Chromatin structural gene expression stratifies cardiac cell populations in health and disease [Dataset]

Supplementary Figure 1. Reanalysis of human snRNA-seq data confirms previously reported findings. Unsupervised UMAP clustering of the dataset from Koenig et al.11 reproduces the original clustering patterns observed between healthy donors and DCM patients. Supplementary Figure 2. (A) Characteristic...

ver descrição completa

Detalhes bibliográficos
Autores: Geng, Xiaoxiao, Pradeep, Rujula, Porter, Riley, García-Gutiérrez, Lucía, Xie, Min, Wende, Adam R., Zhang, Jianyi, Cobo, Isidoro, Nguyen, Thanh, Rosa-Garrido, Manuel
Formato: conjunto de datos
Fecha de publicación:2025
País:España
Recursos:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:dnet:digitalcsic_::6bfb1f0e7b3a31275995cf701c7f047d
Acesso em linha:http://hdl.handle.net/10261/426559
Access Level:acceso abierto
Palavra-chave:Chromatin structure
HMGN3
Cardiac disease
snRNA-seq
ChIP-seq
id ES_98794ef36013f9ba0c672e5d8630f2df
oai_identifier_str oai:dnet:digitalcsic_::6bfb1f0e7b3a31275995cf701c7f047d
network_acronym_str ES
network_name_str España
repository_id_str
dc.title.none.fl_str_mv Chromatin structural gene expression stratifies cardiac cell populations in health and disease [Dataset]
title Chromatin structural gene expression stratifies cardiac cell populations in health and disease [Dataset]
spellingShingle Chromatin structural gene expression stratifies cardiac cell populations in health and disease [Dataset]
Geng, Xiaoxiao
Chromatin structure
HMGN3
Cardiac disease
snRNA-seq
ChIP-seq
title_short Chromatin structural gene expression stratifies cardiac cell populations in health and disease [Dataset]
title_full Chromatin structural gene expression stratifies cardiac cell populations in health and disease [Dataset]
title_fullStr Chromatin structural gene expression stratifies cardiac cell populations in health and disease [Dataset]
title_full_unstemmed Chromatin structural gene expression stratifies cardiac cell populations in health and disease [Dataset]
title_sort Chromatin structural gene expression stratifies cardiac cell populations in health and disease [Dataset]
dc.creator.none.fl_str_mv Geng, Xiaoxiao
Pradeep, Rujula
Porter, Riley
García-Gutiérrez, Lucía
Xie, Min
Wende, Adam R.
Zhang, Jianyi
Cobo, Isidoro
Nguyen, Thanh
Rosa-Garrido, Manuel
author Geng, Xiaoxiao
author_facet Geng, Xiaoxiao
Pradeep, Rujula
Porter, Riley
García-Gutiérrez, Lucía
Xie, Min
Wende, Adam R.
Zhang, Jianyi
Cobo, Isidoro
Nguyen, Thanh
Rosa-Garrido, Manuel
author_role author
author2 Pradeep, Rujula
Porter, Riley
García-Gutiérrez, Lucía
Xie, Min
Wende, Adam R.
Zhang, Jianyi
Cobo, Isidoro
Nguyen, Thanh
Rosa-Garrido, Manuel
author2_role author
author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv University of Alabama at Birmingham
National Institutes of Health (US)
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv Chromatin structure
HMGN3
Cardiac disease
snRNA-seq
ChIP-seq
topic Chromatin structure
HMGN3
Cardiac disease
snRNA-seq
ChIP-seq
description Supplementary Figure 1. Reanalysis of human snRNA-seq data confirms previously reported findings. Unsupervised UMAP clustering of the dataset from Koenig et al.11 reproduces the original clustering patterns observed between healthy donors and DCM patients. Supplementary Figure 2. (A) Characteristic marker genes of each identified cell population. (B) Gene ontology enrichment scatterplot showing the most relevant terms with the lowest p-values for each cell type. (C) Summary of sequencing quality metrics for cardiomyocytes (CM), fibroblasts (FB), endothelial cells (EC), smooth muscle cells (SMC), macrophages (MP), T cells (TC), and neurons (N). For each cell type, the table shows the total number of cells captured, the total number of unique genes detected across all cells, and the median number of genes detected per cell after quality filtering. These metrics reflect both the sequencing depth and transcriptional complexity of each cell population. Supplementary Figure 3. Demographic characteristics of human subjects included in the snRNA-seq dataset. Gender, race, and age information of the human subjects from the snRNA-seq dataset generated and published by Koenig et al., which was used in the analyses presented in this manuscript. AA = African American; W = White. Supplementary Figure 4. Percentage of cells assigned to each cluster identified by Unsupervised Uniform Manifold Approximation and Projection (UMAP) analysis. Clusters include cardiomyocytes (CM), fibroblasts (FB), endothelial cells (EC), smooth muscle cells (SMC), macrophages (MP), T cells (TC). Supplementary Figure 5. Cardiomyocyte marker expression and fibroblast contamination assessment. (A) Immunofluorescence staining of isolated cardiomyocytes showing the cardiomyocyte marker Troponin T (green) with a higher magnification inset of a single cell displaying organized sarcomeric structure. Scale bar: 40µm. (B) Quantitative RT-PCR analysis of HMGN3, Vimentin (fibroblast marker) and Actinin (cardiomyocyte marker) mRNA expression. GAPDH was used to normalize cDNA input, and HMGN3 served as an internal reference to evaluate relative expression levels of Vimentin and Actinin. Data are presented as mean ± SEM, p < 0.01 (**), unpaired two-tailed t-test. (C) Immunofluorescence images showing α-Actinin (red) and nuclear DAPI staining (blue) in isolated cardiomyocytes. Merged images illustrate the organized sarcomeric arrangement of α-Actinin surrounding centrally located nuclei. Scale bar: 20 µm. Supplementary Figure 6. Human subject clinical data. Available data on patients from whom heart samples were obtained is provided. Supplementary Figure 7. Echocardiographic measurements after TAC surgery. Eleven weeks after TAC surgery, treated mice (red) show a significant decrease in ejection fraction (EF) and a significant increase in left ventricular internal dimension during diastole (LVIDd) and systole (LVIDs) compared to SHAM animals (green). Lines indicate the mean value for each parameter, and error bars represent the standard deviation (n = 10 mice per group). Supplementary Figure 8. Transcriptomic changes upon HMGN3 knockdown. (A) PCA plot showing clustering of transcriptomic profiles from scramble control (blue) and siHMGN3 (red) samples, indicating distinct separation between conditions. (B) Volcano plot displaying differential gene expression between scramble and siHMGN3 conditions. The x-axis represents log₂ fold change and the y-axis represents –log₁₀(p-value). Significantly upregulated and downregulated genes are highlighted in orange, with selected genes labeled. Supplementary Figure 9. HMGN3 depletion reduces H3K27ac levels and alters regulatory element activity. (A) Western blot analysis (top) and corresponding quantification (bottom) demonstrate a reduction in global levels of the active histone marks H3K27ac in AC16 cells 72 hours after HMGN3 knockdown. (*p < 0.05). (B) Motif enrichment analysis of differential H3K27ac regions. Shown are transcription factor motifs enriched in regions with decreased (blue) or increased (red) H3K27ac after siHMGN3. The x-axis represents the percentage of sequences above background, and the y-axis represents significance (–log₁₀ FDR). (C) Genomic distribution of differential H3K27ac peaks associated with genes identified as differentially expressed between the scramble and siHMGN3 groups. Pie charts display the proportions of peaks located in promoters, exons, introns, intergenic regions, or other genomic regions for sites losing (left) or gaining (right) H3K27ac after HMGN3 knockdown. Peaks gaining H3K27ac in upregulated genes are predominantly found in regulatory regions (introns and intergenic regions), while peaks losing H3K27ac in downregulated genes are enriched at promoters.
publishDate 2025
dc.date.none.fl_str_mv 2025
2026
2026
dc.type.none.fl_str_mv info:eu-repo/semantics/dataset
http://purl.org/coar/resource_type/c_ddb1
format dataset
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/426559
url http://hdl.handle.net/10261/426559
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Geng, Xiaoxiao; Pradeep, Rujula; Porter, Riley; García-Gutiérrez, Lucía; Xie, Min; Wende, Adam R.; Zhang, Jianyi; Cobo, Isidoro; Nguyen, Thanh; Rosa-Garrido, Manuel. Chromatin structural gene expression stratifies cardiac cell populations in health and disease. https://doi.org/10.1080/15592294.2025.2566505 . http://hdl.handle.net/10261/426484
https://doi.org/10.6084/m9.figshare.30406043
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv image/jpeg
dc.publisher.none.fl_str_mv Taylor & Francis
publisher.none.fl_str_mv Taylor & Francis
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
collection DIGITAL.CSIC. Repositorio Institucional del CSIC
repository.name.fl_str_mv
repository.mail.fl_str_mv
_version_ 1869414195918798848
spelling Chromatin structural gene expression stratifies cardiac cell populations in health and disease [Dataset]Geng, XiaoxiaoPradeep, RujulaPorter, RileyGarcía-Gutiérrez, LucíaXie, MinWende, Adam R.Zhang, JianyiCobo, IsidoroNguyen, ThanhRosa-Garrido, ManuelChromatin structureHMGN3Cardiac diseasesnRNA-seqChIP-seqSupplementary Figure 1. Reanalysis of human snRNA-seq data confirms previously reported findings. Unsupervised UMAP clustering of the dataset from Koenig et al.11 reproduces the original clustering patterns observed between healthy donors and DCM patients. Supplementary Figure 2. (A) Characteristic marker genes of each identified cell population. (B) Gene ontology enrichment scatterplot showing the most relevant terms with the lowest p-values for each cell type. (C) Summary of sequencing quality metrics for cardiomyocytes (CM), fibroblasts (FB), endothelial cells (EC), smooth muscle cells (SMC), macrophages (MP), T cells (TC), and neurons (N). For each cell type, the table shows the total number of cells captured, the total number of unique genes detected across all cells, and the median number of genes detected per cell after quality filtering. These metrics reflect both the sequencing depth and transcriptional complexity of each cell population. Supplementary Figure 3. Demographic characteristics of human subjects included in the snRNA-seq dataset. Gender, race, and age information of the human subjects from the snRNA-seq dataset generated and published by Koenig et al., which was used in the analyses presented in this manuscript. AA = African American; W = White. Supplementary Figure 4. Percentage of cells assigned to each cluster identified by Unsupervised Uniform Manifold Approximation and Projection (UMAP) analysis. Clusters include cardiomyocytes (CM), fibroblasts (FB), endothelial cells (EC), smooth muscle cells (SMC), macrophages (MP), T cells (TC). Supplementary Figure 5. Cardiomyocyte marker expression and fibroblast contamination assessment. (A) Immunofluorescence staining of isolated cardiomyocytes showing the cardiomyocyte marker Troponin T (green) with a higher magnification inset of a single cell displaying organized sarcomeric structure. Scale bar: 40µm. (B) Quantitative RT-PCR analysis of HMGN3, Vimentin (fibroblast marker) and Actinin (cardiomyocyte marker) mRNA expression. GAPDH was used to normalize cDNA input, and HMGN3 served as an internal reference to evaluate relative expression levels of Vimentin and Actinin. Data are presented as mean ± SEM, p < 0.01 (**), unpaired two-tailed t-test. (C) Immunofluorescence images showing α-Actinin (red) and nuclear DAPI staining (blue) in isolated cardiomyocytes. Merged images illustrate the organized sarcomeric arrangement of α-Actinin surrounding centrally located nuclei. Scale bar: 20 µm. Supplementary Figure 6. Human subject clinical data. Available data on patients from whom heart samples were obtained is provided. Supplementary Figure 7. Echocardiographic measurements after TAC surgery. Eleven weeks after TAC surgery, treated mice (red) show a significant decrease in ejection fraction (EF) and a significant increase in left ventricular internal dimension during diastole (LVIDd) and systole (LVIDs) compared to SHAM animals (green). Lines indicate the mean value for each parameter, and error bars represent the standard deviation (n = 10 mice per group). Supplementary Figure 8. Transcriptomic changes upon HMGN3 knockdown. (A) PCA plot showing clustering of transcriptomic profiles from scramble control (blue) and siHMGN3 (red) samples, indicating distinct separation between conditions. (B) Volcano plot displaying differential gene expression between scramble and siHMGN3 conditions. The x-axis represents log₂ fold change and the y-axis represents –log₁₀(p-value). Significantly upregulated and downregulated genes are highlighted in orange, with selected genes labeled. Supplementary Figure 9. HMGN3 depletion reduces H3K27ac levels and alters regulatory element activity. (A) Western blot analysis (top) and corresponding quantification (bottom) demonstrate a reduction in global levels of the active histone marks H3K27ac in AC16 cells 72 hours after HMGN3 knockdown. (*p < 0.05). (B) Motif enrichment analysis of differential H3K27ac regions. Shown are transcription factor motifs enriched in regions with decreased (blue) or increased (red) H3K27ac after siHMGN3. The x-axis represents the percentage of sequences above background, and the y-axis represents significance (–log₁₀ FDR). (C) Genomic distribution of differential H3K27ac peaks associated with genes identified as differentially expressed between the scramble and siHMGN3 groups. Pie charts display the proportions of peaks located in promoters, exons, introns, intergenic regions, or other genomic regions for sites losing (left) or gaining (right) H3K27ac after HMGN3 knockdown. Peaks gaining H3K27ac in upregulated genes are predominantly found in regulatory regions (introns and intergenic regions), while peaks losing H3K27ac in downregulated genes are enriched at promoters.Chromatin structure plays a central role in regulating gene expression and maintaining cellular identity, yet the structural factors driving these processes in cardiac disease remain poorly defined. To investigate whether these factors can distinguish healthy from diseased cardiac cell populations, we generated a comprehensive list of chromatin structural genes based on an extensive literature review. Applying this list to a published single-nuclei RNA sequencing dataset from human hearts with and without dilated cardiomyopathy (DCM), we found that chromatin structural gene expression effectively stratified cardiomyocyte and fibroblast populations by disease status. Diseased cardiomyocytes exhibited reduced expression of contractile genes and increased expression of cardiomyopathy markers, while fibroblasts showed enhanced activation signatures. Among these factors, HMGN3 emerged as a candidate of interest, showing consistent downregulation in cardiomyocytes from DCM human patients, as well as in mouse (pressure overload) and pig (myocardial infarction) models of heart failure. Functional studies in AC16 cells revealed that HMGN3 depletion promoted apoptosis, induced significant changes in gene expression, and reorganized chromatin structure by altering the distribution of the H3K27ac histone mark. These findings identify HMGN3 as a potential regulator of chromatin architecture in diseased cardiomyocytes, highlight the utility of chromatin structural changes in distinguishing pathological cardiac states, and reinforce the role of chromatin organization in shaping the cardiac phenotype.This project was supported by the Department of Biomedical Engineering and the Heersink School of Medicine at UAB, with funding for Manuel Rosa-Garrido, as well as by grants from the National Institutes of Health to Dr.Jianyi Zhang (P01HL160476, 5R01HL131017–08) and Dr.Adam Wende (NIH R01 HL167872).Peer reviewedTaylor & FrancisUniversity of Alabama at BirminghamNational Institutes of Health (US)Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]202620262025info:eu-repo/semantics/datasethttp://purl.org/coar/resource_type/c_ddb1image/jpeghttp://hdl.handle.net/10261/426559reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)InglésGeng, Xiaoxiao; Pradeep, Rujula; Porter, Riley; García-Gutiérrez, Lucía; Xie, Min; Wende, Adam R.; Zhang, Jianyi; Cobo, Isidoro; Nguyen, Thanh; Rosa-Garrido, Manuel. Chromatin structural gene expression stratifies cardiac cell populations in health and disease. https://doi.org/10.1080/15592294.2025.2566505 . http://hdl.handle.net/10261/426484https://doi.org/10.6084/m9.figshare.30406043Síinfo:eu-repo/semantics/openAccessoai:dnet:digitalcsic_::6bfb1f0e7b3a31275995cf701c7f047d2026-05-22T06:33:51Z
score 15,198674

Registos relacionados