSouth San FranciscoUnited States
| | - GV Prateek
- Calico Life Sciences LLC, South San FranciscoSouth San FranciscoUnited States
| | - Andrea Di Francesco
- Calico Life Sciences LLC, South San FranciscoSouth San FranciscoUnited States
| | - Justin Liu
- Calico Life Sciences LLC, South San FranciscoSouth San FranciscoUnited States
| | - Brice E Keyes
- Calico Life Sciences LLC, South San FranciscoSouth San FranciscoUnited States
| | - Ganesh Kolumam
- Calico Life Sciences LLC, South San FranciscoSouth San FranciscoUnited States
| | - Vladimir Jojic
- Calico Life Sciences LLC, South San FranciscoSouth San FranciscoUnited States
| | - Adam Freund
- Calico Life Sciences LLC, South San FranciscoSouth San FranciscoUnited States
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4
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Sayed N, Huang Y, Nguyen K, Krejciova-Rajaniemi Z, Grawe AP, Gao T, Tibshirani R, Hastie T, Alpert A, Cui L, Kuznetsova T, Rosenberg-Hasson Y, Ostan R, Monti D, Lehallier B, Shen-Orr SS, Maecker HT, Dekker CL, Wyss-Coray T, Franceschi C, Jojic V, Haddad F, Montoya JG, Wu JC, Davis MM, Furman D. Author Correction: An inflammatory aging clock (iAge) based on deep learning tracks multimorbidity, immunosenescence, frailty and cardiovascular aging. Nat Aging 2021; 1:748. [PMID: 37117770 DOI: 10.1038/s43587-021-00102-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Affiliation(s)
- Nazish Sayed
- Stanford 1000 Immunomes Project, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Surgery, Division of Vascular Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Yingxiang Huang
- Buck Artificial Intelligence Platform, the Buck Institute for Research on Aging, Novato, CA, USA
| | - Khiem Nguyen
- Buck Artificial Intelligence Platform, the Buck Institute for Research on Aging, Novato, CA, USA
| | | | - Anissa P Grawe
- Buck Artificial Intelligence Platform, the Buck Institute for Research on Aging, Novato, CA, USA
| | - Tianxiang Gao
- Department of Computer Science, University of North Carolina, Chapel Hill, NC, USA
| | - Robert Tibshirani
- Department of Statistics and Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Trevor Hastie
- Department of Statistics and Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Ayelet Alpert
- Faculty of Medicine, Technion, Israel Institute of Technology, Haifa, Israel
| | - Lu Cui
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Tatiana Kuznetsova
- Research Unit Hypertension and Cardiovascular Epidemiology, KU Leuven Department of Cardiovascular Sciences, University of Leuven, Leuven, Belgium
| | - Yael Rosenberg-Hasson
- Human Immune Monitoring Center, Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Rita Ostan
- Interdepartmental Centre L. Galvani (CIG), Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Daniela Monti
- Department of Experimental Clinical and Biomedical Sciences, Mario Serio, University of Florence, Florence, Italy
| | - Benoit Lehallier
- Department of Neurology and Neurological Sciences, Stanford School of Medicine, Stanford, CA, USA
| | - Shai S Shen-Orr
- Faculty of Medicine, Technion, Israel Institute of Technology, Haifa, Israel
| | - Holden T Maecker
- Human Immune Monitoring Center, Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Cornelia L Dekker
- Division of Pediatric Infectious Diseases, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Tony Wyss-Coray
- Department of Neurology and Neurological Sciences, Stanford School of Medicine, Stanford, CA, USA
- Paul F. Glenn Center for Aging Research, Stanford University School of Medicine, Stanford, CA, USA
| | - Claudio Franceschi
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky University, Nizhny, Russia
| | - Vladimir Jojic
- Calico Life Sciences L.L.C, South San Francisco, CA, USA
| | - François Haddad
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - José G Montoya
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Joseph C Wu
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Mark M Davis
- Stanford 1000 Immunomes Project, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - David Furman
- Stanford 1000 Immunomes Project, Stanford University School of Medicine, Stanford, CA, USA.
- Buck Artificial Intelligence Platform, the Buck Institute for Research on Aging, Novato, CA, USA.
- Edifice Health Inc., San Mateo, CA, USA.
- Austral Institute for Applied Artificial Intelligence, Institute for Research in Translational Medicine (IIMT), Universidad Austral, CONICET, Pilar, Buenos Aires, Argentina.
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5
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Sayed N, Huang Y, Nguyen K, Krejciova-Rajaniemi Z, Grawe AP, Gao T, Tibshirani R, Hastie T, Alpert A, Cui L, Kuznetsova T, Rosenberg-Hasson Y, Ostan R, Monti D, Lehallier B, Shen-Orr SS, Maecker HT, Dekker CL, Wyss-Coray T, Franceschi C, Jojic V, Haddad F, Montoya JG, Wu JC, Davis MM, Furman D. An inflammatory aging clock (iAge) based on deep learning tracks multimorbidity, immunosenescence, frailty and cardiovascular aging. ACTA ACUST UNITED AC 2021; 1:598-615. [PMID: 34888528 PMCID: PMC8654267 DOI: 10.1038/s43587-021-00082-y] [Citation(s) in RCA: 153] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
While many diseases of aging have been linked to the immunological system, immune metrics capable of identifying the most at-risk individuals are lacking. From the blood immunome of 1,001 individuals aged 8-96 years, we developed a deep-learning method based on patterns of systemic age-related inflammation. The resulting inflammatory clock of aging (iAge) tracked with multimorbidity, immunosenescence, frailty and cardiovascular aging, and is also associated with exceptional longevity in centenarians. The strongest contributor to iAge was the chemokine CXCL9, which was involved in cardiac aging, adverse cardiac remodeling and poor vascular function. Furthermore, aging endothelial cells in human and mice show loss of function, cellular senescence and hallmark phenotypes of arterial stiffness, all of which are reversed by silencing CXCL9. In conclusion, we identify a key role of CXCL9 in age-related chronic inflammation and derive a metric for multimorbidity that can be utilized for the early detection of age-related clinical phenotypes.
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6
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Soifer L, Fong NL, Yi N, Ireland AT, Lam I, Sooknah M, Paw JS, Peluso P, Concepcion GT, Rank D, Hastie AR, Jojic V, Ruby JG, Botstein D, Roy MA. Fully Phased Sequence of a Diploid Human Genome Determined de Novo from the DNA of a Single Individual. G3 (Bethesda) 2020; 10:2911-2925. [PMID: 32631951 PMCID: PMC7466960 DOI: 10.1534/g3.119.400995] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 06/26/2020] [Indexed: 12/17/2022]
Abstract
In recent years, improved sequencing technology and computational tools have made de novo genome assembly more accessible. Many approaches, however, generate either an unphased or only partially resolved representation of a diploid genome, in which polymorphisms are detected but not assigned to one or the other of the homologous chromosomes. Yet chromosomal phase information is invaluable for the understanding of phenotypic trait inheritance in the cases of compound heterozygosity, allele-specific expression or cis-acting variants. Here we use a combination of tools and sequencing technologies to generate a de novo diploid assembly of the human primary cell line WI-38. First, data from PacBio single molecule sequencing and Bionano Genomics optical mapping were combined to generate an unphased assembly. Next, 10x Genomics linked reads were combined with the hybrid assembly to generate a partially phased assembly. Lastly, we developed and optimized methods to use short-read (Illumina) sequencing of flow cytometry-sorted metaphase chromosomes to provide phase information. The final genome assembly was almost fully (94%) phased with the addition of approximately 2.5-fold coverage of Illumina data from the sequenced metaphase chromosomes. The diploid nature of the final de novo genome assembly improved the resolution of structural variants between the WI-38 genome and the human reference genome. The phased WI-38 sequence data are available for browsing and download at wi38.research.calicolabs.com. Our work shows that assembling a completely phased diploid genome de novo from the DNA of a single individual is now readily achievable.
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Affiliation(s)
- Llya Soifer
- Calico Life Sciences LLC, South San Francisco, CA 94080
| | - Nicole L Fong
- Calico Life Sciences LLC, South San Francisco, CA 94080
| | - Nelda Yi
- Calico Life Sciences LLC, South San Francisco, CA 94080
| | | | - Irene Lam
- Calico Life Sciences LLC, South San Francisco, CA 94080
| | | | | | | | | | - David Rank
- Pacific Biosciences, Menlo Park, CA 94025
| | | | | | - J Graham Ruby
- Calico Life Sciences LLC, South San Francisco, CA 94080
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7
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Abstract
Recent in situ multiplexed profiling techniques provide insight into microenvironment formation, maintenance, and transformation through a lens of localized cellular phenotype distribution. In this article, we introduce a method for recovering signatures of microenvironments from such data. We use topic models to identify characteristic cell types overrepresented in neighborhoods that serve as proxies for microenvironment. Furthermore, by assuming spatial coherence among neighboring microenvironments our model limits the number of parameters that need to be learned and permits data-driven decisions about the size of cellular neighborhoods. We apply this method to uncover anatomically known structures in mouse spleen—identifying distinct population of spleen B cells that are defined by their characteristic neighborhoods. Next, we apply the method to a dataset of triple-negative breast cancer tumors from 41 patients to study the structure of tumor-immune boundary. We uncover previously reported tumor-immune microenvironment near the tumor-immune boundary enriched for immune cells with high Indoleamine-pyrrole 2,3-dioxygenase (IDO) and Programmed death-ligand 1 (PD-L1) and a novel, immunosuppressed, microenvironment-enriched for cells expressing CD45 and FoxP3.
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Affiliation(s)
- Zhenghao Chen
- Calico Life Sciences LLC, South San Francisco, California, USA
| | - Ilya Soifer
- Calico Life Sciences LLC, South San Francisco, California, USA
| | - Hugo Hilton
- Calico Life Sciences LLC, South San Francisco, California, USA
| | - Leeat Keren
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Vladimir Jojic
- Calico Life Sciences LLC, South San Francisco, California, USA
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8
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Hilton HG, Rubinstein ND, Janki P, Ireland AT, Bernstein N, Fong NL, Wright KM, Smith M, Finkle D, Martin-McNulty B, Roy M, Imai DM, Jojic V, Buffenstein R. Single-cell transcriptomics of the naked mole-rat reveals unexpected features of mammalian immunity. PLoS Biol 2019; 17:e3000528. [PMID: 31751331 PMCID: PMC6894886 DOI: 10.1371/journal.pbio.3000528] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 12/05/2019] [Accepted: 11/07/2019] [Indexed: 01/08/2023] Open
Abstract
The immune system comprises a complex network of specialized cells that protects against infection, eliminates cancerous cells, and regulates tissue repair, thus serving a critical role in homeostasis, health span, and life span. The subterranean-dwelling naked mole-rat (NM-R; Heterocephalus glaber) exhibits prolonged life span relative to its body size, is unusually cancer resistant, and manifests few physiological or molecular changes with advancing age. We therefore hypothesized that the immune system of NM-Rs evolved unique features that confer enhanced cancer immunosurveillance and prevent the age-associated decline in homeostasis. Using single-cell RNA-sequencing (scRNA-seq) we mapped the immune system of the NM-R and compared it to that of the short-lived, cancer-prone mouse. In contrast to the mouse, we find that the NM-R immune system is characterized by a high myeloid-to-lymphoid cell ratio that includes a novel, lipopolysaccharide (LPS)-responsive, granulocyte cell subset. Surprisingly, we also find that NM-Rs lack canonical natural killer (NK) cells. Our comparative genomics analyses support this finding, showing that the NM-R genome lacks an expanded gene family that controls NK cell function in several other species. Furthermore, we reconstructed the evolutionary history that likely led to this genomic state. The NM-R thus challenges our current understanding of mammalian immunity, favoring an atypical, myeloid-biased mode of innate immunosurveillance, which may contribute to its remarkable health span.
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Affiliation(s)
- Hugo G. Hilton
- Calico Life Sciences LLC, South San Francisco, California, United States of America
| | - Nimrod D. Rubinstein
- Calico Life Sciences LLC, South San Francisco, California, United States of America
| | - Peter Janki
- Calico Life Sciences LLC, South San Francisco, California, United States of America
| | - Andrea T. Ireland
- Calico Life Sciences LLC, South San Francisco, California, United States of America
| | - Nicholas Bernstein
- Calico Life Sciences LLC, South San Francisco, California, United States of America
| | - Nicole L. Fong
- Calico Life Sciences LLC, South San Francisco, California, United States of America
| | - Kevin M. Wright
- Calico Life Sciences LLC, South San Francisco, California, United States of America
| | - Megan Smith
- Calico Life Sciences LLC, South San Francisco, California, United States of America
| | - David Finkle
- Calico Life Sciences LLC, South San Francisco, California, United States of America
| | - Baby Martin-McNulty
- Calico Life Sciences LLC, South San Francisco, California, United States of America
| | - Margaret Roy
- Calico Life Sciences LLC, South San Francisco, California, United States of America
| | - Denise M. Imai
- Comparative Pathology Laboratory, School of Veterinary Medicine, University of California, Davis, Davis, California, United States of America
| | - Vladimir Jojic
- Calico Life Sciences LLC, South San Francisco, California, United States of America
| | - Rochelle Buffenstein
- Calico Life Sciences LLC, South San Francisco, California, United States of America
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9
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Illing PT, Pymm P, Croft NP, Hilton HG, Jojic V, Han AS, Mendoza JL, Mifsud NA, Dudek NL, McCluskey J, Parham P, Rossjohn J, Vivian JP, Purcell AW. HLA-B57 micropolymorphism defines the sequence and conformational breadth of the immunopeptidome. Nat Commun 2018; 9:4693. [PMID: 30410026 PMCID: PMC6224591 DOI: 10.1038/s41467-018-07109-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 10/12/2018] [Indexed: 12/17/2022] Open
Abstract
Immunophenotypic differences between closely related human leukocyte antigen (HLA) alleles have been associated with divergent clinical outcomes in infection, autoimmunity, transplantation and drug hypersensitivity. Here we explore the impact of micropolymorphism on peptide antigen presentation by three closely related HLA molecules, HLA-B*57:01, HLA-B*57:03 and HLA-B*58:01, that are differentially associated with the HIV elite controller phenotype and adverse drug reactions. For each allotype, we mine HLA ligand data sets derived from the same parental cell proteome to define qualitative differences in peptide presentation using classical peptide binding motifs and an unbiased statistical approach. The peptide repertoires show marked qualitative overlap, with 982 peptides presented by all allomorphs. However, differences in peptide abundance, HLA-peptide stability, and HLA-bound conformation demonstrate that HLA micropolymorphism impacts more than simply the range of peptide ligands. These differences provide grounds for distinct immune reactivity and insights into the capacity of micropolymorphism to diversify immune outcomes. Human leukocyte antigens (HLA) are multi-allelic and polymorphic genes that present antigens to immune cells for inducing protective immunity. Here, using systems biology and structural approaches, the authors show that micropolymorphism of three HLA has effects beyond the modulation of antigen diversity.
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Affiliation(s)
- Patricia T Illing
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Phillip Pymm
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia.,Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, VIC, 3800, Australia
| | - Nathan P Croft
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Hugo G Hilton
- Departments of Structural Biology and Microbiology & Immunology, School of Medicine, Stanford University, Stanford, 94305, CA, USA.,Calico Life Sciences LLC, South San Francisco, 94080, CA, USA
| | - Vladimir Jojic
- Calico Life Sciences LLC, South San Francisco, 94080, CA, USA
| | - Alex S Han
- Department of Genetics, School of Medicine, Stanford University, Stanford, 94305, CA, USA
| | - Juan L Mendoza
- Department of Molecular and Cellular Physiology, School of Medicine, Stanford University, Stanford, 94305, CA, USA.,Institute for Molecular Engineering and Department of Biochemistry & Molecular Biology, University of Chicago, Chicago, 60637, IL, USA
| | - Nicole A Mifsud
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Nadine L Dudek
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - James McCluskey
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Peter Parham
- Departments of Structural Biology and Microbiology & Immunology, School of Medicine, Stanford University, Stanford, 94305, CA, USA
| | - Jamie Rossjohn
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia.,Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, VIC, 3800, Australia.,Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, CF14 4XN, UK
| | - Julian P Vivian
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia. .,Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, VIC, 3800, Australia.
| | - Anthony W Purcell
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia.
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10
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Herrera Paredes S, Gao T, Law TF, Finkel OM, Mucyn T, Teixeira PJPL, Salas González I, Feltcher ME, Powers MJ, Shank EA, Jones CD, Jojic V, Dangl JL, Castrillo G. Design of synthetic bacterial communities for predictable plant phenotypes. PLoS Biol 2018; 16:e2003962. [PMID: 29462153 PMCID: PMC5819758 DOI: 10.1371/journal.pbio.2003962] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 01/17/2018] [Indexed: 01/01/2023] Open
Abstract
Specific members of complex microbiota can influence host phenotypes, depending on both the abiotic environment and the presence of other microorganisms. Therefore, it is challenging to define bacterial combinations that have predictable host phenotypic outputs. We demonstrate that plant-bacterium binary-association assays inform the design of small synthetic communities with predictable phenotypes in the host. Specifically, we constructed synthetic communities that modified phosphate accumulation in the shoot and induced phosphate starvation-responsive genes in a predictable fashion. We found that bacterial colonization of the plant is not a predictor of the plant phenotypes we analyzed. Finally, we demonstrated that characterizing a subset of all possible bacterial synthetic communities is sufficient to predict the outcome of untested bacterial consortia. Our results demonstrate that it is possible to infer causal relationships between microbiota membership and host phenotypes and to use these inferences to rationally design novel communities.
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Affiliation(s)
- Sur Herrera Paredes
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Tianxiang Gao
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Theresa F. Law
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Omri M. Finkel
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Tatiana Mucyn
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Paulo José Pereira Lima Teixeira
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Isaí Salas González
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Meghan E. Feltcher
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Matthew J. Powers
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Elizabeth A. Shank
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Corbin D. Jones
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Vladimir Jojic
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Jeffery L. Dangl
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Gabriel Castrillo
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
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11
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Abstract
Many microbes associate with higher eukaryotes and impact their vitality. To engineer microbiomes for host benefit, we must understand the rules of community assembly and maintenance that, in large part, demand an understanding of the direct interactions among community members. Toward this end, we have developed a Poisson-multivariate normal hierarchical model to learn direct interactions from the count-based output of standard metagenomics sequencing experiments. Our model controls for confounding predictors at the Poisson layer and captures direct taxon-taxon interactions at the multivariate normal layer using an ℓ1 penalized precision matrix. We show in a synthetic experiment that our method handily outperforms state-of-the-art methods such as SparCC and the graphical lasso (glasso). In a real in planta perturbation experiment of a nine-member bacterial community, we show our model, but not SparCC or glasso, correctly resolves a direct interaction structure among three community members that associates with Arabidopsis thaliana roots. We conclude that our method provides a structured, accurate, and distributionally reasonable way of modeling correlated count-based random variables and capturing direct interactions among them.
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Affiliation(s)
- Surojit Biswas
- 1 Department of Statistics, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina
| | - Meredith Mcdonald
- 2 Department of Biology, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina
| | - Derek S Lundberg
- 2 Department of Biology, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina
| | - Jeffery L Dangl
- 2 Department of Biology, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina.,3 Howard Hughes Medical Institute, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina.,4 Department of Immunology, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina
| | - Vladimir Jojic
- 5 Department of Computer Science, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina
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12
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Biswas S, Kerner K, Teixeira PJPL, Dangl JL, Jojic V, Wigge PA. Tradict enables accurate prediction of eukaryotic transcriptional states from 100 marker genes. Nat Commun 2017; 8:15309. [PMID: 28474674 PMCID: PMC5424156 DOI: 10.1038/ncomms15309] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 03/15/2017] [Indexed: 12/21/2022] Open
Abstract
Transcript levels are a critical determinant of the proteome and hence cellular function. Because the transcriptome is an outcome of the interactions between genes and their products, it may be accurately represented by a subset of transcript abundances. We develop a method, Tradict (transcriptome predict), capable of learning and using the expression measurements of a small subset of 100 marker genes to predict transcriptome-wide gene abundances and the expression of a comprehensive, but interpretable list of transcriptional programs that represent the major biological processes and pathways of the cell. By analyzing over 23,000 publicly available RNA-Seq data sets, we show that Tradict is robust to noise and accurate. Coupled with targeted RNA sequencing, Tradict may therefore enable simultaneous transcriptome-wide screening and mechanistic investigation at large scales.
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Affiliation(s)
- Surojit Biswas
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Konstantin Kerner
- Botanical Institute, Biocenter, University of Cologne, D-50674 Cologne, Germany
| | - Paulo José Pereira Lima Teixeira
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Jeffery L. Dangl
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Carolina Center for Genome Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Vladimir Jojic
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Philip A. Wigge
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, UK
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13
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Furman D, Chang J, Lartigue L, Bolen CR, Haddad F, Gaudilliere B, Ganio EA, Fragiadakis GK, Spitzer MH, Douchet I, Daburon S, Moreau JF, Nolan GP, Blanco P, Déchanet-Merville J, Dekker CL, Jojic V, Kuo CJ, Davis MM, Faustin B. Expression of specific inflammasome gene modules stratifies older individuals into two extreme clinical and immunological states. Nat Med 2017; 23:174-184. [PMID: 28092664 DOI: 10.1038/nm.4267] [Citation(s) in RCA: 265] [Impact Index Per Article: 37.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 12/13/2016] [Indexed: 12/13/2022]
Abstract
Low-grade, chronic inflammation has been associated with many diseases of aging, but the mechanisms responsible for producing this inflammation remain unclear. Inflammasomes can drive chronic inflammation in the context of an infectious disease or cellular stress, and they trigger the maturation of interleukin-1β (IL-1β). Here we find that the expression of specific inflammasome gene modules stratifies older individuals into two extremes: those with constitutive expression of IL-1β, nucleotide metabolism dysfunction, elevated oxidative stress, high rates of hypertension and arterial stiffness; and those without constitutive expression of IL-1β, who lack these characteristics. Adenine and N4-acetylcytidine, nucleotide-derived metabolites that are detectable in the blood of the former group, prime and activate the NLRC4 inflammasome, induce the production of IL-1β, activate platelets and neutrophils and elevate blood pressure in mice. In individuals over 85 years of age, the elevated expression of inflammasome gene modules was associated with all-cause mortality. Thus, targeting inflammasome components may ameliorate chronic inflammation and various other age-associated conditions.
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Affiliation(s)
- David Furman
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, California, USA.,Department of Systems Biology, Division of Translational Medicine, Sidra Medical and Research Center, Doha, Qatar
| | - Junlei Chang
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, California, USA
| | - Lydia Lartigue
- INSERM U916 VINCO, Institut Bergonié, Bordeaux Cedex, France
| | - Christopher R Bolen
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - François Haddad
- Institute of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Brice Gaudilliere
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Edward A Ganio
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Gabriela K Fragiadakis
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Matthew H Spitzer
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Isabelle Douchet
- CIRID, UMR CNRS 5164, Université Bordeaux 2, Bordeaux Cedex, France
| | - Sophie Daburon
- CIRID, UMR CNRS 5164, Université Bordeaux 2, Bordeaux Cedex, France
| | | | - Garry P Nolan
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Patrick Blanco
- CIRID, UMR CNRS 5164, Université Bordeaux 2, Bordeaux Cedex, France
| | | | - Cornelia L Dekker
- Department of Pediatrics, Division of Infectious Diseases, Stanford University, Stanford, California, USA
| | - Vladimir Jojic
- Department of Computer Science, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Calvin J Kuo
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, California, USA
| | - Mark M Davis
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, California, USA.,Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, USA
| | - Benjamin Faustin
- CIRID, UMR CNRS 5164, Université Bordeaux 2, Bordeaux Cedex, France
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14
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Abstract
Motivation: The interactions between microbial colonies through chemical signaling are not well understood. A microbial colony can use different molecules to inhibit or accelerate the growth of other colonies. A better understanding of the molecules involved in these interactions could lead to advancements in health and medicine. Imaging mass spectrometry (IMS) applied to co-cultured microbial communities aims to capture the spatial characteristics of the colonies’ molecular fingerprints. These data are high-dimensional and require computational analysis methods to interpret. Results: Here, we present a dictionary learning method that deconvolves spectra of different molecules from IMS data. We call this method MOLecular Dictionary Learning (MOLDL). Unlike standard dictionary learning methods which assume Gaussian-distributed data, our method uses the Poisson distribution to capture the count nature of the mass spectrometry data. Also, our method incorporates universally applicable information on common ion types of molecules in MALDI mass spectrometry. This greatly reduces model parameterization and increases deconvolution accuracy by eliminating spurious solutions. Moreover, our method leverages the spatial nature of IMS data by assuming that nearby locations share similar abundances, thus avoiding overfitting to noise. Tests on simulated datasets show that this method has good performance in recovering molecule dictionaries. We also tested our method on real data measured on a microbial community composed of two species. We confirmed through follow-up validation experiments that our method recovered true and complete signatures of molecules. These results indicate that our method can discover molecules in IMS data reliably, and hence can help advance the study of interaction of microbial colonies. Availability and implementation: The code used in this paper is available at: https://github.com/frizfealer/IMS_project. Contact:vjojic@cs.unc.edu Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Y-C Harn
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA, Department of Biology, University of North Carolina, Chapel Hill, NC 27599-32800, USA, Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599-7290, USA and Curriculum of Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA
| | - M J Powers
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA, Department of Biology, University of North Carolina, Chapel Hill, NC 27599-32800, USA, Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599-7290, USA and Curriculum of Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA
| | - E A Shank
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA, Department of Biology, University of North Carolina, Chapel Hill, NC 27599-32800, USA, Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599-7290, USA and Curriculum of Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA, Department of Biology, University of North Carolina, Chapel Hill, NC 27599-32800, USA, Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599-7290, USA and Curriculum of Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA, Department of Biology, University of North Carolina, Chapel Hill, NC 27599-32800, USA, Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599-7290, USA and Curriculum of Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA
| | - V Jojic
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA, Department of Biology, University of North Carolina, Chapel Hill, NC 27599-32800, USA, Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599-7290, USA and Curriculum of Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA
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15
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Furman D, Jojic V, Sharma S, Shen-Orr SS, Angel CJL, Onengut-Gumuscu S, Kidd BA, Maecker HT, Concannon P, Dekker CL, Thomas PG, Davis MM. Cytomegalovirus infection enhances the immune response to influenza. Sci Transl Med 2015; 7:281ra43. [PMID: 25834109 DOI: 10.1126/scitranslmed.aaa2293] [Citation(s) in RCA: 233] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Cytomegalovirus (CMV) is a β-herpesvirus present in a latent form in most people worldwide. In immunosuppressed individuals, CMV can reactivate and cause serious clinical complications, but the effect of the latent state on healthy people remains elusive. We undertook a systems approach to understand the differences between seropositive and negative subjects and measured hundreds of immune system components from blood samples including cytokines and chemokines, immune cell phenotyping, gene expression, ex vivo cell responses to cytokine stimuli, and the antibody response to seasonal influenza vaccination. As expected, we found decreased responses to vaccination and an overall down-regulation of immune components in aged individuals regardless of CMV status. In contrast, CMV-seropositive young adults exhibited enhanced antibody responses to influenza vaccination, increased CD8(+) T cell sensitivity, and elevated levels of circulating interferon-γ compared to seronegative individuals. Experiments with young mice infected with murine CMV also showed significant protection from an influenza virus challenge compared with uninfected animals, although this effect declined with time. These data show that CMV and its murine equivalent can have a beneficial effect on the immune response of young, healthy individuals, which may explain the ubiquity of CMV infection in humans and many other species.
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Affiliation(s)
- David Furman
- Department of Microbiology and Immunology, School of Medicine, Stanford University, Stanford, CA 94305, USA.
| | - Vladimir Jojic
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Shalini Sharma
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Shai S Shen-Orr
- Department of Immunology, Rappaport Institute of Medical Research, Faculty of Medicine and Faculty of Biology, Technion, Haifa 32000, Israel
| | - Cesar J L Angel
- Department of Microbiology and Immunology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Suna Onengut-Gumuscu
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22903, USA
| | - Brian A Kidd
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Holden T Maecker
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Patrick Concannon
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22903, USA. Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22903, USA
| | - Cornelia L Dekker
- Division of Infectious Diseases, Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Mark M Davis
- Department of Microbiology and Immunology, School of Medicine, Stanford University, Stanford, CA 94305, USA. Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA 94305, USA. The Howard Hughes Medical Institute.
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16
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Brodin P, Jojic V, Gao T, Bhattacharya S, Angel CJL, Furman D, Shen-Orr S, Dekker CL, Swan GE, Butte AJ, Maecker HT, Davis MM. Variation in the human immune system is largely driven by non-heritable influences. Cell 2015; 160:37-47. [PMID: 25594173 DOI: 10.1016/j.cell.2014.12.020] [Citation(s) in RCA: 680] [Impact Index Per Article: 75.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 10/20/2014] [Accepted: 11/14/2014] [Indexed: 12/31/2022]
Abstract
There is considerable heterogeneity in immunological parameters between individuals, but its sources are largely unknown. To assess the relative contribution of heritable versus non-heritable factors, we have performed a systems-level analysis of 210 healthy twins between 8 and 82 years of age. We measured 204 different parameters, including cell population frequencies, cytokine responses, and serum proteins, and found that 77% of these are dominated (>50% of variance) and 58% almost completely determined (>80% of variance) by non-heritable influences. In addition, some of these parameters become more variable with age, suggesting the cumulative influence of environmental exposure. Similarly, the serological responses to seasonal influenza vaccination are also determined largely by non-heritable factors, likely due to repeated exposure to different strains. Lastly, in MZ twins discordant for cytomegalovirus infection, more than half of all parameters are affected. These results highlight the largely reactive and adaptive nature of the immune system in healthy individuals.
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Affiliation(s)
- Petter Brodin
- Science for Life Laboratory, Department of Medicine, Solna, Karolinska Institutet, 17121 Solna, Sweden; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA; Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Vladimir Jojic
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Tianxiang Gao
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Sanchita Bhattacharya
- Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Cesar J Lopez Angel
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA; Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - David Furman
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA; Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Shai Shen-Orr
- Department of Immunology, Faculty of Medicine, Technion, Haifa 31096, Israel
| | - Cornelia L Dekker
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Gary E Swan
- Stanford Prevention Research Center, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Atul J Butte
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94304, USA; Center for Pediatric Bioinformatics, Lucille Packard Children's Hospital, Stanford University, Stanford, CA 94304, USA
| | - Holden T Maecker
- Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94304, USA; Human Immune Monitoring Center, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Mark M Davis
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA; Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94304, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94304, USA.
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17
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Gao T, Brodin P, Davis MM, Jojic V. Drug-induced mRNA signatures are enriched for the minority of genes that are highly heritable. Pac Symp Biocomput 2015:395-406. [PMID: 25592599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The blood gene expression signatures are used as biomarkers for immunological and non- immunological diseases. Therefore, it is important to understand the variation in blood gene expression patterns and the factors (heritable/non-heritable) that underlie this variation. In this paper, we study the relationship between drug effects on the one hand, and heritable and non-heritable factors influencing gene expression on the other. Understanding of this relationship can help select appropriate targets for drugs aimed at reverting disease phenotypes to healthy states. In order to estimate heritable and non-heritable effects on gene expression, we use Twin-ACE model on a gene expression dataset MuTHER, measured in blood samples from monozygotic and dizygotic twins. In order to associate gene expression with drug effects, we use CMap database. We show that, even though the expressions of most genes are driven by non-heritable factors, drugs are more likely to influence expression of genes, driven by heritable rather than non-heritable factors. We further study this finding in the context of a gene regulatory network. We investigate the relationship between the drug effects on gene expression and propagation of heritable and non-heritable factors through regulatory networks. We find that the decisive factor in determining whether a gene will be influenced by a drug is the flow of heritable effects supplied to the gene through regulatory network.
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Affiliation(s)
- Tianxiang Gao
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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18
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Jojic V, Shay T, Sylvia K, Zuk O, Sun X, Kang J, Regev A, Koller D. Identification of transcriptional regulators in the mouse immune system. Nat Immunol 2013; 14:633-43. [PMID: 23624555 PMCID: PMC3690947 DOI: 10.1038/ni.2587] [Citation(s) in RCA: 151] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 03/13/2013] [Indexed: 12/12/2022]
Abstract
The differentiation of hematopoietic stem cells into cells of the immune system has been studied extensively in mammals, but the transcriptional circuitry that controls it is still only partially understood. Here, the Immunological Genome Project gene-expression profiles across mouse immune lineages allowed us to systematically analyze these circuits. To analyze this data set we developed Ontogenet, an algorithm for reconstructing lineage-specific regulation from gene-expression profiles across lineages. Using Ontogenet, we found differentiation stage-specific regulators of mouse hematopoiesis and identified many known hematopoietic regulators and 175 previously unknown candidate regulators, as well as their target genes and the cell types in which they act. Among the previously unknown regulators, we emphasize the role of ETV5 in the differentiation of γδ T cells. As the transcriptional programs of human and mouse cells are highly conserved, it is likely that many lessons learned from the mouse model apply to humans.
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Affiliation(s)
- Vladimir Jojic
- Computer Science Department, Stanford University, 353 Serra Mall, Stanford California 94305-9010, USA
| | - Tal Shay
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Katelyn Sylvia
- Department of Pathology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, Massachusetts 01655, USA
| | - Or Zuk
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Xin Sun
- Laboratory of Genetics, University of Wisconsin-Madison, 425 Henry Mall, Madison, Wisconsin 53706, USA
| | - Joonsoo Kang
- Department of Pathology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, Massachusetts 01655, USA
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Daphne Koller
- Computer Science Department, Stanford University, 353 Serra Mall, Stanford California 94305-9010, USA
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19
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Furman D, Jojic V, Kidd B, Shen-Orr S, Price J, Jarrell J, Tse T, Huang H, Lund P, Maecker HT, Utz PJ, Dekker CL, Koller D, Davis MM. Apoptosis and other immune biomarkers predict influenza vaccine responsiveness. Mol Syst Biol 2013; 9:659. [PMID: 23591775 PMCID: PMC3658270 DOI: 10.1038/msb.2013.15] [Citation(s) in RCA: 145] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Accepted: 03/07/2013] [Indexed: 12/17/2022] Open
Abstract
Despite the importance of the immune system in many diseases, there are currently no objective benchmarks of immunological health. In an effort to identifying such markers, we used influenza vaccination in 30 young (20-30 years) and 59 older subjects (60 to >89 years) as models for strong and weak immune responses, respectively, and assayed their serological responses to influenza strains as well as a wide variety of other parameters, including gene expression, antibodies to hemagglutinin peptides, serum cytokines, cell subset phenotypes and in vitro cytokine stimulation. Using machine learning, we identified nine variables that predict the antibody response with 84% accuracy. Two of these variables are involved in apoptosis, which positively associated with the response to vaccination and was confirmed to be a contributor to vaccine responsiveness in mice. The identification of these biomarkers provides new insights into what immune features may be most important for immune health.
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Affiliation(s)
- David Furman
- Department of Microbiology and Immunology, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Vladimir Jojic
- Department of Computer Science, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Brian Kidd
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Shai Shen-Orr
- Department of Immunology, Faculty of Medicine, Technion, Technion City, Haifa, Israel
| | - Jordan Price
- Department of Microbiology and Immunology, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Justin Jarrell
- Division of Immunology and Rheumatology, Department of Medicine, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Tiffany Tse
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Huang Huang
- Department of Microbiology and Immunology, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Peder Lund
- Department of Microbiology and Immunology, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Holden T Maecker
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Paul J Utz
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Palo Alto, CA, USA
- Division of Immunology and Rheumatology, Department of Medicine, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Cornelia L Dekker
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Palo Alto, CA, USA
- Department of Pediatrics, Division of Infectious Diseases, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Daphne Koller
- Department of Computer Science, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Mark M Davis
- Department of Microbiology and Immunology, School of Medicine, Stanford University, Palo Alto, CA, USA
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Palo Alto, CA, USA
- The Howard Hughes Medical Institute, Chevy Chase, MD, USA
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20
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Abstract
We propose a robust multimodal dictionary learning method for multimodal images. Joint dictionary learning for both modalities may be impaired by lack of correspondence between image modalities in training data, for example due to areas of low quality in one of the modalities. Dictionaries learned with such non-corresponding data will induce uncertainty about image representation. In this paper, we propose a probabilistic model that accounts for image areas that are poorly corresponding between the image modalities. We cast the problem of learning a dictionary in presence of problematic image patches as a likelihood maximization problem and solve it with a variant of the EM algorithm. Our algorithm iterates identification of poorly corresponding patches and refinements of the dictionary. We tested our method on synthetic and real data. We show improvements in image prediction quality and alignment accuracy when using the method for multimodal image registration.
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Affiliation(s)
- Tian Cao
- University of North Carolina at Chapel Hill, NC, USA.
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21
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Biswas S, Jojic V. AMP: Assembly Matching Pursuit. Pac Symp Biocomput 2013:175-187. [PMID: 23424123 DOI: 10.1142/9789814447973_0018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Metagenomics, the study of the total genetic material isolated from a biological host, promises to reveal host-microbe or microbe-microbe interactions that may help to personalize medicine or improve agronomic practice. We introduce a method that discovers metagenomic units (MGUs) relevant for phenotype prediction through sequence-based dictionary learning. The method aggregates patient-specific dictionaries and estimates MGU abundances in order to summarize a whole population and yield universally predictive biomarkers. We analyze the impact of Gaussian, Poisson, and Negative Binomial read count models in guiding dictionary construction by examining classification efficiency on a number of synthetic datasets and a real dataset from Ref. 1. Each outperforms standard methods of dictionary composition, such as random projection and orthogonal matching pursuit. Additionally, the predictive MGUs they recover are biologically relevant.
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Affiliation(s)
- S Biswas
- Department of Statistics and Operations Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
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22
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Miller JC, Brown BD, Shay T, Gautier EL, Jojic V, Cohain A, Pandey G, Leboeuf M, Elpek KG, Helft J, Hashimoto D, Chow A, Price J, Greter M, Bogunovic M, Bellemare-Pelletier A, Frenette PS, Randolph GJ, Turley SJ, Merad M. Deciphering the transcriptional network of the dendritic cell lineage. Nat Immunol 2012; 13:888-99. [PMID: 22797772 PMCID: PMC3985403 DOI: 10.1038/ni.2370] [Citation(s) in RCA: 577] [Impact Index Per Article: 48.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Accepted: 06/08/2012] [Indexed: 12/12/2022]
Abstract
Although much progress has been made in the understanding of the ontogeny and function of dendritic cells (DCs), the transcriptional regulation of the lineage commitment and functional specialization of DCs in vivo remains poorly understood. We made a comprehensive comparative analysis of CD8(+), CD103(+), CD11b(+) and plasmacytoid DC subsets, as well as macrophage DC precursors and common DC precursors, across the entire immune system. Here we characterized candidate transcriptional activators involved in the commitment of myeloid progenitor cells to the DC lineage and predicted regulators of DC functional diversity in tissues. We identified a molecular signature that distinguished tissue DCs from macrophages. We also identified a transcriptional program expressed specifically during the steady-state migration of tissue DCs to the draining lymph nodes that may control tolerance to self tissue antigens.
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Affiliation(s)
- Jennifer C Miller
- Immunology Institute, Mount Sinai School of Medicine, New York, New York, USA
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23
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Adam SJ, Yetil A, Gevaert O, Jojic V, Gentles A, Felsher DW. Abstract 4879: Distinct roles of p53 and p19ARF in MYC-dependent tumor oncogene addiction. Cancer Res 2012. [DOI: 10.1158/1538-7445.am2012-4879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Acute T-cell lymphoblastic leukemia (T-ALL) is a pediatric malignancy in which the MYC oncogene is frequently overexpressed. Although, T-ALL responds to standard therapies, in 20% of cases, treatment fails to induce sustained remission, resulting in reduced patient survival. Inhibition or restoration of the mutant gene products that drive tumorigenesis can reverse the aberrant cell growth and result in elimination of tumor cells through the phenomenon of oncogene addiction. In order to recapitulate tumor regression and recurrence, we have developed conditional mouse models of MYC-dependent T-ALL, thereby allowing for the investigation of therapeutic resistance. Recently, we have shown oncogene addiction in our MYC-driven murine model of T-ALL occurs through both tumor cell-intrinsic mechanisms, such as cellular senescence and apoptosis, and tumor cell-extrinsic, host-dependent mechanisms, including inhibition of angiogenesis, immune system-dependent tumor clearance, and autocrine/paracrine survival signaling. We now present evidence that loss of either p53 or p19ARF facilitates tumor recurrence through distinct mechanisms. p53 utilizes host-dependent mechanisms by allowing tumors to maintain angiogenesis, while p19ARF employs tumor-cell intrinsic mechanisms to circumvent senescence upon oncogene inactivation in vivo. To further interrogate the mechanisms that underlie p53- and p19ARF-dependent tumor recurrence, we performed gene expression analysis on MYC wild-type, MYC/p53-/-, and MYC/p19-/- tumors before and after MYC inactivation. Utilizing novel computational techniques to compare gene expression from our T-ALL cells to gene expression of normal hematopoietic differentiation from the Immunologic Genome Project, we have delineated the regulatory pathways underlying the effects of tumor suppressor loss in human MYC-driven lymphoma cells in the presence of targeted MYC-inactivation. We have also utilized expression analysis to establish gene signatures from unique to our MYC/p53-/- and MYC/p19-/- murine T-ALL models and shown them to be prognostic for specific human T-ALL subtypes, as well as patient relapse-free survival. Overall, we have utilized whole transcriptomic analysis to further define the underlying cell signaling by which loss of p53 and p19 facilitate tumor recurrence and demonstrated that loss of these tumor suppressors can predict outcome in human patients.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4879. doi:1538-7445.AM2012-4879
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24
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Abstract
Next-generation sequencing technologies produce a large number of noisy reads from the DNA in a sample. Metagenomics and population sequencing aim to recover the genomic sequences of the species in the sample, which could be of high diversity. Methods geared towards single sequence reconstruction are not sensitive enough when applied in this setting. We introduce a generative probabilistic model of read generation from environmental samples and present Genovo, a novel de novo sequence assembler that discovers likely sequence reconstructions under the model. A nonparametric prior accounts for the unknown number of genomes in the sample. Inference is performed by applying a series of hill-climbing steps iteratively until convergence. We compare the performance of Genovo to three other short read assembly programs in a series of synthetic experiments and across nine metagenomic datasets created using the 454 platform, the largest of which has 311k reads. Genovo's reconstructions cover more bases and recover more genes than the other methods, even for low-abundance sequences, and yield a higher assembly score. Supplementary Material is available at www.liebertoinline.com/cmb .
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Affiliation(s)
- Jonathan Laserson
- Department of Computer Science, Stanford University, Stanford, California, USA
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25
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Nickle DC, Jojic N, Heckerman D, Jojic V, Kirovski D, Rolland M, Kosakovsky Pond S, Mullins JI. Comparison of immunogen designs that optimize peptide coverage: reply to Fischer et al. PLoS Comput Biol 2008; 4:e25. [PMID: 18463692 PMCID: PMC2217581 DOI: 10.1371/journal.pcbi.0040025] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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26
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Jojic V, Hertz T, Jojic N. Population sequencing using short reads: HIV as a case study. Pac Symp Biocomput 2008:114-125. [PMID: 18229680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Despite many drawbacks, traditional sequencing technologies have proven to be invaluable in modern medical research, even when the targeted genomes are highly variable. While it is often known in such cases that multiple slightly different sequences are present in the analyzed sample in concentrations that vary dramatically, the traditional techniques typically allow only the most dominant strain to be extracted from a single chromatogram. These limitations made some research directions rather difficult to pursue. For example, the analysis of HIV evolution (including the emergence of drug resistance) in a single patient is expected to benefit from a comprehensive catalog of the patient's HIV population. In this paper, we show how the new generation of sequencing technologies, based on high throughput of short reads, can be used to link site variants and reconstruct multiple full strains of the targeted gene, including those of low concentration in the sample. Our algorithm is based on a generative model of the sequencing process, and uses a tailored probabilistic inference and learning procedure to fit the model to the obtained reads.
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27
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Rolland M, Nickle DC, Deng W, Frahm N, Brander C, Learn GH, Heckerman D, Jojic N, Jojic V, Walker BD, Mullins JI. Recognition of HIV-1 peptides by host CTL is related to HIV-1 similarity to human proteins. PLoS One 2007; 2:e823. [PMID: 17786195 PMCID: PMC1952107 DOI: 10.1371/journal.pone.0000823] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2007] [Accepted: 05/18/2007] [Indexed: 12/03/2022] Open
Abstract
Background While human immunodeficiency virus type 1 (HIV-1)-specific cytotoxic T lymphocytes preferentially target specific regions of the viral proteome, HIV-1 features that contribute to immune recognition are not well understood. One hypothesis is that similarities between HIV and human proteins influence the host immune response, i.e., resemblance between viral and host peptides could preclude reactivity against certain HIV epitopes. Methodology/Principal Findings We analyzed the extent of similarity between HIV-1 and the human proteome. Proteins from the HIV-1 B consensus sequence from 2001 were dissected into overlapping k-mers, which were then probed against a non-redundant database of the human proteome in order to identify segments of high similarity. We tested the relationship between HIV-1 similarity to host encoded peptides and immune recognition in HIV-infected individuals, and found that HIV immunogenicity could be partially modulated by the sequence similarity to the host proteome. ELISpot responses to peptides spanning the entire viral proteome evaluated in 314 individuals showed a trend indicating an inverse relationship between the similarity to the host proteome and the frequency of recognition. In addition, analysis of responses by a group of 30 HIV-infected individuals against 944 overlapping peptides representing a broad range of individual HIV-1B Nef variants, affirmed that the degree of similarity to the host was significantly lower for peptides with reactive epitopes than for those that were not recognized. Conclusions/Significance Our results suggest that antigenic motifs that are scarcely represented in human proteins might represent more immunogenic CTL targets not selected against in the host. This observation could provide guidance in the design of more effective HIV immunogens, as sequences devoid of host-like features might afford superior immune reactivity.
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Affiliation(s)
- Morgane Rolland
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - David C. Nickle
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Wenjie Deng
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Nicole Frahm
- Partners AIDS Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts, United States of America
| | - Christian Brander
- Partners AIDS Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts, United States of America
| | - Gerald H. Learn
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - David Heckerman
- Machine Learning and Applied Statistics Group, Microsoft Research, Redmond, Washington, United States of America
| | - Nebosja Jojic
- Machine Learning and Applied Statistics Group, Microsoft Research, Redmond, Washington, United States of America
| | - Vladimir Jojic
- Machine Learning and Applied Statistics Group, Microsoft Research, Redmond, Washington, United States of America
| | - Bruce D. Walker
- Partners AIDS Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts, United States of America
| | - James I. Mullins
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
- * To whom correspondence should be addressed. E-mail:
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28
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Jojic V, Jojic N, Meek C, Geiger D, Siepel A, Haussler D, Heckerman D. Efficient approximations for learning phylogenetic HMM models from data. Bioinformatics 2007; 20 Suppl 1:i161-8. [PMID: 15262795 DOI: 10.1093/bioinformatics/bth917] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION We consider models useful for learning an evolutionary or phylogenetic tree from data consisting of DNA sequences corresponding to the leaves of the tree. In particular, we consider a general probabilistic model described in Siepel and Haussler that we call the phylogenetic-HMM model which generalizes the classical probabilistic models of Neyman and Felsenstein. Unfortunately, computing the likelihood of phylogenetic-HMM models is intractable. We consider several approximations for computing the likelihood of such models including an approximation introduced in Siepel and Haussler, loopy belief propagation and several variational methods. RESULTS We demonstrate that, unlike the other approximations, variational methods are accurate and are guaranteed to lower bound the likelihood. In addition, we identify a particular variational approximation to be best-one in which the posterior distribution is variationally approximated using the classic Neyman-Felsenstein model. The application of our best approximation to data from the cystic fibrosis transmembrane conductance regulator gene region across nine eutherian mammals reveals a CpG effect.
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29
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Peng WT, Robinson MD, Mnaimneh S, Krogan NJ, Cagney G, Morris Q, Davierwala AP, Grigull J, Yang X, Zhang W, Mitsakakis N, Ryan OW, Datta N, Jojic V, Pal C, Canadien V, Richards D, Beattie B, Wu LF, Altschuler SJ, Roweis S, Frey BJ, Emili A, Greenblatt JF, Hughes TR. A panoramic view of yeast noncoding RNA processing. Cell 2003; 113:919-33. [PMID: 12837249 DOI: 10.1016/s0092-8674(03)00466-5] [Citation(s) in RCA: 199] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Predictive analysis using publicly available yeast functional genomics and proteomics data suggests that many more proteins may be involved in biogenesis of ribonucleoproteins than are currently known. Using a microarray that monitors abundance and processing of noncoding RNAs, we analyzed 468 yeast strains carrying mutations in protein-coding genes, most of which have not previously been associated with RNA or RNP synthesis. Many strains mutated in uncharacterized genes displayed aberrant noncoding RNA profiles. Ten factors involved in noncoding RNA biogenesis were verified by further experimentation, including a protein required for 20S pre-rRNA processing (Tsr2p), a protein associated with the nuclear exosome (Lrp1p), and a factor required for box C/D snoRNA accumulation (Bcd1p). These data present a global view of yeast noncoding RNA processing and confirm that many currently uncharacterized yeast proteins are involved in biogenesis of noncoding RNA.
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Affiliation(s)
- Wen Tao Peng
- Banting and Best Department of Medical Research, University of Toronto, 112 College Street, M5G 1L6, Toronto, Ontario, Canada
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