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Ahern DT, Bansal P, Faustino IV, Glatt-Deeley HR, Massey R, Kondaveeti Y, Banda EC, Pinter SF. Isogenic hiPSC models of Turner syndrome development reveal shared roles of inactive X and Y in the human cranial neural crest network. bioRxiv 2024:2023.03.08.531747. [PMID: 36945647 PMCID: PMC10028916 DOI: 10.1101/2023.03.08.531747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2023]
Abstract
Modeling the developmental etiology of viable human aneuploidy can be challenging in rodents due to syntenic boundaries, or primate-specific biology. In humans, monosomy-X (45,X) causes Turner syndrome (TS), altering craniofacial, skeletal, endocrine, and cardiovascular development, which in contrast remain unaffected in 39,X-mice. To learn how human monosomy-X may impact early embryonic development, we turned to human 45,X and isogenic euploid induced pluripotent stem cells (hiPSCs) from male and female mosaic donors. Because neural crest (NC) derived cell types are hypothesized to underpin craniofacial and cardiovascular changes in TS, we performed a highly-powered differential expression study on hiPSC-derived anterior neural crest cells (NCCs). Across three independent isogenic panels, 45,X NCCs show impaired acquisition of PAX7+SOX10+ markers, and disrupted expression of other NCC-specific genes, relative to their isogenic euploid controls. In particular, 45,X NCCs increase cholesterol biosynthesis genes while reducing transcripts that feature 5' terminal oligopyrimidine (TOP) motifs, including those of ribosomal protein and nuclear-encoded mitochondrial genes. Such metabolic pathways are also over-represented in weighted co-expression gene modules that are preserved in monogenic neurocristopathy. Importantly, these gene modules are also significantly enriched in 28% of all TS-associated terms of the human phenotype ontology. Our analysis identifies specific sex-linked genes that are expressed from two copies in euploid males and females alike and qualify as candidate haploinsufficient drivers of TS phenotypes in NC-derived lineages. This study demonstrates that isogenic hiPSC-derived NCC panels representing monosomy-X can serve as a powerful model of early NC development in TS and inform new hypotheses towards its etiology.
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Affiliation(s)
- Darcy T. Ahern
- Graduate Program in Genetics and Developmental Biology, UCONN Health, University of Connecticut, Farmington, CT, United States
- Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, United States
| | - Prakhar Bansal
- Graduate Program in Genetics and Developmental Biology, UCONN Health, University of Connecticut, Farmington, CT, United States
- Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, United States
| | - Isaac V. Faustino
- Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, United States
| | - Heather R. Glatt-Deeley
- Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, United States
| | - Rachael Massey
- Graduate Program in Genetics and Developmental Biology, UCONN Health, University of Connecticut, Farmington, CT, United States
- Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, United States
- Institute for Systems Genomics, University of Connecticut, Farmington, CT, United States
| | - Yuvabharath Kondaveeti
- Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, United States
| | - Erin C. Banda
- Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, United States
| | - Stefan F. Pinter
- Graduate Program in Genetics and Developmental Biology, UCONN Health, University of Connecticut, Farmington, CT, United States
- Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, United States
- Institute for Systems Genomics, University of Connecticut, Farmington, CT, United States
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Keilich SR, Cadar AN, Ahern DT, Torrance BL, Lorenzo EC, Martin DE, Haynes L, Bartley JM. Correction to: Altered T cell infiltration and enrichment of leukocyte regulating pathways within aged skeletal muscle are associated with impaired muscle function following influenza infection. GeroScience 2023; 45:3097. [PMID: 37256521 PMCID: PMC10643704 DOI: 10.1007/s11357-023-00838-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023] Open
Affiliation(s)
- Spencer R Keilich
- UConn Center On Aging, University of Connecticut School of Medicine, Farmington, CT, 06030, USA
- Department of Immunology, University of Connecticut School of Medicine, Farmington, CT, 06030, USA
- Millipore Sigma, 400 Summit Drive, Burlington, MA, 01803, USA
| | - Andreia N Cadar
- UConn Center On Aging, University of Connecticut School of Medicine, Farmington, CT, 06030, USA
- Department of Immunology, University of Connecticut School of Medicine, Farmington, CT, 06030, USA
| | - Darcy T Ahern
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT, 06030, USA
- Intellia Therapeutics, 40 Erie St, Cambridge, MA, 02139, USA
| | - Blake L Torrance
- UConn Center On Aging, University of Connecticut School of Medicine, Farmington, CT, 06030, USA
- Department of Immunology, University of Connecticut School of Medicine, Farmington, CT, 06030, USA
| | - Erica C Lorenzo
- UConn Center On Aging, University of Connecticut School of Medicine, Farmington, CT, 06030, USA
- Department of Immunology, University of Connecticut School of Medicine, Farmington, CT, 06030, USA
| | - Dominique E Martin
- UConn Center On Aging, University of Connecticut School of Medicine, Farmington, CT, 06030, USA
- Department of Immunology, University of Connecticut School of Medicine, Farmington, CT, 06030, USA
| | - Laura Haynes
- UConn Center On Aging, University of Connecticut School of Medicine, Farmington, CT, 06030, USA.
- Department of Immunology, University of Connecticut School of Medicine, Farmington, CT, 06030, USA.
| | - Jenna M Bartley
- UConn Center On Aging, University of Connecticut School of Medicine, Farmington, CT, 06030, USA.
- Department of Immunology, University of Connecticut School of Medicine, Farmington, CT, 06030, USA.
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Keilich SR, Cadar AN, Ahern DT, Torrance BL, Lorenzo EC, Martin DE, Haynes L, Bartley JM. Altered T cell infiltration and enrichment of leukocyte regulating pathways within aged skeletal muscle are associated impaired muscle function following influenza infection. GeroScience 2023; 45:1197-1213. [PMID: 36580167 PMCID: PMC9886695 DOI: 10.1007/s11357-022-00715-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 12/09/2022] [Indexed: 12/30/2022] Open
Abstract
Older adults have diminished immune responses that increase susceptibility to infectious diseases, such as influenza (flu). In older adults, flu infection can lead to hospitalization, catastrophic disability, and mortality. We previously demonstrated severe and prolonged muscle degradation and atrophy in aged mice during flu infection. Here, we utilized an unbiased transcriptomic analysis to elucidate mechanisms of flu-induced muscular declines in a mouse model. Our results showed age-related gene expression differences including downregulation of genes associated with muscle regeneration and organization and upregulation of genes associated with pro-inflammatory cytokines and migratory immune pathways in aged mice when compared to young. Pathway analysis revealed significant enrichment of leukocyte migration and T cell activation pathways in the aged muscle during infection. Intramuscular CD4 T cells increased in both young and aged mice during infection, while intramuscular CD8 T cells increased exclusively in aged muscle. CD4 T cells in young muscle were regulatory T cells (Treg), while those in aged were T follicular helper (Tfh) and Th2 cells. Correspondingly, IL-33, an important cytokine for Treg accumulation within tissue, increased only in young flu-infected muscle. Conversely, CXCL10 (IP-10) increased only in aged muscle suggesting a continued recruitment of CD8 T cells into the aged muscle during flu infection. Overall, our findings elucidate a link between flu-induced disability and dysregulated intracellular T cell recruitment into flu-injured muscle with aging. Furthermore, we uncovered potential pathways involved that can be targeted to develop preventative and therapeutic interventions to avert disability and maintain independence following infection.
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Affiliation(s)
- Spencer R Keilich
- UConn Center On Aging, University of Connecticut School of Medicine, Farmington, CT, 06030, USA
- Department of Immunology, University of Connecticut School of Medicine, Farmington, CT, 06030, USA
- Millipore Sigma, 400 Summit Drive, Burlington, MA, 01803, USA
| | - Andreia N Cadar
- UConn Center On Aging, University of Connecticut School of Medicine, Farmington, CT, 06030, USA
- Department of Immunology, University of Connecticut School of Medicine, Farmington, CT, 06030, USA
| | - Darcy T Ahern
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT, 06030, USA
- Intellia Therapeutics, 40 Erie St, Cambridge, MA, 02139, USA
| | - Blake L Torrance
- UConn Center On Aging, University of Connecticut School of Medicine, Farmington, CT, 06030, USA
- Department of Immunology, University of Connecticut School of Medicine, Farmington, CT, 06030, USA
| | - Erica C Lorenzo
- UConn Center On Aging, University of Connecticut School of Medicine, Farmington, CT, 06030, USA
- Department of Immunology, University of Connecticut School of Medicine, Farmington, CT, 06030, USA
| | - Dominique E Martin
- UConn Center On Aging, University of Connecticut School of Medicine, Farmington, CT, 06030, USA
- Department of Immunology, University of Connecticut School of Medicine, Farmington, CT, 06030, USA
| | - Laura Haynes
- UConn Center On Aging, University of Connecticut School of Medicine, Farmington, CT, 06030, USA.
- Department of Immunology, University of Connecticut School of Medicine, Farmington, CT, 06030, USA.
| | - Jenna M Bartley
- UConn Center On Aging, University of Connecticut School of Medicine, Farmington, CT, 06030, USA.
- Department of Immunology, University of Connecticut School of Medicine, Farmington, CT, 06030, USA.
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Bansal P, Ahern DT, Kondaveeti Y, Qiu CW, Pinter SF. Contiguous erosion of the inactive X in human pluripotency concludes with global DNA hypomethylation. Cell Rep 2021; 35:109215. [PMID: 34107261 PMCID: PMC8267460 DOI: 10.1016/j.celrep.2021.109215] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 05/25/2020] [Revised: 08/18/2020] [Accepted: 05/13/2021] [Indexed: 01/21/2023] Open
Abstract
Female human pluripotent stem cells (hPSCs) routinely undergo inactive X (Xi) erosion. This progressive loss of key repressive features follows the loss of XIST expression, the long non-coding RNA driving X inactivation, and causes reactivation of silenced genes across the eroding X (Xe). To date, the sporadic and progressive nature of erosion has obscured its scale, dynamics, and key transition events. To address this problem, we perform an integrated analysis of DNA methylation (DNAme), chromatin accessibility, and gene expression across hundreds of hPSC samples. Differential DNAme orders female hPSCs across a trajectory from initiation to terminal Xi erosion. Our results identify a cis-regulatory element crucial for XIST expression, trace contiguously growing reactivated domains to a few euchromatic origins, and indicate that the late-stage Xe impairs DNAme genome-wide. Surprisingly, from this altered regulatory landscape emerge select features of naive pluripotency, suggesting that its link to X dosage may be partially conserved in human embryonic development. Reactivation of the silenced X in human female iPSC/ESCs compromises their utility. Bansal et al. perform an integrated genomics analysis to reveal a prevalent X erosion trajectory that they validate in long-term culture. Starting with XIST loss, this trajectory indicates that reactivation may spread contiguously from escapees to silenced genes.
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Affiliation(s)
- Prakhar Bansal
- Graduate Program in Genetics and Developmental Biology, UCONN Health, University of Connecticut, Farmington, CT, USA; Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, USA
| | - Darcy T Ahern
- Graduate Program in Genetics and Developmental Biology, UCONN Health, University of Connecticut, Farmington, CT, USA; Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, USA
| | - Yuvabharath Kondaveeti
- Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, USA
| | - Catherine W Qiu
- Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, USA
| | - Stefan F Pinter
- Graduate Program in Genetics and Developmental Biology, UCONN Health, University of Connecticut, Farmington, CT, USA; Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, USA; Institute for Systems Genomics, University of Connecticut, Farmington, CT, USA.
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