1
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De Ridder K, Che H, Leroy K, Thienpont B. Benchmarking of methods for DNA methylome deconvolution. Nat Commun 2024; 15:4134. [PMID: 38755121 PMCID: PMC11099101 DOI: 10.1038/s41467-024-48466-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 04/30/2024] [Indexed: 05/18/2024] Open
Abstract
Defining the number and abundance of different cell types in tissues is important for understanding disease mechanisms as well as for diagnostic and prognostic purposes. Typically, this is achieved by immunohistological analyses, cell sorting, or single-cell RNA-sequencing. Alternatively, cell-specific DNA methylome information can be leveraged to deconvolve cell fractions from a bulk DNA mixture. However, comprehensive benchmarking of deconvolution methods and modalities was not yet performed. Here we evaluate 16 deconvolution algorithms, developed either specifically for DNA methylome data or more generically. We assess the performance of these algorithms, and the effect of normalization methods, while modeling variables that impact deconvolution performance, including cell abundance, cell type similarity, reference panel size, method for methylome profiling (array or sequencing), and technical variation. We observe differences in algorithm performance depending on each these variables, emphasizing the need for tailoring deconvolution analyses. The complexity of the reference, marker selection method, number of marker loci and, for sequencing-based assays, sequencing depth have a marked influence on performance. By developing handles to select the optimal analysis configuration, we provide a valuable source of information for studies aiming to deconvolve array- or sequencing-based methylation data.
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Affiliation(s)
- Kobe De Ridder
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium
| | - Huiwen Che
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium
| | - Kaat Leroy
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium
| | - Bernard Thienpont
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium.
- KU Leuven Institute for Single Cell Omics (LISCO), KU Leuven, 3000, Leuven, Belgium.
- KU Leuven Cancer Institute (LKI), KU Leuven, 3000, Leuven, Belgium.
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2
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Zhou M, Tamburini I, Van C, Molendijk J, Nguyen CM, Chang IYY, Johnson C, Velez LM, Cheon Y, Yeo R, Bae H, Le J, Larson N, Pulido R, Nascimento-Filho CHV, Jang C, Marazzi I, Justice J, Pannunzio N, Hevener AL, Sparks L, Kershaw EE, Nicholas D, Parker BL, Masri S, Seldin MM. Leveraging inter-individual transcriptional correlation structure to infer discrete signaling mechanisms across metabolic tissues. eLife 2024; 12:RP88863. [PMID: 38224289 PMCID: PMC10945578 DOI: 10.7554/elife.88863] [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] [Indexed: 01/16/2024] Open
Abstract
Inter-organ communication is a vital process to maintain physiologic homeostasis, and its dysregulation contributes to many human diseases. Given that circulating bioactive factors are stable in serum, occur naturally, and are easily assayed from blood, they present obvious focal molecules for therapeutic intervention and biomarker development. Recently, studies have shown that secreted proteins mediating inter-tissue signaling could be identified by 'brute force' surveys of all genes within RNA-sequencing measures across tissues within a population. Expanding on this intuition, we reasoned that parallel strategies could be used to understand how individual genes mediate signaling across metabolic tissues through correlative analyses of gene variation between individuals. Thus, comparison of quantitative levels of gene expression relationships between organs in a population could aid in understanding cross-organ signaling. Here, we surveyed gene-gene correlation structure across 18 metabolic tissues in 310 human individuals and 7 tissues in 103 diverse strains of mice fed a normal chow or high-fat/high-sucrose (HFHS) diet. Variation of genes such as FGF21, ADIPOQ, GCG, and IL6 showed enrichments which recapitulate experimental observations. Further, similar analyses were applied to explore both within-tissue signaling mechanisms (liver PCSK9) and genes encoding enzymes producing metabolites (adipose PNPLA2), where inter-individual correlation structure aligned with known roles for these critical metabolic pathways. Examination of sex hormone receptor correlations in mice highlighted the difference of tissue-specific variation in relationships with metabolic traits. We refer to this resource as gene-derived correlations across tissues (GD-CAT) where all tools and data are built into a web portal enabling users to perform these analyses without a single line of code (gdcat.org). This resource enables querying of any gene in any tissue to find correlated patterns of genes, cell types, pathways, and network architectures across metabolic organs.
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Affiliation(s)
- Mingqi Zhou
- Department of Biological Chemistry, UC IrvineIrvineUnited States
- Center for Epigenetics and Metabolism, UC IrvineIrvineUnited States
| | - Ian Tamburini
- Department of Biological Chemistry, UC IrvineIrvineUnited States
- Center for Epigenetics and Metabolism, UC IrvineIrvineUnited States
| | - Cassandra Van
- Center for Epigenetics and Metabolism, UC IrvineIrvineUnited States
| | - Jeffrey Molendijk
- Department of Anatomy and Physiology, University of MelbourneMelbourneAustralia
| | - Christy M Nguyen
- Department of Biological Chemistry, UC IrvineIrvineUnited States
- Center for Epigenetics and Metabolism, UC IrvineIrvineUnited States
| | | | - Casey Johnson
- Department of Biological Chemistry, UC IrvineIrvineUnited States
- Center for Epigenetics and Metabolism, UC IrvineIrvineUnited States
| | - Leandro M Velez
- Department of Biological Chemistry, UC IrvineIrvineUnited States
- Center for Epigenetics and Metabolism, UC IrvineIrvineUnited States
| | - Youngseo Cheon
- Department of Biological Chemistry, UC IrvineIrvineUnited States
- Center for Epigenetics and Metabolism, UC IrvineIrvineUnited States
| | - Reichelle Yeo
- Translational Research Institute, AdventHealthOrlandoUnited States
| | - Hosung Bae
- Department of Biological Chemistry, UC IrvineIrvineUnited States
- Center for Epigenetics and Metabolism, UC IrvineIrvineUnited States
| | - Johnny Le
- Department of Biological Chemistry, UC IrvineIrvineUnited States
- Center for Epigenetics and Metabolism, UC IrvineIrvineUnited States
| | - Natalie Larson
- Department of Biological Chemistry, UC IrvineIrvineUnited States
- Center for Epigenetics and Metabolism, UC IrvineIrvineUnited States
| | - Ron Pulido
- Department of Biological Chemistry, UC IrvineIrvineUnited States
- Center for Epigenetics and Metabolism, UC IrvineIrvineUnited States
| | - Carlos HV Nascimento-Filho
- Department of Biological Chemistry, UC IrvineIrvineUnited States
- Center for Epigenetics and Metabolism, UC IrvineIrvineUnited States
| | - Cholsoon Jang
- Department of Biological Chemistry, UC IrvineIrvineUnited States
- Center for Epigenetics and Metabolism, UC IrvineIrvineUnited States
| | - Ivan Marazzi
- Department of Biological Chemistry, UC IrvineIrvineUnited States
- Center for Epigenetics and Metabolism, UC IrvineIrvineUnited States
| | - Jamie Justice
- Veterans Administration Greater Los Angeles Healthcare System, Geriatric Research Education and Clinical Center (GRECC)Los AngelesUnited States
| | - Nicholas Pannunzio
- Divison of Hematology/Oncology, Department of Medicine, UC Irvine HealthIrvineUnited States
| | - Andrea L Hevener
- Department of Medicine, Division of Endocrinology, Diabetes, and Hypertension, David Geffen School of Medicine at UCLALos AngelesUnited States
- Iris Cantor-UCLA Women’s Health Research Center, David Geffen School of Medicine at UCLALos AngelesUnited States
| | - Lauren Sparks
- Translational Research Institute, AdventHealthOrlandoUnited States
| | - Erin E Kershaw
- Division of Endocrinology, Department of Medicine, University of PittsburgPittsburghUnited States
| | - Dequina Nicholas
- Department of Biological Chemistry, UC IrvineIrvineUnited States
- Center for Epigenetics and Metabolism, UC IrvineIrvineUnited States
- Department of Molecular Biology and Biochemistry, School of Biological Sciences, University of California IrvineIrvineUnited States
| | - Benjamin L Parker
- Department of Anatomy and Physiology, University of MelbourneMelbourneAustralia
| | - Selma Masri
- Department of Biological Chemistry, UC IrvineIrvineUnited States
- Center for Epigenetics and Metabolism, UC IrvineIrvineUnited States
| | - Marcus M Seldin
- Department of Biological Chemistry, UC IrvineIrvineUnited States
- Center for Epigenetics and Metabolism, UC IrvineIrvineUnited States
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3
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Zhou M, Tamburini IJ, Van C, Molendijk J, Nguyen CM, Chang IYY, Johnson C, Velez LM, Cheon Y, Yeo RX, Bae H, Le J, Larson N, Pulido R, Filho C, Jang C, Marazzi I, Justice JN, Pannunzio N, Hevener A, Sparks LM, Kershaw EE, Nicholas D, Parker B, Masri S, Seldin M. Leveraging inter-individual transcriptional correlation structure to infer discrete signaling mechanisms across metabolic tissues. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.10.540142. [PMID: 37214953 PMCID: PMC10197628 DOI: 10.1101/2023.05.10.540142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Abstract/IntroductionInter-organ communication is a vital process to maintain physiologic homeostasis, and its dysregulation contributes to many human diseases. Beginning with the discovery of insulin over a century ago, characterization of molecules responsible for signal between tissues has required careful and elegant experimentation where these observations have been integral to deciphering physiology and disease. Given that circulating bioactive factors are stable in serum, occur naturally, and are easily assayed from blood, they present obvious focal molecules for therapeutic intervention and biomarker development. For example, physiologic dissection of the actions of soluble proteins such as proprotein convertase subtilisin/kexin type 9 (PCSK9) and glucagon-like peptide 1 (GLP1) have yielded among the most promising therapeutics to treat cardiovascular disease and obesity, respectively1–4. A major obstacle in the characterization of such soluble factors is that defining their tissues and pathways of action requires extensive experimental testing in cells and animal models. Recently, studies have shown that secreted proteins mediating inter-tissue signaling could be identified by “brute-force” surveys of all genes within RNA-sequencing measures across tissues within a population5–9. Expanding on this intuition, we reasoned that parallel strategies could be used to understand how individual genes mediate signaling across metabolic tissues through correlative analyses of gene variation between individuals. Thus, comparison of quantitative levels of gene expression relationships between organs in a population could aid in understanding cross-organ signaling. Here, we surveyed gene-gene correlation structure across 18 metabolic tissues in 310 human individuals and 7 tissues in 103 diverse strains of mice fed a normal chow or HFHS diet. Variation of genes such asFGF21, ADIPOQ, GCGandIL6showed enrichments which recapitulate experimental observations. Further, similar analyses were applied to explore both within-tissue signaling mechanisms (liverPCSK9) as well as genes encoding enzymes producing metabolites (adiposePNPLA2), where inter-individual correlation structure aligned with known roles for these critical metabolic pathways. Examination of sex hormone receptor correlations in mice highlighted the difference of tissue-specific variation in relationships with metabolic traits. We refer to this resource asGene-DerivedCorrelationsAcrossTissues (GD-CAT) where all tools and data are built into a web portal enabling users to perform these analyses without a single line of code (gdcat.org). This resource enables querying of any gene in any tissue to find correlated patterns of genes, cell types, pathways and network architectures across metabolic organs.
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Affiliation(s)
- Mingqi Zhou
- Department of Biological Chemistry, UC Irvine. Irvine, CA, USA
- Center for Epigenetics and Metabolism, UC Irvine. Irvine, CA, USA
| | - Ian J. Tamburini
- Department of Biological Chemistry, UC Irvine. Irvine, CA, USA
- Center for Epigenetics and Metabolism, UC Irvine. Irvine, CA, USA
| | - Cassandra Van
- Department of Biological Chemistry, UC Irvine. Irvine, CA, USA
- Center for Epigenetics and Metabolism, UC Irvine. Irvine, CA, USA
| | - Jeffrey Molendijk
- Department of Anatomy and Physiology, University of Melbourne, Melbourne, VIC, Australia
| | - Christy M Nguyen
- Department of Biological Chemistry, UC Irvine. Irvine, CA, USA
- Center for Epigenetics and Metabolism, UC Irvine. Irvine, CA, USA
| | | | - Casey Johnson
- Department of Biological Chemistry, UC Irvine. Irvine, CA, USA
- Center for Epigenetics and Metabolism, UC Irvine. Irvine, CA, USA
| | - Leandro M. Velez
- Department of Biological Chemistry, UC Irvine. Irvine, CA, USA
- Center for Epigenetics and Metabolism, UC Irvine. Irvine, CA, USA
| | - Youngseo Cheon
- Department of Biological Chemistry, UC Irvine. Irvine, CA, USA
- Center for Epigenetics and Metabolism, UC Irvine. Irvine, CA, USA
| | - Reichelle X. Yeo
- Translational Research Institute, AdventHealth, Orlando, FL, USA
| | - Hosung Bae
- Department of Biological Chemistry, UC Irvine. Irvine, CA, USA
- Center for Epigenetics and Metabolism, UC Irvine. Irvine, CA, USA
| | - Johnny Le
- Department of Biological Chemistry, UC Irvine. Irvine, CA, USA
- Center for Epigenetics and Metabolism, UC Irvine. Irvine, CA, USA
| | - Natalie Larson
- Department of Biological Chemistry, UC Irvine. Irvine, CA, USA
- Center for Epigenetics and Metabolism, UC Irvine. Irvine, CA, USA
| | - Ron Pulido
- Department of Biological Chemistry, UC Irvine. Irvine, CA, USA
- Center for Epigenetics and Metabolism, UC Irvine. Irvine, CA, USA
| | - Carlos Filho
- Department of Biological Chemistry, UC Irvine. Irvine, CA, USA
- Center for Epigenetics and Metabolism, UC Irvine. Irvine, CA, USA
| | - Cholsoon Jang
- Department of Biological Chemistry, UC Irvine. Irvine, CA, USA
- Center for Epigenetics and Metabolism, UC Irvine. Irvine, CA, USA
| | - Ivan Marazzi
- Department of Biological Chemistry, UC Irvine. Irvine, CA, USA
- Center for Epigenetics and Metabolism, UC Irvine. Irvine, CA, USA
| | - Jamie N. Justice
- Veterans Administration Greater Los Angeles Healthcare System, Geriatric Research Education and Clinical Center (GRECC), Los Angeles, CA, USA
| | - Nicholas Pannunzio
- Department of Biological Chemistry, UC Irvine. Irvine, CA, USA
- Center for Epigenetics and Metabolism, UC Irvine. Irvine, CA, USA
| | - Andrea Hevener
- Department of Medicine, Division of Endocrinology, Diabetes, and Hypertension, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Iris Cantor-UCLA Women’s Health Research Center, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Lauren M. Sparks
- Translational Research Institute, AdventHealth, Orlando, FL, USA
| | - Erin E. Kershaw
- Department of Internal Medicine, Section On Gerontology and Geriatric Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Dequina Nicholas
- Division of Endocrinology, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Benjamin Parker
- Department of Anatomy and Physiology, University of Melbourne, Melbourne, VIC, Australia
| | - Selma Masri
- Department of Biological Chemistry, UC Irvine. Irvine, CA, USA
- Center for Epigenetics and Metabolism, UC Irvine. Irvine, CA, USA
| | - Marcus Seldin
- Department of Biological Chemistry, UC Irvine. Irvine, CA, USA
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4
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Nava A, Alves da Quinta D, Prato L, Girotti R, Moron G, Llera AS, Fernández EA. Novel evaluation approach for molecular signature-based deconvolution methods. J Biomed Inform 2023; 142:104387. [PMID: 37172634 DOI: 10.1016/j.jbi.2023.104387] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 03/17/2023] [Accepted: 05/07/2023] [Indexed: 05/15/2023]
Abstract
The tumoral immune microenvironment (TIME) plays a key role in prognosis, therapeutic approach and pathophysiological understanding over oncological processes. Several computational immune cell-type deconvolution methods (DM), supported by diverse molecular signatures (MS), have been developed to uncover such TIME interplay from RNA-seq tumor biopsies. MS-DM pairs were benchmarked against each other by means of different metrics, such as Pearson's correlation, R2 and RMSE, but these only evaluate the linear association of the estimated proportion related to the expected one, missing the analysis of prediction-dependent bias trends and cell identification accuracy. We present a novel protocol composed of four tests allowing appropriate evaluation of the cell type identification performance and proportion prediction accuracy of molecular signature-deconvolution method pair by means of certainty and confidence cell-type identification scores (F1-score, distance to the optimal point and error rates) as well the Bland-Altman method for error-trend analysis. Our protocol was used to benchmark six state-of-the-art DMs (CIBERSORTx, DCQ, DeconRNASeq, EPIC, MIXTURE and quanTIseq) paired to five murine tissue-specific MSs, revealing a systematic overestimation of the number of different cell types across almost all methods.
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Affiliation(s)
- A Nava
- Fundación Instituto Leloir-CONICET, Buenos Aires, Argentina; Fundación Huésped, Buenos Aires, Argentina
| | - D Alves da Quinta
- Fundación Instituto Leloir-CONICET, Buenos Aires, Argentina; Universidad Argentina de la Empresa (UADE). Instituto de Tecnología (INTEC), Buenos Aires, Argentina
| | - L Prato
- Universidad de Villa María, Córdoba, Argentina
| | - R Girotti
- Universidad Argentina de la Empresa (UADE). Instituto de Tecnología (INTEC), Buenos Aires, Argentina
| | - G Moron
- Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina; Centro de Investigaciones en Bioquímica Clínica e Inmunología, CONICET, Córdoba, Argentina
| | - A S Llera
- Fundación Instituto Leloir-CONICET, Buenos Aires, Argentina
| | - E A Fernández
- Facultad de Ingeniería, Carrera de Bioinformática, Universidad Católica de Córdoba (UCC), Córdoba, Argentina; Facultad de Ciencias Exactas Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba, Argentina; Centro de Investigaciòn en Inmunología y Enfermedades Infecciosas, UCC, CONICET, Córdoba, Argentina.
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5
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Hou H, Chan C, Yuki KE, Sokolowski D, Roy A, Qu R, Uusküla-Reimand L, Faykoo-Martinez M, Hudson M, Corre C, Goldenberg A, Zhang Z, Palmert MR, Wilson MD. Postnatal developmental trajectory of sex-biased gene expression in the mouse pituitary gland. Biol Sex Differ 2022; 13:57. [PMID: 36221127 PMCID: PMC9552479 DOI: 10.1186/s13293-022-00467-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 09/30/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The pituitary gland regulates essential physiological processes such as growth, pubertal onset, stress response, metabolism, reproduction, and lactation. While sex biases in these functions and hormone production have been described, the underlying identity, temporal deployment, and cell-type specificity of sex-biased pituitary gene regulatory networks are not fully understood. METHODS To capture sex differences in pituitary gene regulation dynamics during postnatal development, we performed 3' untranslated region sequencing and small RNA sequencing to ascertain gene and microRNA expression, respectively, across five postnatal ages (postnatal days 12, 22, 27, 32, 37) that span the pubertal transition in female and male C57BL/6J mouse pituitaries (n = 5-6 biological replicates for each sex at each age). RESULTS We observed over 900 instances of sex-biased gene expression and 17 sex-biased microRNAs, with the majority of sex differences occurring with puberty. Using miRNA-gene target interaction databases, we identified 18 sex-biased genes that were putative targets of 5 sex-biased microRNAs. In addition, by combining our bulk RNA-seq with publicly available male and female mouse pituitary single-nuclei RNA-seq data, we obtained evidence that cell-type proportion sex differences exist prior to puberty and persist post-puberty for three major hormone-producing cell types: somatotropes, lactotropes, and gonadotropes. Finally, we identified sex-biased genes in these three pituitary cell types after accounting for cell-type proportion differences between sexes. CONCLUSION Our study reveals the identity and postnatal developmental trajectory of sex-biased gene expression in the mouse pituitary. This work also highlights the importance of considering sex biases in cell-type composition when understanding sex differences in the processes regulated by the pituitary gland.
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Affiliation(s)
- Huayun Hou
- Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada
| | - Cadia Chan
- Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Donnelly Centre for Cellular and Biomolecular Research, Toronto, ON, Canada
| | - Kyoko E Yuki
- Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada
| | - Dustin Sokolowski
- Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Anna Roy
- Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada
| | - Rihao Qu
- Interdepartmental Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA.,Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | | | - Mariela Faykoo-Martinez
- Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada.,Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Matt Hudson
- Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Christina Corre
- Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada.,Division of Endocrinology, The Hospital for Sick Children, Toronto, ON, Canada.,Departments of Pediatrics and Physiology, University of Toronto, Toronto, ON, Canada
| | - Anna Goldenberg
- Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada.,Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | - Zhaolei Zhang
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | - Mark R Palmert
- Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada. .,Division of Endocrinology, The Hospital for Sick Children, Toronto, ON, Canada. .,Institute of Medical Science, University of Toronto, Toronto, ON, Canada. .,Departments of Pediatrics and Physiology, University of Toronto, Toronto, ON, Canada.
| | - Michael D Wilson
- Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
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6
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Velez LM, Van C, Moore T, Zhou Z, Johnson C, Hevener AL, Seldin MM. Genetic variation of putative myokine signaling is dominated by biological sex and sex hormones. eLife 2022; 11:e76887. [PMID: 35416774 PMCID: PMC9094747 DOI: 10.7554/elife.76887] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 04/12/2022] [Indexed: 11/18/2022] Open
Abstract
Skeletal muscle plays an integral role in coordinating physiological homeostasis, where signaling to other tissues via myokines allows for coordination of complex processes. Here, we aimed to leverage natural genetic correlation structure of gene expression both within and across tissues to understand how muscle interacts with metabolic tissues. Specifically, we performed a survey of genetic correlations focused on myokine gene regulation, muscle cell composition, cross-tissue signaling, and interactions with genetic sex in humans. While expression levels of a majority of myokines and cell proportions within skeletal muscle showed little relative differences between males and females, nearly all significant cross-tissue enrichments operated in a sex-specific or hormone-dependent fashion; in particular, with estradiol. These sex- and hormone-specific effects were consistent across key metabolic tissues: liver, pancreas, hypothalamus, intestine, heart, visceral, and subcutaneous adipose tissue. To characterize the role of estradiol receptor signaling on myokine expression, we generated male and female mice which lack estrogen receptor α specifically in skeletal muscle (MERKO) and integrated with human data. These analyses highlighted potential mechanisms of sex-dependent myokine signaling conserved between species, such as myostatin enriched for divergent substrate utilization pathways between sexes. Several other putative sex-dependent mechanisms of myokine signaling were uncovered, such as muscle-derived tumor necrosis factor alpha (TNFA) enriched for stronger inflammatory signaling in females compared to males and GPX3 as a male-specific link between glycolytic fiber abundance and hepatic inflammation. Collectively, we provide a population genetics framework for inferring muscle signaling to metabolic tissues in humans. We further highlight sex and estradiol receptor signaling as critical variables when assaying myokine functions and how changes in cell composition are predicted to impact other metabolic organs.
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Affiliation(s)
- Leandro M Velez
- Department of Biological Chemistry, University of California, IrvineIrvineUnited States
- Center for Epigenetics and Metabolism, University of California IrvineIrvineUnited States
| | - Cassandra Van
- Department of Biological Chemistry, University of California, IrvineIrvineUnited States
- Center for Epigenetics and Metabolism, University of California IrvineIrvineUnited States
| | - Timothy Moore
- Department of Medicine, Division of Cardiology, David Geffen School of Medicine at UCLALos AngelesUnited States
| | - Zhenqi Zhou
- Department of Medicine, Division of Endocrinology, Diabetes and Hypertension, David Geffen School of Medicine at UCLALos AngelesUnited States
| | - Casey Johnson
- Department of Biological Chemistry, University of California, IrvineIrvineUnited States
- Center for Epigenetics and Metabolism, University of California IrvineIrvineUnited States
| | - Andrea L Hevener
- Department of Medicine, Division of Endocrinology, Diabetes and Hypertension, David Geffen School of Medicine at UCLALos AngelesUnited States
- Iris Cantor-UCLA Women’s Health Research Center, David Geffen School of Medicine at UCLALos AngelesUnited States
| | - Marcus M Seldin
- Department of Biological Chemistry, University of California, IrvineIrvineUnited States
- Center for Epigenetics and Metabolism, University of California IrvineIrvineUnited States
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7
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Ebersole JL, Kirakodu S, Nguyen L, Gonzalez OA. Gingival Transcriptome of Innate Antimicrobial Factors and the Oral Microbiome With Aging and Periodontitis. FRONTIERS IN ORAL HEALTH 2022; 3:817249. [PMID: 35330821 PMCID: PMC8940521 DOI: 10.3389/froh.2022.817249] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 02/04/2022] [Indexed: 12/30/2022] Open
Abstract
The epithelial barrier at mucosal sites comprises an important mechanical protective feature of innate immunity, and is intimately involved in communicating signals of infection/tissue damage to inflammatory and immune cells in these local environments. A wide array of antimicrobial factors (AMF) exist at mucosal sites and in secretions that contribute to this innate immunity. A non-human primate model of ligature-induced periodontitis was used to explore characteristics of the antimicrobial factor transcriptome (n = 114 genes) of gingival biopsies in health, initiation and progression of periodontal lesions, and in samples with clinical resolution. Age effects and relationship of AMF to the dominant members of the oral microbiome were also evaluated. AMF could be stratified into 4 groups with high (n = 22), intermediate (n = 29), low (n = 18) and very low (n = 45) expression in healthy adult tissues. A subset of AMF were altered in healthy young, adolescent and aged samples compared with adults (e.g., APP, CCL28, DEFB113, DEFB126, FLG2, PRH1) and were affected across multiple age groups. With disease, a greater number of the AMF genes were affected in the adult and aged samples with skewing toward decreased expression, for example WDC12, PGLYRP3, FLG2, DEFB128, and DEF4A/B, with multiple age groups. Few of the AMF genes showed a >2-fold increase with disease in any age group. Selected AMF exhibited significant positive correlations across the array of AMF that varied in health and disease. In contrast, a rather limited number of the AMF significantly correlated with members of the microbiome; most prominent in healthy samples. These correlated microbes were different in younger and older samples and differed in health, disease and resolution samples. The findings supported effects of age on the expression of AMF genes in healthy gingival tissues showing a relationship to members of the oral microbiome. Furthermore, a dynamic expression of AMF genes was related to the disease process and showed similarities across the age groups, except for low/very low expressed genes that were unaffected in young samples. Targeted assessment of AMF members from this large array may provide insight into differences in disease risk and biomolecules that provide some discernment of early transition to disease.
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Affiliation(s)
- Jeffrey L. Ebersole
- Department of Biomedical Sciences, School of Dental Medicine, University of Nevada Las Vegas, Las Vegas, NV, United States
- Center for Oral Health Research, College of Dentistry, University of Kentucky, Lexington, KY, United States
- *Correspondence: Jeffrey L. Ebersole
| | - Sreenatha Kirakodu
- Center for Oral Health Research, College of Dentistry, University of Kentucky, Lexington, KY, United States
| | - Linh Nguyen
- Department of Biomedical Sciences, School of Dental Medicine, University of Nevada Las Vegas, Las Vegas, NV, United States
| | - Octavio A. Gonzalez
- Center for Oral Health Research, College of Dentistry, University of Kentucky, Lexington, KY, United States
- Division of Periodontology, College of Dentistry, University of Kentucky, Lexington, KY, United States
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8
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Ebersole JL, Kirakodu SS, Orraca L, Gonzalez Martinez J, Gonzalez OA. Gingival transcriptomics of follicular T cell footprints in progressing periodontitis. Clin Exp Immunol 2021; 204:373-395. [PMID: 33565609 DOI: 10.1111/cei.13584] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 02/02/2021] [Accepted: 02/04/2021] [Indexed: 12/22/2022] Open
Abstract
Follicular helper T cells (Tfh) cells have been identified in the circulation and in tertiary lymphoid structures in chronic inflammation. Gingival tissues with periodontitis reflect chronic inflammation, so genomic footprints of Tfh cells should occur in these tissues and may differ related to aging effects. Macaca mulatta were used in a ligature-induced periodontitis model [adult group (aged 12-23 years); young group (aged 3-7 years)]. Gingival tissue and subgingival microbiome samples were obtained at matched healthy ligature-induced disease and clinical resolution sites. Microarray analysis examined Tfh genes (n = 54) related to microbiome characteristics documented using 16S MiSeq. An increase in the major transcription factor of Tfh cells, BCL6, was found with disease in both adult and young animals, while master transcription markers of other T cell subsets were either decreased or showed minimal change. Multiple Tfh-related genes, including surface receptors and transcription factors, were also significantly increased during disease. Specific microbiome patterns were significantly associated with profiles indicative of an increased presence/function of Tfh cells. Importantly, unique microbial complexes showed distinctive patterns of interaction with Tfh genes differing in health and disease and with the age of the animals. An increase in Tfh cell responsiveness occurred in the progression of periodontitis, affected by age and related to specific microbial complexes in the oral microbiome. The capacity of gingival Tfh cells to contribute to localized B cell activation and active antibody responses, including affinity maturation, may be critical for controlling periodontal lesions and contributing to limiting and/or resolving the lesions.
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Affiliation(s)
- J L Ebersole
- Department of Biomedical Science, School of Dental Medicine, University of Nevada Las Vegas, Las Vegas, NV, USA
| | - S S Kirakodu
- Center for Oral Health Research, College of Dentistry, University of Kentucky, Lexington, KY, USA
| | - L Orraca
- School of Dental Medicine, University of Puerto Rico, San Juan, PR, USA
| | - J Gonzalez Martinez
- Caribbean Primate Research Center, University of Puerto Rico, Toa Baja, PR, USA
| | - O A Gonzalez
- Center for Oral Health Research, College of Dentistry, University of Kentucky, Lexington, KY, USA.,Division of Periodontology, College of Dentistry, University of Kentucky, Lexington, KY, USA
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9
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Craven KE, Gökmen-Polar Y, Badve SS. CIBERSORT analysis of TCGA and METABRIC identifies subgroups with better outcomes in triple negative breast cancer. Sci Rep 2021; 11:4691. [PMID: 33633150 PMCID: PMC7907367 DOI: 10.1038/s41598-021-83913-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 02/04/2021] [Indexed: 02/07/2023] Open
Abstract
Studies have shown that the presence of tumor infiltrating lymphocytes (TILs) in Triple Negative Breast Cancer (TNBC) is associated with better prognosis. However, the molecular mechanisms underlying these immune cell differences are not well delineated. In this study, analysis of hematoxylin and eosin images from The Cancer Genome Atlas (TCGA) breast cancer cohort failed to show a prognostic benefit of TILs in TNBC, whereas CIBERSORT analysis, which quantifies the proportion of each immune cell type, demonstrated improved overall survival in TCGA TNBC samples with increased CD8 T cells or CD8 plus CD4 memory activated T cells and in Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) TNBC samples with increased gamma delta T cells. Twenty-five genes showed mutational frequency differences between the TCGA high and low T cell groups, and many play important roles in inflammation or immune evasion (ATG2B, HIST1H2BC, PKD1, PIKFYVE, TLR3, NOTCH3, GOLGB1, CREBBP). Identification of these mutations suggests novel mechanisms by which the cancer cells attract immune cells and by which they evade or dampen the immune system during the cancer immunoediting process. This study suggests that integration of mutations with CIBERSORT analysis could provide better prediction of outcomes and novel therapeutic targets in TNBC cases.
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Affiliation(s)
- Kelly E Craven
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Yesim Gökmen-Polar
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Sunil S Badve
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, USA. .,Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, USA. .,Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, IN, 46202, USA.
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10
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Sokolowski DJ, Faykoo-Martinez M, Erdman L, Hou H, Chan C, Zhu H, Holmes MM, Goldenberg A, Wilson MD. Single-cell mapper (scMappR): using scRNA-seq to infer the cell-type specificities of differentially expressed genes. NAR Genom Bioinform 2021; 3:lqab011. [PMID: 33655208 PMCID: PMC7902236 DOI: 10.1093/nargab/lqab011] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 12/23/2020] [Accepted: 02/04/2021] [Indexed: 12/11/2022] Open
Abstract
RNA sequencing (RNA-seq) is widely used to identify differentially expressed genes (DEGs) and reveal biological mechanisms underlying complex biological processes. RNA-seq is often performed on heterogeneous samples and the resulting DEGs do not necessarily indicate the cell-types where the differential expression occurred. While single-cell RNA-seq (scRNA-seq) methods solve this problem, technical and cost constraints currently limit its widespread use. Here we present single cell Mapper (scMappR), a method that assigns cell-type specificity scores to DEGs obtained from bulk RNA-seq by leveraging cell-type expression data generated by scRNA-seq and existing deconvolution methods. After evaluating scMappR with simulated RNA-seq data and benchmarking scMappR using RNA-seq data obtained from sorted blood cells, we asked if scMappR could reveal known cell-type specific changes that occur during kidney regeneration. scMappR appropriately assigned DEGs to cell-types involved in kidney regeneration, including a relatively small population of immune cells. While scMappR can work with user-supplied scRNA-seq data, we curated scRNA-seq expression matrices for ∼100 human and mouse tissues to facilitate its stand-alone use with bulk RNA-seq data from these species. Overall, scMappR is a user-friendly R package that complements traditional differential gene expression analysis of bulk RNA-seq data.
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Affiliation(s)
- Dustin J Sokolowski
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | | | - Lauren Erdman
- Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, M5G 0A4, Canada
| | - Huayun Hou
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Cadia Chan
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Helen Zhu
- Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Melissa M Holmes
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada
| | - Anna Goldenberg
- Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, M5G 0A4, Canada
| | - Michael D Wilson
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
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11
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Chen Z, Wu A. Progress and challenge for computational quantification of tissue immune cells. Brief Bioinform 2021; 22:6065002. [PMID: 33401306 DOI: 10.1093/bib/bbaa358] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 10/23/2020] [Accepted: 11/07/2020] [Indexed: 12/28/2022] Open
Abstract
Tissue immune cells have long been recognized as important regulators for the maintenance of balance in the body system. Quantification of the abundance of different immune cells will provide enhanced understanding of the correlation between immune cells and normal or abnormal situations. Currently, computational methods to predict tissue immune cell compositions from bulk transcriptomes have been largely developed. Therefore, summarizing the advantages and disadvantages is appropriate. In addition, an examination of the challenges and possible solutions for these computational models will assist the development of this field. The common hypothesis of these models is that the expression of signature genes for immune cell types might represent the proportion of immune cells that contribute to the tissue transcriptome. In general, we grouped all reported tools into three groups, including reference-free, reference-based scoring and reference-based deconvolution methods. In this review, a summary of all the currently reported computational immune cell quantification tools and their applications, limitations, and perspectives are presented. Furthermore, some critical problems are found that have limited the performance and application of these models, including inadequate immune cell type, the collinearity problem, the impact of the tissue environment on the immune cell expression level, and the deficiency of standard datasets for model validation. To address these issues, tissue specific training datasets that include all known immune cells, a hierarchical computational framework, and benchmark datasets including both tissue expression profiles and the abundances of all the immune cells are proposed to further promote the development of this field.
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Affiliation(s)
- Ziyi Chen
- Suzhou Institute of Systems Medicine, Center for Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Jiangsu, Suzhou, China
| | - Aiping Wu
- Suzhou Institute of Systems Medicine, Center for Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Jiangsu, Suzhou, China
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12
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Danziger SA, McConnell M, Gockley J, Young MH, Rosenthal A, Schmitz F, Reiss DJ, Farmer P, Alapat DV, Singh A, Ashby C, Bauer M, Ren Y, Smith K, Couto SS, van Rhee F, Davies F, Zangari M, Petty N, Orlowski RZ, Dhodapkar MV, Copeland WB, Fox B, Hoering A, Fitch A, Newhall K, Barlogie B, Trotter MWB, Hershberg RM, Walker BA, Dervan AP, Ratushny AV, Morgan GJ. Bone marrow microenvironments that contribute to patient outcomes in newly diagnosed multiple myeloma: A cohort study of patients in the Total Therapy clinical trials. PLoS Med 2020; 17:e1003323. [PMID: 33147277 PMCID: PMC7641353 DOI: 10.1371/journal.pmed.1003323] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 09/18/2020] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND The tumor microenvironment (TME) is increasingly appreciated as an important determinant of cancer outcome, including in multiple myeloma (MM). However, most myeloma microenvironment studies have been based on bone marrow (BM) aspirates, which often do not fully reflect the cellular content of BM tissue itself. To address this limitation in myeloma research, we systematically characterized the whole bone marrow (WBM) microenvironment during premalignant, baseline, on treatment, and post-treatment phases. METHODS AND FINDINGS Between 2004 and 2019, 998 BM samples were taken from 436 patients with newly diagnosed MM (NDMM) at the University of Arkansas for Medical Sciences in Little Rock, Arkansas, United States of America. These patients were 61% male and 39% female, 89% White, 8% Black, and 3% other/refused, with a mean age of 58 years. Using WBM and matched cluster of differentiation (CD)138-selected tumor gene expression to control for tumor burden, we identified a subgroup of patients with an adverse TME associated with 17 fewer months of progression-free survival (PFS) (95% confidence interval [CI] 5-29, 49-69 versus 70-82 months, χ2 p = 0.001) and 15 fewer months of overall survival (OS; 95% CI -1 to 31, 92-120 versus 113-129 months, χ2 p = 0.036). Using immunohistochemistry-validated computational tools that identify distinct cell types from bulk gene expression, we showed that the adverse outcome was correlated with elevated CD8+ T cell and reduced granulocytic cell proportions. This microenvironment develops during the progression of premalignant to malignant disease and becomes less prevalent after therapy, in which it is associated with improved outcomes. In patients with quantified International Staging System (ISS) stage and 70-gene Prognostic Risk Score (GEP-70) scores, taking the microenvironment into consideration would have identified an additional 40 out of 290 patients (14%, premutation p = 0.001) with significantly worse outcomes (PFS, 95% CI 6-36, 49-73 versus 74-90 months) who were not identified by existing clinical (ISS stage III) and tumor (GEP-70) criteria as high risk. The main limitations of this study are that it relies on computationally identified cell types and that patients were treated with thalidomide rather than current therapies. CONCLUSIONS In this study, we observe that granulocyte signatures in the MM TME contribute to a more accurate prognosis. This implies that future researchers and clinicians treating patients should quantify TME components, in particular monocytes and granulocytes, which are often ignored in microenvironment studies.
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Affiliation(s)
- Samuel A. Danziger
- Bristol Myers Squibb, Seattle, Washington, United States of America
- * E-mail: (SAD); (AVR); (GJM)
| | - Mark McConnell
- Bristol Myers Squibb, Seattle, Washington, United States of America
| | - Jake Gockley
- Sage Bionetworks, Seattle, Washington, United States of America
| | - Mary H. Young
- Sage Bionetworks, Seattle, Washington, United States of America
| | - Adam Rosenthal
- Cancer Research and Biostatistics, Seattle, Washington, United States of America
| | - Frank Schmitz
- Sage Bionetworks, Seattle, Washington, United States of America
| | - David J. Reiss
- Bristol Myers Squibb, Seattle, Washington, United States of America
| | - Phil Farmer
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Daisy V. Alapat
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Amrit Singh
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Cody Ashby
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Michael Bauer
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Yan Ren
- Bristol Myers Squibb, Seattle, Washington, United States of America
| | - Kelsie Smith
- Bristol Myers Squibb, Seattle, Washington, United States of America
| | | | - Frits van Rhee
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Faith Davies
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Maurizio Zangari
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Nathan Petty
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Robert Z. Orlowski
- The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Madhav V. Dhodapkar
- Winship Cancer Institute, Emory University, Atlanta, Georgia, United States of America
| | | | - Brian Fox
- Bristol Myers Squibb, Seattle, Washington, United States of America
| | - Antje Hoering
- Cancer Research and Biostatistics, Seattle, Washington, United States of America
| | - Alison Fitch
- Bristol Myers Squibb, Seattle, Washington, United States of America
| | - Katie Newhall
- Sage Bionetworks, Seattle, Washington, United States of America
| | - Bart Barlogie
- Department of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | | | | | - Brian A. Walker
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | | | - Alexander V. Ratushny
- Bristol Myers Squibb, Seattle, Washington, United States of America
- * E-mail: (SAD); (AVR); (GJM)
| | - Gareth J. Morgan
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
- * E-mail: (SAD); (AVR); (GJM)
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13
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Aguilar B, Gibbs DL, Reiss DJ, McConnell M, Danziger SA, Dervan A, Trotter M, Bassett D, Hershberg R, Ratushny AV, Shmulevich I. A generalizable data-driven multicellular model of pancreatic ductal adenocarcinoma. Gigascience 2020; 9:giaa075. [PMID: 32696951 PMCID: PMC7374045 DOI: 10.1093/gigascience/giaa075] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 02/14/2020] [Accepted: 06/21/2020] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Mechanistic models, when combined with pertinent data, can improve our knowledge regarding important molecular and cellular mechanisms found in cancer. These models make the prediction of tissue-level response to drug treatment possible, which can lead to new therapies and improved patient outcomes. Here we present a data-driven multiscale modeling framework to study molecular interactions between cancer, stromal, and immune cells found in the tumor microenvironment. We also develop methods to use molecular data available in The Cancer Genome Atlas to generate sample-specific models of cancer. RESULTS By combining published models of different cells relevant to pancreatic ductal adenocarcinoma (PDAC), we built an agent-based model of the multicellular pancreatic tumor microenvironment, formally describing cell type-specific molecular interactions and cytokine-mediated cell-cell communications. We used an ensemble-based modeling approach to systematically explore how variations in the tumor microenvironment affect the viability of cancer cells. The results suggest that the autocrine loop involving EGF signaling is a key interaction modulator between pancreatic cancer and stellate cells. EGF is also found to be associated with previously described subtypes of PDAC. Moreover, the model allows a systematic exploration of the effect of possible therapeutic perturbations; our simulations suggest that reducing bFGF secretion by stellate cells will have, on average, a positive impact on cancer apoptosis. CONCLUSIONS The developed framework allows model-driven hypotheses to be generated regarding therapeutically relevant PDAC states with potential molecular and cellular drivers indicating specific intervention strategies.
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Affiliation(s)
- Boris Aguilar
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109, USA
| | - David L Gibbs
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109, USA
| | - David J Reiss
- Bristol-Myers Squibb, 400 Dexter Avenue North, Suite 1200, Seattle, WA 98109, USA
| | - Mark McConnell
- Bristol-Myers Squibb, 400 Dexter Avenue North, Suite 1200, Seattle, WA 98109, USA
| | - Samuel A Danziger
- Bristol-Myers Squibb, 400 Dexter Avenue North, Suite 1200, Seattle, WA 98109, USA
| | - Andrew Dervan
- Bristol-Myers Squibb, 400 Dexter Avenue North, Suite 1200, Seattle, WA 98109, USA
| | - Matthew Trotter
- BMS Center for Innovation and Translational Research Europe (CITRE), Pabellon de Italia, Calle Isaac Newton 4, Sevilla 41092, Spain
| | - Douglas Bassett
- Bristol-Myers Squibb, 400 Dexter Avenue North, Suite 1200, Seattle, WA 98109, USA
| | - Robert Hershberg
- Formerly Celgene Corporation, 400 Dexter Avenue North, Suite 1200, Seattle, WA 98109, USA
| | - Alexander V Ratushny
- Bristol-Myers Squibb, 400 Dexter Avenue North, Suite 1200, Seattle, WA 98109, USA
| | - Ilya Shmulevich
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109, USA
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