1
|
Vargas-Casanova Y, Bravo-Chaucanés CP, Fuentes SDLC, Martinez-Lopez R, Monteoliva L, Gil C, Rivera-Monroy ZJ, Costa GM, Castañeda JEG, Parra-Giraldo CM. Antifungal Synergy: Mechanistic Insights into the R-1-R Peptide and Bidens pilosa Extract as Potent Therapeutics against Candida spp. through Proteomics. Int J Mol Sci 2024; 25:8938. [PMID: 39201622 PMCID: PMC11354716 DOI: 10.3390/ijms25168938] [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: 06/30/2024] [Revised: 08/03/2024] [Accepted: 08/09/2024] [Indexed: 09/02/2024] Open
Abstract
Previous reports have demonstrated that the peptide derived from LfcinB, R-1-R, exhibits anti-Candida activity, which is enhanced when combined with an extract from the Bidens pilosa plant. However, the mechanism of action remains unexplored. In this research, a proteomic study was carried out, followed by a bioinformatic analysis and biological assays in both the SC5314 strain and a fluconazole-resistant isolate of Candida albicans after incubation with R-1-R. The proteomic data revealed that treatment with R-1-R led to the up-regulation of most differentially expressed proteins compared to the controls in both strains. These proteins are primarily involved in membrane and cell wall biosynthesis, membrane transport, oxidative stress response, the mitochondrial respiratory chain, and DNA damage response. Additionally, proteomic analysis of the C. albicans parental strain SC5314 treated with R-1-R combined with an ethanolic extract of B. pilosa was performed. The differentially expressed proteins following this combined treatment were involved in similar functional processes as those treated with the R-1-R peptide alone but were mostly down-regulated (data are available through ProteomeXchange with identifier PXD053558). Biological assays validated the proteomic results, evidencing cell surface damage, reactive oxygen species generation, and decreased mitochondrial membrane potential. These findings provide insights into the complex antifungal mechanisms of the R-1-R peptide and its combination with the B. pilosa extract, potentially informing future studies on natural product derivatives.
Collapse
Affiliation(s)
- Yerly Vargas-Casanova
- Microbiology Department, Faculty of Sciences, Pontificia Universidad Javeriana, Bogotá 110231, Colombia; (Y.V.-C.); (C.P.B.-C.)
| | | | | | - Raquel Martinez-Lopez
- Microbiology and Parasitology Department, Faculty of Pharmacy, Universidad Complutense de Madrid, 28040 Madrid, Spain; (R.M.-L.); (L.M.); (C.G.)
| | - Lucía Monteoliva
- Microbiology and Parasitology Department, Faculty of Pharmacy, Universidad Complutense de Madrid, 28040 Madrid, Spain; (R.M.-L.); (L.M.); (C.G.)
| | - Concha Gil
- Microbiology and Parasitology Department, Faculty of Pharmacy, Universidad Complutense de Madrid, 28040 Madrid, Spain; (R.M.-L.); (L.M.); (C.G.)
| | - Zuly Jenny Rivera-Monroy
- Faculty of Sciences, Universidad Nacional of Colombia, Bogotá 111321, Colombia; (Z.J.R.-M.); (J.E.G.C.)
| | - Geison Modesti Costa
- Chemistry Department, Faculty of Sciences, Pontificia Universidad Javeriana, Bogotá 110231, Colombia;
| | | | - Claudia Marcela Parra-Giraldo
- Microbiology Department, Faculty of Sciences, Pontificia Universidad Javeriana, Bogotá 110231, Colombia; (Y.V.-C.); (C.P.B.-C.)
- Microbiology and Parasitology Department, Faculty of Pharmacy, Universidad Complutense de Madrid, 28040 Madrid, Spain; (R.M.-L.); (L.M.); (C.G.)
| |
Collapse
|
2
|
Usey MM, Ruberto AA, Huet D. The Toxoplasma gondii homolog of ATPase inhibitory factor 1 is critical for mitochondrial cristae maintenance and stress response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.09.607411. [PMID: 39149366 PMCID: PMC11326266 DOI: 10.1101/2024.08.09.607411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
The production of energy in the form of ATP by the mitochondrial ATP synthase must be tightly controlled. One well-conserved form of regulation is mediated via ATPase inhibitory factor 1 (IF1), which governs ATP synthase activity and gene expression patterns through a cytoprotective process known as mitohormesis. In apicomplexans, the processes regulating ATP synthase activity are not fully elucidated. Using the model apicomplexan Toxoplasma gondii, we found that knockout and overexpression of TgIF1, the structural homolog of IF1, significantly affected gene expression. Additionally, TgIF1 overexpression resulted in the formation of a stable TgIF1 oligomer that increased the presence of higher order ATP synthase oligomers. We also show that parasites lacking TgIF1 exhibit reduced mitochondrial cristae density, and that while TgIF1 levels do not affect growth in conventional culture conditions, they are crucial for parasite survival under hypoxia. Interestingly, TgIF1 overexpression enhances recovery from oxidative stress, suggesting a mitohormetic function. In summary, while TgIF1 does not appear to play a role in metabolic regulation under conventional growth conditions, our work highlights its importance for adapting to stressors faced by T. gondii and other apicomplexans throughout their intricate life cycles.
Collapse
Affiliation(s)
- Madelaine M. Usey
- Department of Cellular Biology, University of Georgia, Athens, GA, USA
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, USA
| | - Anthony A. Ruberto
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, USA
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Diego Huet
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA, USA
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, USA
| |
Collapse
|
3
|
Mikucki EE, O’Leary TS, Lockwood BL. Heat tolerance, oxidative stress response tuning and robust gene activation in early-stage Drosophila melanogaster embryos. Proc Biol Sci 2024; 291:20240973. [PMID: 39163981 PMCID: PMC11335408 DOI: 10.1098/rspb.2024.0973] [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: 04/26/2024] [Revised: 06/11/2024] [Accepted: 07/26/2024] [Indexed: 08/22/2024] Open
Abstract
In organisms with complex life cycles, life stages that are most susceptible to environmental stress may determine species persistence in the face of climate change. Early embryos of Drosophila melanogaster are particularly sensitive to acute heat stress, yet tropical embryos have higher heat tolerance than temperate embryos, suggesting adaptive variation in embryonic heat tolerance. We compared transcriptomic responses to heat stress among tropical and temperate embryos to elucidate the gene regulatory basis of divergence in embryonic heat tolerance. The transcriptomes of tropical and temperate embryos differed in both constitutive and heat-stress-induced responses of the expression of relatively few genes, including genes involved in oxidative stress. Most of the transcriptomic response to heat stress was shared among all embryos. Embryos shifted the expression of thousands of genes, including increases in the expression of heat shock genes, suggesting robust zygotic gene activation and demonstrating that, contrary to previous reports, early embryos are not transcriptionally silent. The involvement of oxidative stress genes corroborates recent reports on the critical role of redox homeostasis in coordinating developmental transitions. By characterizing adaptive variation in the transcriptomic basis of embryonic heat tolerance, this study is a novel contribution to the literature on developmental physiology and developmental genetics.
Collapse
Affiliation(s)
- Emily E. Mikucki
- Department of Biology, University of Vermont, Burlington, VT, USA
| | | | | |
Collapse
|
4
|
Elasbali AM, Al-Soud WA, Adnan M, Alhassan HH, Mohammad T, Hassan MI. Discovering Promising Biomarkers and Therapeutic Targets for Duchenne Muscular Dystrophy: a Multiomics Meta-Analysis Approach. Mol Neurobiol 2024; 61:5117-5128. [PMID: 38165583 DOI: 10.1007/s12035-023-03868-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Accepted: 12/08/2023] [Indexed: 01/04/2024]
Abstract
Duchenne muscular dystrophy (DMD) is a genetic disorder that causes muscle weakness and degeneration. In this study, we identified potential biomarkers and drug targets for DMD through a comprehensive meta-analysis of mRNA profiles. We conducted an in-depth analysis of three microarray datasets from the GEO database, utilizing the Affymetrix platform. A rigorous data pre-processing pipeline encompassed background correction, normalization, log2 transformation and probe-to-gene symbol mapping. Robust multi-array average method followed by Limma package in R was employed to ensure differential expression analysis within individual datasets, yielding gene-specific p-values. We identified 63 genes exhibiting statistically significant differential expression across the three datasets (p < 0.05) and an absolute log fold change > 1.5. Functional enrichment analyses of these differentially expressed genes were done, followed by pathway analyses. Our results suggested pertinent biological processes, molecular functions and cellular components associated with DMD. Finally, eight hub genes-COL6A3, COL1A1, COL3A1, COL1A2, POSTN, TIMP1, THBS2 and SPP1-were pinpointed as central players in the network. Two differentially expressed genes with substantial absolute log-fold changes, namely, DMD, downregulated and MYH3, upregulated, were identified as potential therapeutic candidates. In light of these findings, our work contributes not only to understanding DMD at the molecular level but also presents potential targets for therapeutic strategies. Finally, our study facilitates the development of therapeutic interventions that can effectively control and mitigate the impact of DMD.
Collapse
Affiliation(s)
- Abdelbaset Mohamed Elasbali
- Department of Clinical Laboratory Science, College of Applied Medical Sciences-Qurayyat, Jouf University, Sakakah, Saudi Arabia
| | - Waleed Abu Al-Soud
- Department of Clinical Laboratory Science, College of Applied Sciences-Sakaka, Jouf University, Sakakah, Saudi Arabia
- Molekylärbiologi, Klinisk Mikrobiologi och vårdhygien, Region Skåne, Sölvegatan 23B, 221 85, Lund, Sweden
| | - Mohd Adnan
- Department of Biology, College of Science, University of Ha'il, Ha'il, Saudi Arabia
| | - Hassan H Alhassan
- Department of Clinical Laboratory Science, College of Applied Medical Sciences, Jouf University, Jouf, Saudi Arabia
| | - Taj Mohammad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India.
| |
Collapse
|
5
|
Lee J, Yoon JH, Lee E, Lee HY, Jeong S, Park S, Jo YS, Kwak JY. Immune response and mesenchymal transition of papillary thyroid carcinoma reflected in ultrasonography features assessed by radiologists and deep learning. J Adv Res 2024; 62:219-228. [PMID: 37783270 PMCID: PMC11331164 DOI: 10.1016/j.jare.2023.09.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 09/07/2023] [Accepted: 09/29/2023] [Indexed: 10/04/2023] Open
Abstract
INTRODUCTION Ultrasonography (US) features of papillary thyroid cancers (PTCs) are used to select nodules for biopsy due to their association with tumor behavior. However, the molecular biological mechanisms that lead to the characteristic US features of PTCs are largely unknown. OBJECTIVES This study aimed to investigate the molecular biological mechanisms behind US features assessed by radiologists and three convolutional neural networks (CNN) through transcriptome analysis. METHODS Transcriptome data from 273 PTC tissue samples were generated and differentially expressed genes (DEGs) were identified according to US feature. Pathway enrichment analyses were also conducted by gene set enrichment analysis (GSEA) and ClusterProfiler according to assessments made by radiologists and three CNNs - CNN1 (ResNet50), CNN2 (ResNet101) and CNN3 (VGG16). Signature gene scores for PTCs were calculated by single-sample GSEA (ssGSEA). RESULTS Individual suspicious US features consistently suggested an upregulation of genes related to immune response and epithelial-mesenchymal transition (EMT). Likewise, PTCs assessed as positive by radiologists and three CNNs showed the coordinate enrichment of similar gene sets with abundant immune and stromal components. However, PTCs assessed as positive by radiologists had the highest number of DEGs, and those assessed as positive by CNN3 had more diverse DEGs and gene sets compared to CNN1 or CNN2. The percentage of PTCs assessed as positive or negative concordantly by radiologists and three CNNs was 85.6% (231/273) and 7.1% (3/273), respectively. CONCLUSION US features assessed by radiologists and CNNs revealed molecular biologic features and tumor microenvironment in PTCs.
Collapse
Affiliation(s)
- Jandee Lee
- Department of Surgery, Open NBI Convergence Technology Research Laboratory, Yonsei Cancer Center, Severance Hospital, Yonsei University College of Medicine, Seoul 03722, South Korea
| | - Jung Hyun Yoon
- Department of Radiology, Severance Hospital, Research Institute of Radiological Science, Yonsei University, College of Medicine, Seoul 03722, South Korea
| | - Eunjung Lee
- School of Mathematics and Computing (Computational Science and Engineering), Yonsei University, Seoul 03722, South Korea
| | - Hwa Young Lee
- Department of Surgery, Open NBI Convergence Technology Research Laboratory, Yonsei Cancer Center, Severance Hospital, Yonsei University College of Medicine, Seoul 03722, South Korea
| | - Seonhyang Jeong
- Department of Internal Medicine, Open NBI Convergence Technology Research Laboratory, Yonsei University College of Medicine, Seoul 03722, South Korea
| | - Sunmi Park
- Department of Internal Medicine, Open NBI Convergence Technology Research Laboratory, Yonsei University College of Medicine, Seoul 03722, South Korea
| | - Young Suk Jo
- Department of Internal Medicine, Open NBI Convergence Technology Research Laboratory, Yonsei University College of Medicine, Seoul 03722, South Korea.
| | - Jin Young Kwak
- Department of Radiology, Severance Hospital, Research Institute of Radiological Science, Yonsei University, College of Medicine, Seoul 03722, South Korea.
| |
Collapse
|
6
|
Gómez-Pascual A, Rocamora-Pérez G, Ibanez L, Botía JA. Targeted co-expression networks for the study of traits. Sci Rep 2024; 14:16675. [PMID: 39030261 PMCID: PMC11271532 DOI: 10.1038/s41598-024-67329-7] [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: 12/28/2023] [Accepted: 07/10/2024] [Indexed: 07/21/2024] Open
Abstract
Weighted Gene Co-expression Network Analysis (WGCNA) is a widely used approach for the generation of gene co-expression networks. However, networks generated with this tool usually create large modules with a large set of functional annotations hard to decipher. We have developed TGCN, a new method to create Targeted Gene Co-expression Networks. This method identifies the transcripts that best predict the trait of interest based on gene expression using a refinement of the LASSO regression. Then, it builds the co-expression modules around those transcripts. Algorithm properties were characterized using the expression of 13 brain regions from the Genotype-Tissue Expression project. When comparing our method with WGCNA, TGCN networks lead to more precise modules that have more specific and yet rich biological meaning. Then, we illustrate its applicability by creating an APP-TGCN on The Religious Orders Study and Memory and Aging Project dataset, aiming to identify the molecular pathways specifically associated with APP role in Alzheimer's disease. Main biological findings were further validated in two independent cohorts. In conclusion, we provide a new framework that serves to create targeted networks that are smaller, biologically relevant and useful in high throughput hypothesis driven research. The TGCN R package is available on Github: https://github.com/aliciagp/TGCN .
Collapse
Affiliation(s)
- A Gómez-Pascual
- Communications Engineering and Information Department, University of Murcia, 30100, Murcia, Spain
| | - G Rocamora-Pérez
- Department of Genetics and Genomic Medicine Research and Teaching, UCL GOS Institute of Child Health, London, WC1N 1EH, UK
| | - L Ibanez
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO, 63110, USA
- Department of Neurology, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - J A Botía
- Communications Engineering and Information Department, University of Murcia, 30100, Murcia, Spain.
| |
Collapse
|
7
|
Apostolides M, Choi B, Navickas A, Saberi A, Soto LM, Goodarzi H, Najafabadi HS. Accurate isoform quantification by joint short- and long-read RNA-sequencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.11.603067. [PMID: 39026819 PMCID: PMC11257535 DOI: 10.1101/2024.07.11.603067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Accurate quantification of transcript isoforms is crucial for understanding gene regulation, functional diversity, and cellular behavior. Existing RNA sequencing methods have significant limitations: short-read (SR) sequencing provides high depth but struggles with isoform deconvolution, whereas long-read (LR) sequencing offers isoform resolution at the cost of lower depth, higher noise, and technical biases. Addressing this gap, we introduce Multi-Platform Aggregation and Quantification of Transcripts (MPAQT), a generative model that combines the complementary strengths of different sequencing platforms to achieve state-of-the-art isoform-resolved transcript quantification, as demonstrated by extensive simulations and experimental benchmarks. By applying MPAQT to an in vitro model of human embryonic stem cell differentiation into cortical neurons, followed by machine learning-based modeling of transcript abundances, we show that untranslated regions (UTRs) are major determinants of isoform proportion and exon usage; this effect is mediated through isoform-specific sequence features embedded in UTRs, which likely interact with RNA-binding proteins that modulate mRNA stability. These findings highlight MPAQT's potential to enhance our understanding of transcriptomic complexity and underline the role of splicing-independent post-transcriptional mechanisms in shaping the isoform and exon usage landscape of the cell.
Collapse
Affiliation(s)
- Michael Apostolides
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Victor P. Dahdaleh Institute of Genomic Medicine, Montreal, QC, Canada
| | - Benedict Choi
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Albertas Navickas
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
- Present address: Institut Curie, PSL Research University, CNRS UMR3348, INSERM U1278, Orsay, France
| | - Ali Saberi
- Victor P. Dahdaleh Institute of Genomic Medicine, Montreal, QC, Canada
- Department of Electrical and Computer Engineering, McGill University, Montreal, Canada
| | - Larisa M. Soto
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Victor P. Dahdaleh Institute of Genomic Medicine, Montreal, QC, Canada
| | - Hani Goodarzi
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
- Arc Institute, 3181 Porter Drive, Palo Alto, CA, USA
| | - Hamed S. Najafabadi
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Victor P. Dahdaleh Institute of Genomic Medicine, Montreal, QC, Canada
- McGill Centre for RNA Sciences, McGill University, Montreal, Canada
| |
Collapse
|
8
|
Rose EC, Simon JM, Gomez-Martinez I, Magness ST, Odle J, Blikslager AT, Ziegler AL. Single-cell transcriptomics predict novel potential regulators of acute epithelial restitution in the ischemia-injured intestine. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.28.601271. [PMID: 38979337 PMCID: PMC11230382 DOI: 10.1101/2024.06.28.601271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Intestinal ischemic injury damages the epithelial barrier predisposes patients to life-threatening sepsis unless that barrier is rapidly restored. There is an age-dependency of intestinal recovery in that neonates are the most susceptible to succumb to disease of the intestinal barrier versus older patients. We have developed a pig model that demonstrates age-dependent failure of intestinal barrier restitution in neonatal pigs which can be rescued by the direct application of juvenile pig mucosal tissue, but the mechanisms of rescue remain undefined. We hypothesized that by identifying a subpopulation of restituting enterocytes by their expression of cell migration transcriptional pathways, we can then predict novel upstream regulators of age-dependent restitution response programs. Superficial mucosal epithelial cells from recovering ischemic jejunum of juvenile pigs were processed for single cell RNA sequencing analysis, and predicted upstream regulators were assessed in a porcine intestinal epithelial cell line (IPEC-J2) and banked tissues. A subcluster of absorptive enterocytes expressed several cell migration pathways key to restitution. Differentially expressed genes in this subcluster predicted their upstream regulation included colony stimulating factor-1 (CSF-1). We validated age-dependent induction of CSF-1 by ischemia and documented that CSF-1 and CSF1R co-localized in ischemic juvenile, but not neonatal, wound-adjacent epithelial cells and in the restituted epithelium of juveniles and rescued (but not control) neonates. Further, the CSF1R inhibitor BLZ945 reduced restitution in scratch wounded IPEC-J2 cells. These studies validate an approach to inform potential novel therapeutic targets, such as CSF-1, to improve outcomes in neonates with intestinal injury in a unique pig model. NEW & NOTEWORTHY These studies validate an approach to identify and predict upstream regulation of restituting epithelium in a unique pig intestinal ischemic injury model. Identification of potential molecular mediators of restitution, such as CSF-1, will inform the development of targeted therapeutic interventions for medical management of patients with ischemia-mediated intestinal injury.
Collapse
|
9
|
Gluck-Thaler E, Forsythe A, Puerner C, Stajich JE, Croll D, Cramer RA, Vogan AA. Giant transposons promote strain heterogeneity in a major fungal pathogen. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.28.601215. [PMID: 38979181 PMCID: PMC11230402 DOI: 10.1101/2024.06.28.601215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Fungal infections are difficult to prevent and treat in large part due to heterogeneity in clinically relevant phenotypes. However, the genetic mechanisms driving pathogen variation remain poorly understood. Here, we determined the extent to which Starships -giant transposons capable of mobilizing numerous fungal genes-generate genetic and phenotypic variability in the human pathogen Aspergillus fumigatus . We analyzed 519 diverse strains, including 12 newly sequenced with long-read technology, to reveal 20 distinct Starships that generate genomic heterogeneity over timescales impacting experimental reproducibility. Starship -mobilized genes encode diverse functions, including biofilm-related virulence factors and biosynthetic gene clusters, and many are differentially expressed during infection and antifungal exposure in a strain-specific manner. These findings support a new model of fungal pathogenesis wherein Starships mediate variation in virulence-related gene content and expression. Together, our results demonstrate that Starships are a foundational mechanism generating disease-relevant genotypic and, in turn, phenotypic heterogeneity in a major human fungal pathogen.
Collapse
|
10
|
Nicholas CA, Tensun FA, Evans SA, Toole KP, Broncucia H, Hesselberth JR, Gottlieb PA, Wells KL, Smith MJ. Islet-antigen reactive B cells display a unique phenotype and BCR repertoire in autoantibody positive and recent-onset type 1 diabetes patients. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.20.599914. [PMID: 38979376 PMCID: PMC11230262 DOI: 10.1101/2024.06.20.599914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Autoreactive B cells play an important but ill-defined role in autoimmune type 1 diabetes (T1D). To better understand their contribution, we performed single cell gene and BCR-seq analysis on pancreatic islet antigen-reactive (IAR) B cells from the peripheral blood of nondiabetic (ND), autoantibody positive prediabetic (AAB), and recent-onset T1D individuals. We found that the frequency of IAR B cells was increased in AAB and T1D. IAR B cells from these donors had altered expression of B cell signaling, pro-inflammatory, infection, and antigen processing and presentation genes. Both AAB and T1D donors demonstrated a significant increase in certain heavy and light chain V genes, and these V genes were enriched in islet-reactivity. Public clones of IAR B cells were restricted almost entirely to AAB and T1D donors. IAR B cells were clonally expanded in the autoimmune donors, particularly the AAB group. Notably, a substantial fraction of IAR B cells in AAB and T1D donors appeared to be polyreactive, which was corroborated by analysis of recombinant monoclonal antibodies. These results expand our understanding of autoreactive B cell activation during T1D and identify unique BCR repertoire changes that may serve as biomarkers for increased disease risk.
Collapse
Affiliation(s)
- Catherine A. Nicholas
- Barbara Davis Center for Diabetes, University of Colorado School of Medicine, Aurora, CO 80045, USA
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
- Molecular Biology Graduate Program, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Fatima A. Tensun
- Barbara Davis Center for Diabetes, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Spencer A. Evans
- Barbara Davis Center for Diabetes, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Kevin P. Toole
- Barbara Davis Center for Diabetes, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Hali Broncucia
- Barbara Davis Center for Diabetes, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Jay R Hesselberth
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
- Molecular Biology Graduate Program, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Peter A. Gottlieb
- Barbara Davis Center for Diabetes, University of Colorado School of Medicine, Aurora, CO 80045, USA
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Kristen L. Wells
- Barbara Davis Center for Diabetes, University of Colorado School of Medicine, Aurora, CO 80045, USA
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Mia J. Smith
- Barbara Davis Center for Diabetes, University of Colorado School of Medicine, Aurora, CO 80045, USA
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO 80045, USA
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| |
Collapse
|
11
|
Marconi A, Vernaz G, Karunaratna A, Ngochera MJ, Durbin R, Santos ME. Genetic and developmental divergence in the neural crest programme between cichlid fish species. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.30.578004. [PMID: 38352436 PMCID: PMC10862805 DOI: 10.1101/2024.01.30.578004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Neural crest (NC) is a vertebrate-specific embryonic progenitor cell population at the basis of important vertebrate features such as the craniofacial skeleton and pigmentation patterns. Despite the wide-ranging variation of NC-derived traits across vertebrates, the contribution of NC to species diversification remains underexplored. Here, leveraging the adaptive diversity of African Great Lakes' cichlid species, we combined comparative transcriptomics and population genomics to investigate the evolution of the NC genetic programme in the context of their morphological divergence. Our analysis revealed substantial differences in transcriptional landscapes across somitogenesis, an embryonic period coinciding with NC development and migration. This included dozens of genes with described functions in the vertebrate NC gene regulatory network, several of which showed signatures of positive selection. Among candidates showing between-species expression divergence, we focused on teleost-specific paralogs of the NC-specifier sox10 (sox10a and sox10b) as prime candidates to influence NC development. These genes, expressed in NC cells, displayed remarkable spatio-temporal variation in cichlids, suggesting their contribution to inter-specific morphological differences. Finally, through CRISPR/Cas9 mutagenesis, we demonstrated the functional divergence between cichlid sox10 paralogs, with the acquisition of a novel skeletogenic function by sox10a. When compared to the teleost models zebrafish and medaka, our findings reveal that sox10 duplication, although retained in most teleost lineages, had variable functional fates across their phylogeny. Altogether, our study suggests that NC-related processes - particularly those controlled by sox10s - might be involved in generating morphological diversification between species and lays the groundwork for further investigations into mechanisms underpinning vertebrate NC diversification.
Collapse
Affiliation(s)
| | | | | | - Maxon J. Ngochera
- Senga Bay Fisheries Research Center, Malawi Fisheries Department, P.O. Box 316, Salima, Malawi
| | - Richard Durbin
- Department of Genetics, University of Cambridge, United Kingdom
| | | |
Collapse
|
12
|
Wang L, Fu Y, Yuan Z, Wang J, Guan Y. Identification and analysis of short-term and long-term salt-associated lncRNAs in the leaf of Avicennia marina. BMC PLANT BIOLOGY 2024; 24:500. [PMID: 38840244 PMCID: PMC11151563 DOI: 10.1186/s12870-024-05216-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 05/29/2024] [Indexed: 06/07/2024]
Abstract
As a highly salt-resistant mangrove, Avicennia marina can thrive in the hypersaline water. The leaves of Avicennia marina play a crucial role in salinity stress adaptability by secreting salt. Although the functions of long non-coding RNAs (lncRNAs) in leaves remain unknown, they have emerged as regulators in leaf development, aging and salt response. In this study, we employed transcriptomic data of both short-term and long-term salt treated leaves to identify salt-associated lncRNAs of leaf tissue. As a result, 687 short-term and 797 long-term salt-associated lncRNAs were identified. Notably, both short-term and long-term salt-associated lncRNAs exhibited slightly longer lengths and larger exons, but smaller introns compared with salt-non-associated lncRNAs. Furthermore, salt-associated lncRNAs also displayed higher tissue-specificity than salt-non-associated lncRNAs. Most of the salt-associated lncRNAs were common to short- and long-term salt treatments. And about one fifth of the downregulated salt-associated lncRNAs identified both in two terms were leaf tissue-specific lncRNAs. Besides, these leaf-specific lncRNAs were found to be involved in the oxidation-reduction and photosynthesis processes, as well as several metabolic processes, suggesting the noticeable functions of salt-associated lncRNAs in regulating salt responses of Avicennia marina leaves.
Collapse
Affiliation(s)
- Lingling Wang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, 571158, China.
| | - Yixuan Fu
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, 571158, China
| | - Zixin Yuan
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, 571158, China
| | - Jingyi Wang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, 571158, China
| | - Yali Guan
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, 571158, China.
- Hainan Observation and Research Station of Dongzhaigang Mangrove Wetland Ecosystem, Haikou, 571158, China.
| |
Collapse
|
13
|
Soelter TM, Howton TC, Wilk EJ, Whitlock JH, Clark AD, Birnbaum A, Patterson DC, Cortes CJ, Lasseigne BN. Evaluation of altered cell-cell communication between glia and neurons in the hippocampus of 3xTg-AD mice at two time points. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.21.595199. [PMID: 38826305 PMCID: PMC11142088 DOI: 10.1101/2024.05.21.595199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Alzheimer's disease (AD) is the most common form of dementia and is characterized by progressive memory loss and cognitive decline, affecting behavior, speech, and motor abilities. The neuropathology of AD includes the formation of extracellular amyloid-β plaque and intracellular neurofibrillary tangles of phosphorylated tau, along with neuronal loss. While neuronal loss is an AD hallmark, cell-cell communication between neuronal and non-neuronal cell populations maintains neuronal health and brain homeostasis. To study changes in cell-cell communication during disease progression, we performed snRNA-sequencing of the hippocampus from female 3xTg-AD and wild-type littermates at 6 and 12 months. We inferred differential cell-cell communication between 3xTg-AD and wild-type mice across time points and between senders (astrocytes, microglia, oligodendrocytes, and OPCs) and receivers (excitatory and inhibitory neurons) of interest. We also assessed the downstream effects of altered glia-neuron communication using pseudobulk differential gene expression, functional enrichment, and gene regulatory analyses. We found that glia-neuron communication is increasingly dysregulated in 12-month 3xTg-AD mice. We also identified 23 AD-associated ligand-receptor pairs that are upregulated in the 12-month-old 3xTg-AD hippocampus. Our results suggest increased AD association of interactions originating from microglia. Signaling mediators were not significantly differentially expressed but showed altered gene regulation and TF activity. Our findings indicate that altered glia-neuron communication is increasingly dysregulated and affects the gene regulatory mechanisms in neurons of 12-month-old 3xTg-AD mice.
Collapse
Affiliation(s)
- Tabea M. Soelter
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Timothy C. Howton
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Elizabeth J. Wilk
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Jordan H. Whitlock
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Amanda D. Clark
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Allison Birnbaum
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Dalton C. Patterson
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Constanza J. Cortes
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California, United States of America
| | - Brittany N. Lasseigne
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| |
Collapse
|
14
|
Pan Y, Chiu TP, Zhou L, Chan P, Kuo TT, Battaglin F, Soni S, Jayachandran P, Li JJ, Lenz HJ, Mumenthaler SM, Rohs R, Torres ER, Kay SA. Targeting circadian transcriptional programs in triple negative breast cancer through a cis-regulatory mechanism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.26.590360. [PMID: 38746115 PMCID: PMC11092448 DOI: 10.1101/2024.04.26.590360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Circadian clock genes are emerging targets in many types of cancer, but their mechanistic contributions to tumor progression are still largely unknown. This makes it challenging to stratify patient populations and develop corresponding treatments. In this work, we show that in breast cancer, the disrupted expression of circadian genes has the potential to serve as biomarkers. We also show that the master circadian transcription factors (TFs) BMAL1 and CLOCK are required for the proliferation of metastatic mesenchymal stem-like (mMSL) triple-negative breast cancer (TNBC) cells. Using currently available small molecule modulators, we found that a stabilizer of cryptochrome 2 (CRY2), the direct repressor of BMAL1 and CLOCK transcriptional activity, synergizes with inhibitors of proteasome, which is required for BMAL1 and CLOCK function, to repress a transcriptional program comprising circadian cycling genes in mMSL TNBC cells. Omics analyses on drug-treated cells implied that this repression of transcription is mediated by the transcription factor binding sites (TFBSs) features in the cis-regulatory elements (CRE) of clock-controlled genes. Through a massive parallel reporter assay, we defined a set of CRE features that are potentially repressed by the specific drug combination. The identification of cis -element enrichment may serve as a new way of defining and targeting tumor types through the modulation of cis -regulatory programs, and ultimately provide a new paradigm of therapy design for cancer types with unclear drivers like TNBC.
Collapse
|
15
|
Fisher JL, Wilk EJ, Oza VH, Gary SE, Howton TC, Flanary VL, Clark AD, Hjelmeland AB, Lasseigne BN. Signature reversion of three disease-associated gene signatures prioritizes cancer drug repurposing candidates. FEBS Open Bio 2024; 14:803-830. [PMID: 38531616 PMCID: PMC11073506 DOI: 10.1002/2211-5463.13796] [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: 02/11/2024] [Revised: 03/13/2024] [Accepted: 03/14/2024] [Indexed: 03/28/2024] Open
Abstract
Drug repurposing is promising because approving a drug for a new indication requires fewer resources than approving a new drug. Signature reversion detects drug perturbations most inversely related to the disease-associated gene signature to identify drugs that may reverse that signature. We assessed the performance and biological relevance of three approaches for constructing disease-associated gene signatures (i.e., limma, DESeq2, and MultiPLIER) and prioritized the resulting drug repurposing candidates for four low-survival human cancers. Our results were enriched for candidates that had been used in clinical trials or performed well in the PRISM drug screen. Additionally, we found that pamidronate and nimodipine, drugs predicted to be efficacious against the brain tumor glioblastoma (GBM), inhibited the growth of a GBM cell line and cells isolated from a patient-derived xenograft (PDX). Our results demonstrate that by applying multiple disease-associated gene signature methods, we prioritized several drug repurposing candidates for low-survival cancers.
Collapse
Affiliation(s)
- Jennifer L. Fisher
- Department of Cell, Developmental and Integrative Biology, Heersink School of MedicineThe University of Alabama at BirminghamALUSA
| | - Elizabeth J. Wilk
- Department of Cell, Developmental and Integrative Biology, Heersink School of MedicineThe University of Alabama at BirminghamALUSA
| | - Vishal H. Oza
- Department of Cell, Developmental and Integrative Biology, Heersink School of MedicineThe University of Alabama at BirminghamALUSA
| | - Sam E. Gary
- Department of Cell, Developmental and Integrative Biology, Heersink School of MedicineThe University of Alabama at BirminghamALUSA
| | - Timothy C. Howton
- Department of Cell, Developmental and Integrative Biology, Heersink School of MedicineThe University of Alabama at BirminghamALUSA
| | - Victoria L. Flanary
- Department of Cell, Developmental and Integrative Biology, Heersink School of MedicineThe University of Alabama at BirminghamALUSA
| | - Amanda D. Clark
- Department of Cell, Developmental and Integrative Biology, Heersink School of MedicineThe University of Alabama at BirminghamALUSA
| | - Anita B. Hjelmeland
- Department of Cell, Developmental and Integrative Biology, Heersink School of MedicineThe University of Alabama at BirminghamALUSA
| | - Brittany N. Lasseigne
- Department of Cell, Developmental and Integrative Biology, Heersink School of MedicineThe University of Alabama at BirminghamALUSA
| |
Collapse
|
16
|
Hill CM, Indeglia A, Picone F, Murphy ME, Cipriano C, Maki RG, Gardini A. NAB2-STAT6 drives an EGR1-dependent neuroendocrine program in Solitary Fibrous Tumors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.15.589533. [PMID: 38659891 PMCID: PMC11042251 DOI: 10.1101/2024.04.15.589533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
The pathogenesis of many rare tumor types is poorly understood, preventing the design of effective treatments. Solitary fibrous tumors (SFTs) are neoplasms of mesenchymal origin that affect 1/1,000,000 individuals every year and are clinically assimilated to soft tissue sarcomas. SFTs can arise throughout the body and are usually managed surgically. However, 30-40% of SFTs will relapse local-regionally or metastasize. There are no systemic therapies with durable activity for malignant SFTs to date. The molecular hallmark of SFTs is a gene fusion between the NAB2 and STAT6 loci on chromosome 12, resulting in a chimeric protein of poorly characterized function called NAB2-STAT6. We use primary samples and an inducible cell model to discover that NAB2-STAT6 operates as a transcriptional coactivator for a specific set of enhancers and promoters that are normally targeted by the EGR1 transcription factor. In physiological conditions, NAB2 is primarily localized to the cytoplasm and only a small nuclear fraction is available to operate as a co-activator of EGR1 targets. NAB2-STAT6 redirects NAB1, NAB2, and additional EGR1 to the nucleus and bolster the expression of neuronal EGR1 targets. The STAT6 moiety of the fusion protein is a major driver of its nuclear localization and further contributes to NAB2's co-activating abilities. In primary tumors, NAB2-STAT6 activates a neuroendocrine gene signature that sets it apart from most sarcomas. These discoveries provide new insight into the pathogenesis of SFTs and reveal new targets with therapeutic potential.
Collapse
Affiliation(s)
- Connor M Hill
- The Wistar Institute, Philadelphia, PA, US
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, U.S
| | - Alexandra Indeglia
- The Wistar Institute, Philadelphia, PA, US
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, U.S
| | | | | | - Cara Cipriano
- Department of Orthopedic Surgery, University of Pennsylvania, Philadelphia, PA, U.S
| | - Robert G Maki
- Department of Orthopedic Surgery, University of Pennsylvania, Philadelphia, PA, U.S
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, U.S
| | | |
Collapse
|
17
|
Benfica LF, Brito LF, do Bem RD, de Oliveira LF, Mulim HA, Braga LG, Cyrillo JNSG, Bonilha SFM, Mercadante MEZ. Detection and characterization of copy number variation in three differentially-selected Nellore cattle populations. Front Genet 2024; 15:1377130. [PMID: 38694873 PMCID: PMC11061390 DOI: 10.3389/fgene.2024.1377130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 04/05/2024] [Indexed: 05/04/2024] Open
Abstract
Introduction: Nellore cattle (Bos taurus indicus) is the main beef cattle breed raised in Brazil. This breed is well adapted to tropical conditions and, more recently, has experienced intensive genetic selection for multiple performance traits. Over the past 43 years, an experimental breeding program has been developed in the Institute of Animal Science (IZ, Sertaozinho, SP, Brazil), which resulted in three differentially-selected lines known as Nellore Control (NeC), Nellore Selection (NeS), and Nellore Traditional (NeT). The primary goal of this selection experiment was to determine the response to selection for yearling weight (YW) and residual feed intake (RFI) on Nellore cattle. The main objectives of this study were to: 1) identify copy number variation (CNVs) in Nellore cattle from three selection lines; 2) identify and characterize CNV regions (CNVR) on these three lines; and 3) perform functional enrichment analyses of the CNVR identified. Results: A total of 14,914 unique CNVs and 1,884 CNVRs were identified when considering all lines as a single population. The CNVRs were non-uniformly distributed across the chromosomes of the three selection lines included in the study. The NeT line had the highest number of CNVRs (n = 1,493), followed by the NeS (n = 823) and NeC (n = 482) lines. The CNVRs covered 23,449,890 bp (0.94%), 40,175,556 bp (1.61%), and 63,212,273 bp (2.54%) of the genome of the NeC, NeS, and NeT lines, respectively. Two CNVRs were commonly identified between the three lines, and six, two, and four exclusive regions were identified for NeC, NeS, and NeT, respectively. All the exclusive regions overlap with important genes, such as SMARCD3, SLC15A1, and MAPK1. Key biological processes associated with the candidate genes were identified, including pathways related to growth and metabolism. Conclusion: This study revealed large variability in CNVs and CNVRs across three Nellore lines differentially selected for YW and RFI. Gene annotation and gene ontology analyses of the exclusive CNVRs to each line revealed specific genes and biological processes involved in the expression of growth and feed efficiency traits. These findings contribute to the understanding of the genetic mechanisms underlying the phenotypic differences among the three Nellore selection lines.
Collapse
Affiliation(s)
- Lorena F. Benfica
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
- Department of Animal Science, Faculty of Agricultural and Veterinary Sciences, Sao Paulo State University, Jaboticabal, São Paulo, Brazil
| | - Luiz F. Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
| | - Ricardo D. do Bem
- Department of Animal Science, Faculty of Agricultural and Veterinary Sciences, Sao Paulo State University, Jaboticabal, São Paulo, Brazil
| | | | - Henrique A. Mulim
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
| | - Larissa G. Braga
- Department of Animal Science, Faculty of Agricultural and Veterinary Sciences, Sao Paulo State University, Jaboticabal, São Paulo, Brazil
- Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | | | - Sarah F. M. Bonilha
- Beef Cattle Research Center, Institute of Animal Science, Sertaozinho, São Paulo, Brazil
| | - Maria Eugenia Z. Mercadante
- Department of Animal Science, Faculty of Agricultural and Veterinary Sciences, Sao Paulo State University, Jaboticabal, São Paulo, Brazil
- Beef Cattle Research Center, Institute of Animal Science, Sertaozinho, São Paulo, Brazil
| |
Collapse
|
18
|
Ceylan B, Düz E, Çakir T. Personalized Protein-Protein Interaction Networks Towards Unraveling the Molecular Mechanisms of Alzheimer's Disease. Mol Neurobiol 2024; 61:2120-2135. [PMID: 37855983 DOI: 10.1007/s12035-023-03690-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 10/02/2023] [Indexed: 10/20/2023]
Abstract
Alzheimer's disease (AD) is a highly heterogenous neurodegenerative disease, and several omic-based datasets were generated in the last decade from the patients with the disease. However, the vast majority of studies evaluate these datasets in bulk by considering all the patients as a single group, which obscures the molecular differences resulting from the heterogeneous nature of the disease. In this study, we adopted a personalized approach and analyzed the transcriptome data from 403 patients individually by mapping the data on a human protein-protein interaction network. Patient-specific subnetworks were discovered and analyzed in terms of the genes in the subnetworks, enriched functional terms, and known AD genes. We identified several affected pathways that could not be captured by the bulk comparison. We also showed that our personalized findings point to patterns of alterations consistent with the recently suggested AD subtypes.
Collapse
Affiliation(s)
- Betül Ceylan
- Department of Bioengineering, Gebze Technical University, 41400, Gebze, Kocaeli, Turkey
| | - Elif Düz
- Department of Bioengineering, Gebze Technical University, 41400, Gebze, Kocaeli, Turkey
| | - Tunahan Çakir
- Department of Bioengineering, Gebze Technical University, 41400, Gebze, Kocaeli, Turkey.
| |
Collapse
|
19
|
Quirion L, Robert A, Boulais J, Huang S, Bernal Astrain G, Strakhova R, Jo CH, Kherdjemil Y, Thibault MP, Faubert D, Kmita M, Baskin JM, Gingras AC, Smith MJ, Cote JF. Mapping the global interactome of the ARF family reveals spatial organization in cellular signaling pathways. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.03.01.530598. [PMID: 36909472 PMCID: PMC10002736 DOI: 10.1101/2023.03.01.530598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
The ADP-ribosylation factors (ARFs) and ARF-like (ARLs) GTPases serve as essential molecular switches governing a wide array of cellular processes. In this study, we utilized proximity-dependent biotin identification (BioID) to comprehensively map the interactome of 28 out of 29 ARF and ARL proteins in two cellular models. Through this approach, we identified ~3000 high-confidence proximal interactors, enabling us to assign subcellular localizations to the family members. Notably, we uncovered previously undefined localizations for ARL4D and ARL10. Clustering analyses further exposed the distinctiveness of the interactors identified with these two GTPases. We also reveal that the expression of the understudied member ARL14 is confined to the stomach and intestines. We identified phospholipase D1 (PLD1) and the ESCPE-1 complex, more precisely SNX1, as proximity interactors. Functional assays demonstrated that ARL14 can activate PLD1 in cellulo and is involved in cargo trafficking via the ESCPE-1 complex. Overall, the BioID data generated in this study provide a valuable resource for dissecting the complexities of ARF and ARL spatial organization and signaling.
Collapse
|
20
|
Fan X, Huang K, Wu Y, Jin S, Pang L, Wang Y, Jin B, Sun X. A specific inflammatory suppression fibroblast subpopulation characterized by MHCII expression in human dilated cardiomyopathy. Mol Cell Biochem 2024:10.1007/s11010-024-04939-9. [PMID: 38462549 DOI: 10.1007/s11010-024-04939-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 01/12/2024] [Indexed: 03/12/2024]
Abstract
Dilated cardiomyopathy (DCM) is a significant cause of heart failure that requires heart transplantation. Fibroblasts play a central role in the fibro-inflammatory microenvironment of DCM. However, their cellular heterogeneity and interaction with immune cells have not been well identified. An integrative analysis was conducted on single-cell RNA sequencing (ScRNA-Seq) data from human left ventricle tissues, which comprised 4 hearts from healthy donors and 6 hearts with DCM. The specific antigen-presenting fibroblast (apFB) was explored as a subtype of fibroblasts characterized by expressing MHCII genes, the existence of which was confirmed by immunofluorescence staining of 3 cardiac tissues from DCM patients with severe heart failure. apFB highly expressed the genes that response to IFN-γ, and it also have a high activity of the JAK-STAT pathway and the transcription factor RFX5. In addition, the analysis of intercellular communication between apFBs and CD4+T cells revealed that the anti-inflammatory ligand-receptor pairs TGFB-TGFR, CLEC2B-KLRB1, and CD46-JAG1 were upregulated in DCM. The apFB signature exhibited a positive correlation with immunosuppression and demonstrated diagnostic and prognostic value when evaluated using a bulk RNA dataset comprising 166 donors and 166 DCM samples. In conclusion, the present study identified a novel subpopulation of fibroblasts that specifically expresses MHCII-encoding genes. This specific apFBs can suppress the inflammation occurring in DCM. Our findings further elucidate the composition of the fibro-inflammatory microenvironment in DCM, and provide a novel therapeutic target.
Collapse
Affiliation(s)
- Xi Fan
- Department of Cardiothoracic Surgery, Huashan Hospital of Fudan University, 12 Wulumuqi Rd, Shanghai, 200040, China
| | - Kai Huang
- Department of Cardiothoracic Surgery, Huashan Hospital of Fudan University, 12 Wulumuqi Rd, Shanghai, 200040, China
| | - Yuming Wu
- Department of Physiology, Hebei Medical University, Shijiazhuang, China
| | - Sheng Jin
- Department of Physiology, Hebei Medical University, Shijiazhuang, China
| | - Liewen Pang
- Department of Cardiothoracic Surgery, Huashan Hospital of Fudan University, 12 Wulumuqi Rd, Shanghai, 200040, China
| | - Yiqing Wang
- Department of Cardiothoracic Surgery, Huashan Hospital of Fudan University, 12 Wulumuqi Rd, Shanghai, 200040, China.
| | - Bo Jin
- Department of Cardiology, Huashan Hospital of Fudan University, 12 Wulumuqi Rd, Shanghai, 200040, China.
| | - Xiaotian Sun
- Department of Cardiothoracic Surgery, Huashan Hospital of Fudan University, 12 Wulumuqi Rd, Shanghai, 200040, China.
| |
Collapse
|
21
|
Kolic J, Sun WG, Cen HH, Ewald J, Rogalski JC, Sasaki S, Sun H, Rajesh V, Xia YH, Moravcova R, Skovsø S, Spigelman AF, Manning Fox JE, Lyon J, Beet L, Xia J, Lynn FC, Gloyn AL, Foster LJ, MacDonald PE, Johnson JD. Proteomic predictors of individualized nutrient-specific insulin secretion in health and disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.05.24.23290298. [PMID: 38496562 PMCID: PMC10942505 DOI: 10.1101/2023.05.24.23290298] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Population level variation and molecular mechanisms behind insulin secretion in response to carbohydrate, protein, and fat remain uncharacterized despite ramifications for personalized nutrition. Here, we define prototypical insulin secretion dynamics in response to the three macronutrients in islets from 140 cadaveric donors, including those diagnosed with type 2 diabetes. While islets from the majority of donors exhibited the expected relative response magnitudes, with glucose being highest, amino acid moderate, and fatty acid small, 9% of islets stimulated with amino acid and 8% of islets stimulated with fatty acids had larger responses compared with high glucose. We leveraged this insulin response heterogeneity and used transcriptomics and proteomics to identify molecular correlates of specific nutrient responsiveness, as well as those proteins and mRNAs altered in type 2 diabetes. We also examine nutrient-responsiveness in stem cell-derived islet clusters and observe that they have dysregulated fuel sensitivity, which is a hallmark of functionally immature cells. Our study now represents the first comparison of dynamic responses to nutrients and multi-omics analysis in human insulin secreting cells. Responses of different people's islets to carbohydrate, protein, and fat lay the groundwork for personalized nutrition. ONE-SENTENCE SUMMARY Deep phenotyping and multi-omics reveal individualized nutrient-specific insulin secretion propensity.
Collapse
|
22
|
Lawarde A, Sharif Rahmani E, Nath A, Lavogina D, Jaal J, Salumets A, Modhukur V. ExplORRNet: An interactive web tool to explore stage-wise miRNA expression profiles and their interactions with mRNA and lncRNA in human breast and gynecological cancers. Noncoding RNA Res 2024; 9:125-140. [PMID: 38035042 PMCID: PMC10686811 DOI: 10.1016/j.ncrna.2023.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 12/02/2023] Open
Abstract
Background MicroRNAs (miRNAs) are key regulators of gene expression that have been implicated in gynecological and breast cancers. Understanding the cancer stage-wise expression patterns of miRNAs and their interactions with other RNA molecules in cancer is crucial to improve cancer diagnosis and treatment planning. Comprehensive web tools that integrate data on the transcriptome, circulating miRNAs, and their validated targets to derive beneficial conclusions in cancer research are lacking. Methods Using the Shiny R package, we developed a web tool called ExplORRNet that integrates transcriptomic profiles from The Cancer Genome Atlas and miRNA expression data derived from various sources, including tissues, cell lines, exosomes, serum, and plasma, available in the Gene Expression Omnibus database. Differential expression analyses between normal and tumor tissue samples as well as different stages of cancer, accompanied by gene enrichment and survival analyses, can be performed using specialized R packages. Additionally, a miRNA-messenger RNA (mRNA)-long non-coding RNA (lncRNA) networks are constructed to identify regulatory modules. Results Our tool identifies cancer stage-wise differentially regulated miRNAs, mRNAs, and lncRNAs in gynecological and breast cancers. Survival analysis identifies miRNAs associated with patient survival, and functional enrichment analysis provides insights into dysregulated miRNA-related biological processes and pathways. The miRNA-mRNA-lncRNA networks highlight interconnected regulatory molecular modules driving cancer progression. Case studies demonstrate the utility of the ExplORRNet for studying gynecological and breast cancers. Conclusion ExplORRNet is an intuitive and user-friendly web tool that provides a deeper understanding of dysregulated miRNAs and their functional implications in gynecological and breast cancers. We hope our ExplORRNet tool has potential utility among the clinical and basic researchers and will be beneficial to the entire cancer genomics community to encourage and facilitate mining the rapidly growing public databases to progress the field of precision oncology. The ExplORRNet is available at https://mirna.cs.ut.ee.
Collapse
Affiliation(s)
- Ankita Lawarde
- Competence Centre on Health Technologies, Tartu, Estonia
- Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | | | - Adhiraj Nath
- Bioengineering Research Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, North Guwahati, Assam, India
| | - Darja Lavogina
- Competence Centre on Health Technologies, Tartu, Estonia
- Institute of Clinical Medicine, Faculty of Medicine, University of Tartu, Estonia
- Institute of Chemistry, University of Tartu, Estonia
| | - Jana Jaal
- Institute of Clinical Medicine, Faculty of Medicine, University of Tartu, Estonia
- Haematology and Oncology Clinic, Tartu University Hospital, Tartu, Estonia
| | - Andres Salumets
- Competence Centre on Health Technologies, Tartu, Estonia
- Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
- Division of Obstetrics and Gynecology, Department of Clinical Science, Intervention and Technology, Karolinska Institute and Karolinska University Hospital, Stockholm, Sweden
| | - Vijayachitra Modhukur
- Competence Centre on Health Technologies, Tartu, Estonia
- Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| |
Collapse
|
23
|
Kasap C, Izgutdina A, Patiño-Escobar B, Kang A, Chilakapati N, Akagi N, Johnson H, Rashid T, Werner J, Barpanda A, Geng H, Lin YHT, Rampersaud S, Gil-Alós D, Sobh A, Dupéré-Richer D, Wicaksono G, Kawehi Kelii K, Dalal R, Ramos E, Vijayanarayanan A, Salangsang F, Phojanakong P, Serrano JAC, Zakraoui O, Tariq I, Steri V, Shanmugam M, Boise LH, Kortemme T, Stieglitz E, Licht JD, Karlon WJ, Barwick BG, Wiita AP. Targeting high-risk multiple myeloma genotypes with optimized anti-CD70 CAR-T cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.24.581875. [PMID: 38463958 PMCID: PMC10925123 DOI: 10.1101/2024.02.24.581875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Despite the success of BCMA-targeting CAR-Ts in multiple myeloma, patients with high-risk cytogenetic features still relapse most quickly and are in urgent need of additional therapeutic options. Here, we identify CD70, widely recognized as a favorable immunotherapy target in other cancers, as a specifically upregulated cell surface antigen in high risk myeloma tumors. We use a structure-guided design to define a CD27-based anti-CD70 CAR-T design that outperforms all tested scFv-based CARs, leading to >80-fold improved CAR-T expansion in vivo. Epigenetic analysis via machine learning predicts key transcription factors and transcriptional networks driving CD70 upregulation in high risk myeloma. Dual-targeting CAR-Ts against either CD70 or BCMA demonstrate a potential strategy to avoid antigen escape-mediated resistance. Together, these findings support the promise of targeting CD70 with optimized CAR-Ts in myeloma as well as future clinical translation of this approach.
Collapse
Affiliation(s)
- Corynn Kasap
- Dept. of Medicine, Division of Hematology/Oncology, University of California, San Francisco, CA
- Dept. of Laboratory Medicine, University of California, San Francisco, CA
| | - Adila Izgutdina
- Dept. of Laboratory Medicine, University of California, San Francisco, CA
| | | | - Amrik Kang
- Dept. of Laboratory Medicine, University of California, San Francisco, CA
- Medical Scientist Training Program, University of California, San Francisco, CA
| | - Nikhil Chilakapati
- Dept. of Laboratory Medicine, University of California, San Francisco, CA
| | - Naomi Akagi
- Dept. of Laboratory Medicine, University of California, San Francisco, CA
| | - Haley Johnson
- Dept. of Laboratory Medicine, University of California, San Francisco, CA
| | - Tasfia Rashid
- Dept. of Laboratory Medicine, University of California, San Francisco, CA
| | - Juwita Werner
- Dept. of Pediatrics, Division of Oncology, University of California, San Francisco, CA
| | - Abhilash Barpanda
- Dept. of Laboratory Medicine, University of California, San Francisco, CA
| | - Huimin Geng
- Dept. of Laboratory Medicine, University of California, San Francisco, CA
| | - Yu-Hsiu T. Lin
- Dept. of Laboratory Medicine, University of California, San Francisco, CA
| | - Sham Rampersaud
- Dept. of Laboratory Medicine, University of California, San Francisco, CA
| | - Daniel Gil-Alós
- Dept. of Laboratory Medicine, University of California, San Francisco, CA
- Dept of Hematology, Hospital 12 de Octubre, Madrid, Spain
| | - Amin Sobh
- University of Florida Health Cancer Center, The University of Florida Cancer and Genetics Research Complex, Gainesville, Florida
- Division of Hematology/Oncology, The University of Florida College of Medicine, Gainesville, Florida
| | - Daphné Dupéré-Richer
- University of Florida Health Cancer Center, The University of Florida Cancer and Genetics Research Complex, Gainesville, Florida
- Division of Hematology/Oncology, The University of Florida College of Medicine, Gainesville, Florida
| | - Gianina Wicaksono
- Dept. of Laboratory Medicine, University of California, San Francisco, CA
| | - K.M. Kawehi Kelii
- Dept. of Laboratory Medicine, University of California, San Francisco, CA
| | - Radhika Dalal
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA
| | - Emilio Ramos
- Dept. of Laboratory Medicine, University of California, San Francisco, CA
| | | | - Fernando Salangsang
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
| | - Paul Phojanakong
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
| | | | - Ons Zakraoui
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
| | - Isa Tariq
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
| | - Veronica Steri
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
| | - Mala Shanmugam
- Department of Hematology and Medical Oncology, Winship Cancer Institute, School of Medicine, Emory University, Atlanta, GA
| | - Lawrence H. Boise
- Department of Hematology and Medical Oncology, Winship Cancer Institute, School of Medicine, Emory University, Atlanta, GA
| | - Tanja Kortemme
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA
- Chan Zuckerberg Biohub San Francisco, San Francisco, CA
| | - Elliot Stieglitz
- Dept. of Pediatrics, Division of Oncology, University of California, San Francisco, CA
| | - Jonathan D. Licht
- University of Florida Health Cancer Center, The University of Florida Cancer and Genetics Research Complex, Gainesville, Florida
- Division of Hematology/Oncology, The University of Florida College of Medicine, Gainesville, Florida
| | - William J. Karlon
- Dept. of Laboratory Medicine, University of California, San Francisco, CA
| | - Benjamin G. Barwick
- Department of Hematology and Medical Oncology, Winship Cancer Institute, School of Medicine, Emory University, Atlanta, GA
| | - Arun P. Wiita
- Dept. of Laboratory Medicine, University of California, San Francisco, CA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Chan Zuckerberg Biohub San Francisco, San Francisco, CA
| |
Collapse
|
24
|
Tremblay BJM, Santini CP, Cheng Y, Zhang X, Rosa S, Qüesta JI. Interplay between coding and non-coding regulation drives the Arabidopsis seed-to-seedling transition. Nat Commun 2024; 15:1724. [PMID: 38409232 PMCID: PMC10897432 DOI: 10.1038/s41467-024-46082-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 02/14/2024] [Indexed: 02/28/2024] Open
Abstract
Translation of seed stored mRNAs is essential to trigger germination. However, when RNAPII re-engages RNA synthesis during the seed-to-seedling transition has remained in question. Combining csRNA-seq, ATAC-seq and smFISH in Arabidopsis thaliana we demonstrate that active transcription initiation is detectable during the entire germination process. Features of non-coding regulation such as dynamic changes in chromatin accessible regions, antisense transcription, as well as bidirectional non-coding promoters are widespread throughout the Arabidopsis genome. We show that sensitivity to exogenous ABSCISIC ACID (ABA) during germination depends on proximal promoter accessibility at ABA-responsive genes. Moreover, we provide genetic validation of the existence of divergent transcription in plants. Our results reveal that active enhancer elements are transcribed producing non-coding enhancer RNAs (eRNAs) as widely documented in metazoans. In sum, this study defining the extent and role of coding and non-coding transcription during key stages of germination expands our understanding of transcriptional mechanisms underlying plant developmental transitions.
Collapse
Affiliation(s)
- Benjamin J M Tremblay
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain
| | - Cristina P Santini
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain
| | - Yajiao Cheng
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain
| | - Xue Zhang
- Plant Biology Department, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Stefanie Rosa
- Plant Biology Department, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Julia I Qüesta
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain.
| |
Collapse
|
25
|
Lien HJT, Pedersen TT, Jakobsen B, Flatberg A, Chawla K, Sætrom P, Fenstad MH. Single-cell resolution of longitudinal blood transcriptome profiles in rheumatoid arthritis, systemic lupus erythematosus and healthy control pregnancies. Ann Rheum Dis 2024; 83:300-311. [PMID: 38049980 PMCID: PMC10894842 DOI: 10.1136/ard-2023-224644] [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: 06/28/2023] [Accepted: 11/10/2023] [Indexed: 12/06/2023]
Abstract
OBJECTIVES Comparative longitudinal analyses of cellular composition and peripheral blood gene expression in Rheumatoid arthritis (RA), systemic lupus erythematosus (SLE) and healthy pregnancies. METHODS In total, 335 whole blood samples from 84 RA, SLE and healthy controls before pregnancy, at each trimester, 6 weeks, 6 months and 12 months post partum were analysed. We combined bulk and single cell RNA analyses for cell-type estimation, validated by flow cytometry, before combining this in a cell-type adjusted analysis for an improved resolution of unrecognised gene expression changes associated with RA and SLE pregnancies. RESULTS Patients were well regulated throughout pregnancy, and few had pregnancy complications. In SLE, the interferon signature was augmented during pregnancy, and the pregnancy signature was continued post partum. An altered cell type composition strongly influences the profile. In the pregnancy signature, transcripts involved in galactosylation potentially altering the effector functions of autoantibodies became more evident. Several genes in the adjusted RA signature are expressed in mucosal associated invariant T cells. CONCLUSION We found distinct RA, SLE and pregnancy signatures, and no expression patterns could be attributed to medication or disease activity. Our results support the need for close postpartum follow-up of patients with SLE. Gene expression patterns in RA were closer to healthy controls than to SLE, and primarily became evident after cell-type adjustment. Adjusting for cell abundance unravelled gene expression signatures less associated with variation in cell-composition and highlighted genes with expression profiles associated with changes in specialised cell populations.
Collapse
Affiliation(s)
- Hilde Julie T Lien
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Tina T Pedersen
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
- Norwegian National Advisory Unit on Pregnancy and Rheumatic Diseases, Department of Rheumatology, St. Olavs hospital, Trondheim University Hospital, Trondheim, Norway
| | - Bente Jakobsen
- Norwegian National Advisory Unit on Pregnancy and Rheumatic Diseases, Department of Rheumatology, St. Olavs hospital, Trondheim University Hospital, Trondheim, Norway
| | - Arnar Flatberg
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
- Genomics Core Facility, HF, Sentral Stab, St. Olavs hospital, Trondheim University Hospital, Trondheim, Norway
| | - Konika Chawla
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
- BioCore - Bioinformatics Core Facility, HF, Sentral stab, St. Olavs hospital, Trondheim University Hospital, Trondheim, Norway
| | - Pål Sætrom
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Computer Science, Norwegian University of Science and Technology, Trondheim, Norway
| | - Mona H Fenstad
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Immunology and Transfusion Medicine, St. Olavs hospital, Trondheim University Hospital, Trondheim, Norway
| |
Collapse
|
26
|
Piron A, Szymczak F, Papadopoulou T, Alvelos MI, Defrance M, Lenaerts T, Eizirik DL, Cnop M. RedRibbon: A new rank-rank hypergeometric overlap for gene and transcript expression signatures. Life Sci Alliance 2024; 7:e202302203. [PMID: 38081640 PMCID: PMC10709657 DOI: 10.26508/lsa.202302203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
High-throughput omics technologies have generated a wealth of large protein, gene, and transcript datasets that have exacerbated the need for new methods to analyse and compare big datasets. Rank-rank hypergeometric overlap is an important threshold-free method to combine and visualize two ranked lists of P-values or fold-changes, usually from differential gene expression analyses. Here, we introduce a new rank-rank hypergeometric overlap-based method aimed at gene level and alternative splicing analyses at transcript or exon level, hitherto unreachable as transcript numbers are an order of magnitude larger than gene numbers. We tested the tool on synthetic and real datasets at gene and transcript levels to detect correlation and anticorrelation patterns and found it to be fast and accurate, even on very large datasets thanks to an evolutionary algorithm-based minimal P-value search. The tool comes with a ready-to-use permutation scheme allowing the computation of adjusted P-values at low time cost. The package compatibility mode is a drop-in replacement to previous packages. RedRibbon holds the promise to accurately extricate detailed information from large comparative analyses.
Collapse
Affiliation(s)
- Anthony Piron
- https://ror.org/01r9htc13 ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels (IB2), Brussels, Belgium
- https://ror.org/01r9htc13 Machine Learning Group, Université Libre de Bruxelles, Brussels, Belgium
| | - Florian Szymczak
- https://ror.org/01r9htc13 ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels (IB2), Brussels, Belgium
| | - Theodora Papadopoulou
- https://ror.org/01r9htc13 ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels (IB2), Brussels, Belgium
| | - Maria Inês Alvelos
- https://ror.org/01r9htc13 ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles, Brussels, Belgium
| | - Matthieu Defrance
- Interuniversity Institute of Bioinformatics in Brussels (IB2), Brussels, Belgium
- https://ror.org/01r9htc13 Machine Learning Group, Université Libre de Bruxelles, Brussels, Belgium
| | - Tom Lenaerts
- Interuniversity Institute of Bioinformatics in Brussels (IB2), Brussels, Belgium
- https://ror.org/01r9htc13 Machine Learning Group, Université Libre de Bruxelles, Brussels, Belgium
- Artificial Intelligence Lab, Vrije Universiteit Brussel, Brussels, Belgium
| | - Décio L Eizirik
- https://ror.org/01r9htc13 ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles, Brussels, Belgium
| | - Miriam Cnop
- https://ror.org/01r9htc13 ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles, Brussels, Belgium
- https://ror.org/01r9htc13 Division of Endocrinology, Erasmus Hospital, Université Libre de Bruxelles, Brussels, Belgium
| |
Collapse
|
27
|
Huau G, Liaubet L, Gourdine JL, Riquet J, Renaudeau D. Multi-tissue metabolic and transcriptomic responses to a short-term heat stress in swine. BMC Genomics 2024; 25:99. [PMID: 38262957 PMCID: PMC10804606 DOI: 10.1186/s12864-024-09999-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 01/09/2024] [Indexed: 01/25/2024] Open
Abstract
BACKGROUND Heat stress (HS) is an increasing threat for pig production with a wide range of impacts. When submitted to high temperatures, pigs will use a variety of strategies to alleviate the effect of HS. While systemic adaptations are well known, tissue-specific changes remain poorly understood. In this study, thirty-two pigs were submitted to a 5-day HS at 32 °C. RESULTS Transcriptomic and metabolomic analyses were performed on several tissues. The results revealed differentially expressed genes and metabolites in different tissues. Specifically, 481, 1774, 71, 1572, 17, 164, and 169 genes were differentially expressed in muscle, adipose tissue, liver, blood, thyroid, pituitary, and adrenal glands, respectively. Regulatory glands (pituitary, thyroid, and adrenal) had a lower number of regulated genes, perhaps indicating an earlier sensitivity to HS. In addition, 7, 8, 2, and 8 metabolites were differentially produced in muscle, liver, plasma, and urine, respectively. The study also focused on the oxidative stress pathway in muscle and liver by performing a correlation analysis between genes and metabolites. CONCLUSIONS This study has identified various adaptation mechanisms in swine that enable them to cope with heat stress (HS). These mechanisms include a global decrease in energetic metabolism, as well as changes in metabolic precursors that are linked with protein and lipid catabolism and anabolism. Notably, the adaptation mechanisms differ significantly between regulatory (pituitary, thyroid and adrenal glands) and effector tissues (muscle, adipose tissue, liver and blood). Our findings provide new insights into the comprehension of HS adaptation mechanisms in swine.
Collapse
Affiliation(s)
- Guilhem Huau
- GenPhySE, Université de Toulouse, INRAE, INPT, ENVT, 31326, Castanet Tolosan, France
- PEGASE, INRAE, Institut Agro, 35590, Saint-Gilles, France
| | - Laurence Liaubet
- GenPhySE, Université de Toulouse, INRAE, INPT, ENVT, 31326, Castanet Tolosan, France
| | | | - Juliette Riquet
- GenPhySE, Université de Toulouse, INRAE, INPT, ENVT, 31326, Castanet Tolosan, France
| | | |
Collapse
|
28
|
Southwell N, Manzo O, Zhao D, Sayles NM, Dash J, Fujita K, D'Aurelio M, Di Lorenzo A, Manfredi G, Kawamata H. High fat diet ameliorates mitochondrial cardiomyopathy in CHCHD10 mutant mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.22.529577. [PMID: 36865125 PMCID: PMC9980108 DOI: 10.1101/2023.02.22.529577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
Mutations in CHCHD10 , a mitochondrial protein with undefined functions, are associated with autosomal dominant mitochondrial diseases. Chchd10 knock-in mice harboring a heterozygous S55L mutation (equivalent to human pathogenic S59L) develop a fatal mitochondrial cardiomyopathy caused by CHCHD10 aggregation and proteotoxic mitochondrial integrated stress response (mtISR). In mutant hearts, mtISR is accompanied by a metabolic rewiring characterized by increased reliance on glycolysis rather than fatty acid oxidation. To counteract this metabolic rewiring, heterozygous S55L mice were subjected to chronic high fat diet (HFD) to decrease insulin sensitivity and glucose uptake and enhance fatty acid utilization in the heart. HFD ameliorated the ventricular dysfunction of mutant hearts and significantly extended the survival of mutant female mice affected by severe pregnancy-induced cardiomyopathy. Gene expression profiles confirmed that HFD increased fatty acid utilization and ameliorated cardiomyopathy markers. Importantly, HFD also decreased accumulation of aggregated CHCHD10 in the S55L heart, suggesting activation of quality control mechanisms. Overall, our findings indicate that metabolic therapy can be effective in mitochondrial cardiomyopathies associated with proteotoxic stress.
Collapse
|
29
|
Grieco SF, Johnston KG, Gao P, Garduño BM, Tang B, Yi E, Sun Y, Horwitz GD, Yu Z, Holmes TC, Xu X. Anatomical and molecular characterization of parvalbumin-cholecystokinin co-expressing inhibitory interneurons: implications for neuropsychiatric conditions. Mol Psychiatry 2023; 28:5293-5308. [PMID: 37443194 DOI: 10.1038/s41380-023-02153-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 05/15/2023] [Accepted: 06/19/2023] [Indexed: 07/15/2023]
Abstract
Inhibitory interneurons are crucial to brain function and their dysfunction is implicated in neuropsychiatric conditions. Emerging evidence indicates that cholecystokinin (CCK)-expressing interneurons (CCK+) are highly heterogenous. We find that a large subset of parvalbumin-expressing (PV+) interneurons express CCK strongly; between 40 and 56% of PV+ interneurons in mouse hippocampal CA1 express CCK. Primate interneurons also exhibit substantial PV/CCK co-expression. Mouse PV+/CCK+ and PV+/CCK- cells show distinguishable electrophysiological and molecular characteristics. Analysis of single nuclei RNA-seq and ATAC-seq data shows that PV+/CCK+ cells are a subset of PV+ cells, not of synuclein gamma positive (SNCG+) cells, and that they strongly express oxidative phosphorylation (OXPHOS) genes. We find that mitochondrial complex I and IV-associated OXPHOS gene expression is strongly correlated with CCK expression in PV+ interneurons at both the transcriptomic and protein levels. Both PV+ interneurons and dysregulation of OXPHOS processes are implicated in neuropsychiatric conditions, including autism spectrum (ASD) disorder and schizophrenia (SCZ). Analysis of human brain samples from patients with these conditions shows alterations in OXPHOS gene expression. Together these data reveal important molecular characteristics of PV-CCK co-expressing interneurons and support their implication in neuropsychiatric conditions.
Collapse
Affiliation(s)
- Steven F Grieco
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, CA, 92697, USA
- Center for Neural Circuit Mapping, University of California, Irvine, CA, 92697, USA
| | - Kevin G Johnston
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, CA, 92697, USA
- Department of Mathematics, School of Physical Sciences, University of California, Irvine, CA, 92697, USA
| | - Pan Gao
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, CA, 92697, USA
| | - B Maximiliano Garduño
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, CA, 92697, USA
| | - Bryan Tang
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, CA, 92697, USA
| | - Elsie Yi
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, CA, 92697, USA
| | - Yanjun Sun
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, CA, 92697, USA
| | - Gregory D Horwitz
- Center for Neural Circuit Mapping, University of California, Irvine, CA, 92697, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, 98195, USA
| | - Zhaoxia Yu
- Center for Neural Circuit Mapping, University of California, Irvine, CA, 92697, USA
- Department of Statistics, Donald Bren School of Information and Computer Sciences, University of California, Irvine, CA, 92697, USA
| | - Todd C Holmes
- Center for Neural Circuit Mapping, University of California, Irvine, CA, 92697, USA
- Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA, 92697, USA
| | - Xiangmin Xu
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, CA, 92697, USA.
- Center for Neural Circuit Mapping, University of California, Irvine, CA, 92697, USA.
- Department of Microbiology and Molecular Genetics, University of California, Irvine, CA, 92697, USA.
- Department of Biomedical Engineering, University of California, Irvine, CA, 92697, USA.
- Department of Computer Science, University of California, Irvine, CA, 92697, USA.
| |
Collapse
|
30
|
Stauffer EM, Bethlehem RAI, Dorfschmidt L, Won H, Warrier V, Bullmore ET. The genetic relationships between brain structure and schizophrenia. Nat Commun 2023; 14:7820. [PMID: 38016951 PMCID: PMC10684873 DOI: 10.1038/s41467-023-43567-7] [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: 04/06/2023] [Accepted: 11/14/2023] [Indexed: 11/30/2023] Open
Abstract
Genetic risks for schizophrenia are theoretically mediated by genetic effects on brain structure but it has been unclear which genes are associated with both schizophrenia and cortical phenotypes. We accessed genome-wide association studies (GWAS) of schizophrenia (N = 69,369 cases; 236,642 controls), and of three magnetic resonance imaging (MRI) metrics (surface area, cortical thickness, neurite density index) measured at 180 cortical areas (N = 36,843, UK Biobank). Using Hi-C-coupled MAGMA, 61 genes were significantly associated with both schizophrenia and one or more MRI metrics. Whole genome analysis with partial least squares demonstrated significant genetic covariation between schizophrenia and area or thickness of most cortical regions. Genetic similarity between cortical areas was strongly coupled to their phenotypic covariance, and genetic covariation between schizophrenia and brain phenotypes was strongest in the hubs of structural covariance networks. Pleiotropically associated genes were enriched for neurodevelopmental processes and positionally concentrated in chromosomes 3p21, 17q21 and 11p11. Mendelian randomization analysis indicated that genetically determined variation in a posterior cingulate cortical area could be causal for schizophrenia. Parallel analyses of GWAS on bipolar disorder, Alzheimer's disease and height showed that pleiotropic association with MRI metrics was stronger for schizophrenia compared to other disorders.
Collapse
Affiliation(s)
| | - Richard A I Bethlehem
- Department of Psychiatry, University of Cambridge, Cambridge, UK
- Department of Psychology, University of Cambridge, Cambridge, UK
| | - Lena Dorfschmidt
- Department of Psychiatry, University of Cambridge, Cambridge, UK
| | - Hyejung Won
- Department of Genetics and the Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Varun Warrier
- Department of Psychiatry, University of Cambridge, Cambridge, UK
- Department of Psychology, University of Cambridge, Cambridge, UK
| | - Edward T Bullmore
- Department of Psychiatry, University of Cambridge, Cambridge, UK
- Cambridgeshire & Peterborough NHS Foundation Trust, Cambridge, UK
| |
Collapse
|
31
|
Olusakin J, Kumar G, Basu M, Calarco CA, Fox ME, Alipio JB, Haga C, Turner MD, Keller A, Ament SA, Lobo MK. Transcriptomic profiling of reward and sensory brain areas in perinatal fentanyl exposed juvenile mice. Neuropsychopharmacology 2023; 48:1724-1734. [PMID: 37400565 PMCID: PMC10579237 DOI: 10.1038/s41386-023-01639-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 06/14/2023] [Accepted: 06/16/2023] [Indexed: 07/05/2023]
Abstract
Use of the synthetic opioid fentanyl increased ~300% in the last decade, including among women of reproductive ages. Adverse neonatal outcomes and long-term behavioral disruptions are associated with perinatal opioid exposure. Our previous work demonstrated that perinatal fentanyl exposed mice displayed enhanced negative affect and somatosensory circuit and behavioral disruptions during adolescence. However, little is known about molecular adaptations across brain regions that underlie these outcomes. We performed RNA sequencing across three reward and two sensory brain areas to study transcriptional programs in perinatal fentanyl exposed juvenile mice. Pregnant dams received 10 μg/ml fentanyl in the drinking water from embryonic day 0 (E0) through gestational periods until weaning at postnatal day 21 (P21). RNA was extracted from nucleus accumbens (NAc), prelimbic cortex (PrL), ventral tegmental area (VTA), somatosensory cortex (S1) and ventrobasal thalamus (VBT) from perinatal fentanyl exposed mice of both sexes at P35. RNA sequencing was performed, followed by analysis of differentially expressed genes (DEGs) and gene co-expression networks. Transcriptome analysis revealed DEGs and gene modules significantly associated with exposure to perinatal fentanyl in a sex-wise manner. The VTA had the most DEGs, while robust gene enrichment occurred in NAc. Genes enriched in mitochondrial respiration were pronounced in NAc and VTA of perinatal fentanyl exposed males, extracellular matrix (ECM) and neuronal migration enrichment were pronounced in NAc and VTA of perinatal fentanyl exposed males, while genes associated with vesicular cycling and synaptic signaling were markedly altered in NAc of perinatal fentanyl exposed female mice. In sensory areas from perinatal fentanyl exposed females, we found alterations in mitochondrial respiration, synaptic and ciliary organization processes. Our findings demonstrate distinct transcriptomes across reward and sensory brain regions, with some showing discordance between sexes. These transcriptome adaptations may underlie structural, functional, and behavioral changes observed in perinatal fentanyl exposed mice.
Collapse
Affiliation(s)
- Jimmy Olusakin
- Department of Neurobiology, University of Maryland School of Medicine, Baltimore, MD, USA
- Program in Neuroscience, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Gautam Kumar
- Department of Neurobiology, University of Maryland School of Medicine, Baltimore, MD, USA
- Program in Neuroscience, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Mahashweta Basu
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Cali A Calarco
- Department of Neurobiology, University of Maryland School of Medicine, Baltimore, MD, USA
- Program in Neuroscience, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Megan E Fox
- Department of Anesthesiology, Penn State College of Medicine, Hershey, PA, USA
| | - Jason B Alipio
- Department of Neurobiology, University of Maryland School of Medicine, Baltimore, MD, USA
- Program in Neuroscience, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Catherine Haga
- Department of Neurobiology, University of Maryland School of Medicine, Baltimore, MD, USA
- Program in Neuroscience, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Makeda D Turner
- Department of Neurobiology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Asaf Keller
- Department of Neurobiology, University of Maryland School of Medicine, Baltimore, MD, USA
- Program in Neuroscience, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Seth A Ament
- Program in Neuroscience, University of Maryland School of Medicine, Baltimore, MD, USA
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Mary Kay Lobo
- Department of Neurobiology, University of Maryland School of Medicine, Baltimore, MD, USA.
- Program in Neuroscience, University of Maryland School of Medicine, Baltimore, MD, USA.
- Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD, USA.
| |
Collapse
|
32
|
Grams KJ, Neumueller SE, Mouradian GC, Burgraff NJ, Hodges MR, Pan L, Forster HV. Mild and moderate chronic hypercapnia elicit distinct transcriptomic responses of immune function in cardiorespiratory nuclei. Physiol Genomics 2023; 55:487-503. [PMID: 37602394 PMCID: PMC11178267 DOI: 10.1152/physiolgenomics.00038.2023] [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: 05/11/2023] [Revised: 08/03/2023] [Accepted: 08/17/2023] [Indexed: 08/22/2023] Open
Abstract
Chronic hypercapnia (CH) is a hallmark of respiratory-related diseases, and the level of hypercapnia can acutely or progressively become more severe. Previously, we have shown time-dependent adaptations in steady-state physiology during mild (arterial Pco2 ∼55 mmHg) and moderate (∼60 mmHg) CH in adult goats, including transient (mild CH) or sustained (moderate CH) suppression of acute chemosensitivity suggesting limitations in adaptive respiratory control mechanisms as the level of CH increases. Changes in specific markers of glutamate receptor plasticity, interleukin-1ß, and serotonergic modulation within key nodes of cardiorespiratory control do not fully account for the physiological adaptations to CH. Here, we used an unbiased approach (bulk tissue RNA sequencing) to test the hypothesis that mild or moderate CH elicits distinct gene expression profiles in important brain stem regions of cardiorespiratory control, which may explain the contrasting responses to CH. Gene expression profiles from the brain regions validated the accuracy of tissue biopsy methodology. Differential gene expression analyses revealed greater effects of CH on brain stem sites compared with the medial prefrontal cortex. Mild CH elicited an upregulation of predominantly immune-related genes and predicted activation of immune-related pathways and functions. In contrast, moderate CH broadly led to downregulation of genes and predicted inactivation of cellular pathways related to the immune response and vascular function. These data suggest that mild CH leads to a steady-state activation of neuroinflammatory pathways within the brain stem, whereas moderate CH drives the opposite response. Transcriptional shifts in immune-related functions may underlie the cardiorespiratory network's capability to respond to acute, more severe hypercapnia when in a state of progressively increased CH.NEW & NOTEWORTHY Mild chronic hypercapnia (CH) broadly upregulated immune-related genes and a predicted activation of biological pathways related to immune cell activity and the overall immune response. In contrast, moderate CH primarily downregulated genes related to major histocompatibility complex signaling and vasculature function that led to a predicted inactivation of pathways involving the immune response and vascular endothelial function. The severity-dependent effect on immune responses suggests that neuroinflammation has an important role in CH and may be important in the maintenance of proper ventilatory responses to acute and chronic hypercapnia.
Collapse
Affiliation(s)
- Kirstyn J Grams
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, United States
| | - Suzanne E Neumueller
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, United States
| | - Gary C Mouradian
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, United States
| | - Nicholas J Burgraff
- Center for Integrated Brain Research, Seattle Children's Research Institute, Seattle, Washington, United States
| | - Matthew R Hodges
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, United States
| | - Lawrence Pan
- Department of Physical Therapy, Marquette University, Milwaukee, Wisconsin, United States
| | - Hubert V Forster
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, United States
- Zablocki Veterans Affairs Medical Center, Milwaukee, Wisconsin, United States
| |
Collapse
|
33
|
Mansouri S, Pessoni AM, Marroquín-Rivera A, Parise EM, Tamminga CA, Turecki G, Nestler EJ, Chen TH, Labonté B. Transcriptional dissection of symptomatic profiles across the brain of men and women with depression. Nat Commun 2023; 14:6835. [PMID: 37884562 PMCID: PMC10603117 DOI: 10.1038/s41467-023-42686-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 10/18/2023] [Indexed: 10/28/2023] Open
Abstract
Major depressive disorder (MDD) is one of the most important causes of disability worldwide. While recent work provides insights into the molecular alterations in the brain of patients with MDD, whether these molecular signatures can be associated with the expression of specific symptom domains remains unclear. Here, we identified sex-specific gene modules associated with the expression of MDD, combining differential gene expression and co-expression network analyses in six cortical and subcortical brain regions. Our results show varying levels of network homology between males and females across brain regions, although the associations between these structures and the expression of MDD remain highly sex specific. We refined these associations to several symptom domains and identified transcriptional signatures associated with distinct functional pathways, including GABAergic and glutamatergic neurotransmission, metabolic processes and intracellular signal transduction, across brain regions associated with distinct symptomatic profiles in a sex-specific fashion. In most cases, these associations were specific to males or to females with MDD, although a subset of gene modules associated with common symptomatic features in both sexes were also identified. Together, our findings suggest that the expression of distinct MDD symptom domains associates with sex-specific transcriptional structures across brain regions.
Collapse
Affiliation(s)
- Samaneh Mansouri
- CERVO Brain Research Centre, Quebec, QC, Canada
- Department of Social and Preventive Medicine, Faculty of Medicine, Université Laval, Québec, QC, Canada
| | - André M Pessoni
- CERVO Brain Research Centre, Quebec, QC, Canada
- Department of Psychiatry and Neurosciences, Faculty of Medicine, Université Laval, Quebec, QC, Canada
| | - Arturo Marroquín-Rivera
- CERVO Brain Research Centre, Quebec, QC, Canada
- Department of Psychiatry and Neurosciences, Faculty of Medicine, Université Laval, Quebec, QC, Canada
| | - Eric M Parise
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Carol A Tamminga
- Department of Psychiatry, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Gustavo Turecki
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, Montreal, Canada
- Department of Psychiatry, McGill University, Montreal, Canada
| | - Eric J Nestler
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ting-Huei Chen
- CERVO Brain Research Centre, Quebec, QC, Canada
- Department of Mathematics and Statistics, Laval University, Québec, QC, Canada
| | - Benoit Labonté
- CERVO Brain Research Centre, Quebec, QC, Canada.
- Department of Psychiatry and Neurosciences, Faculty of Medicine, Université Laval, Quebec, QC, Canada.
| |
Collapse
|
34
|
Caldwell BA, Wu Y, Wang J, Li L. Altered DNA methylation underlies monocyte dysregulation and innate exhaustion memory in sepsis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.30.555580. [PMID: 37693554 PMCID: PMC10491170 DOI: 10.1101/2023.08.30.555580] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Innate immune memory is the process by which pathogen exposure elicits cell-intrinsic states to alter the strength of future immune challenges. Such altered memory states drive monocyte dysregulation during sepsis, promoting pathogenic behavior characterized by pro-inflammatory, immunosuppressive gene expression in concert with emergency hematopoiesis. Epigenetic changes, notably in the form of histone modifications, have been shown to underlie innate immune memory, but the contribution of DNA methylation to this process remains poorly understood. Using an ex vivo sepsis model, we discovered broad changes in DNA methylation throughout the genome of exhausted monocytes, including at several genes previously implicated as major drivers of immune dysregulation during sepsis and Covid-19 infection (e.g. Plac8 ). Methylome alterations are driven in part by Wnt signaling inhibition in exhausted monocytes, and can be reversed through treatment with DNA methyltransferase inhibitors, Wnt agonists, or immune training molecules. Importantly, these changes are recapitulated in septic mice following cecal slurry injection, resulting in stable changes at critical immune genes that support the involvement of DNA methylation in acute and long-term monocyte dysregulation during sepsis.
Collapse
|
35
|
Sonti S, Littleton SH, Pahl MC, Zimmerman AJ, Chesi A, Palermo J, Lasconi C, Brown EB, Pippin JA, Wells AD, Doldur-Balli F, Pack AI, Gehrman PR, Keene AC, Grant SFA. Perturbation of the insomnia WDR90 GWAS locus pinpoints rs3752495 as a causal variant influencing distal expression of neighboring gene, PIG-Q. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.17.553739. [PMID: 37645863 PMCID: PMC10462147 DOI: 10.1101/2023.08.17.553739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Although genome wide association studies (GWAS) have been crucial for the identification of loci associated with sleep traits and disorders, the method itself does not directly uncover the underlying causal variants and corresponding effector genes. The overwhelming majority of such variants reside in non-coding regions and are therefore presumed to impact the activity of cis-regulatory elements, such as enhancers. Our previously reported 'variant-to-gene mapping' effort in human induced pluripotent stem cell (iPSC)-derived neural progenitor cells (NPCs), combined with validation in both Drosophila and zebrafish, implicated PIG-Q as a functionally relevant gene at the insomnia 'WDR90' locus. However, importantly that effort did not characterize the corresponding underlying causal variant at this GWAS signal. Specifically, our genome-wide ATAC-seq and high-resolution promoter-focused Capture C datasets generated in this cell setting brought our attention to a shortlist of three tightly neighboring single nucleotide polymorphisms (SNPs) in strong linkage disequilibrium in a candidate intronic enhancer region of WDR90 that contacted the open PIG-Q promoter. The objective of this study was to investigate the influence of the proxy SNPs collectively and then individually on PIG-Q modulation and to pinpoint the causal "regulatory" variant among the three SNPs. Starting at a gross level perturbation, deletion of the entire region harboring all three SNPs in human iPSC-derived neural progenitor cells via CRISPR-Cas9 editing and subsequent RNA sequencing revealed expression changes in specific PIG-Q transcripts. Results from more refined individual luciferase reporter assays for each of the three SNPs in iPSCs revealed that the intronic region with the rs3752495 risk allele induced a ~2.5-fold increase in luciferase expression (n=10). Importantly, rs3752495 also exhibited an allele specific effect, with the risk allele increasing the luciferase expression by ~2-fold compared to the non-risk allele. In conclusion, our variant-to-function approach and subsequent in vitro validation implicates rs3752495 as a causal insomnia risk variant embedded at the WDR90-PIG-Q locus.
Collapse
Affiliation(s)
- Shilpa Sonti
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Sheridan H Littleton
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Matthew C Pahl
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Amber J Zimmerman
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Division of Sleep Medicine, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Alessandra Chesi
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Pathology and Laboratory Medicine University of Pennsylvania Perelman School of Medicine Philadelphia PA USA
| | - Justin Palermo
- Department of Biology, Texas A&M University, College Station, TX, USA
| | - Chiara Lasconi
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Elizabeth B Brown
- Division of Sleep Medicine, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - James A Pippin
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Andrew D Wells
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Fusun Doldur-Balli
- Division of Sleep Medicine, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Allan I Pack
- Division of Sleep Medicine, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Phillip R Gehrman
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Alex C Keene
- Department of Biology, Texas A&M University, College Station, TX, USA
| | - S F A Grant
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Pediatrics, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
- Divisions of Human Genetics and Endocrinology & Diabetes, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| |
Collapse
|
36
|
Glass MR, Waxman EA, Yamashita S, Lafferty M, Beltran A, Farah T, Patel NK, Matoba N, Ahmed S, Srivastava M, Drake E, Davis LT, Yeturi M, Sun K, Love MI, Hashimoto-Torii K, French DL, Stein JL. Cross-site reproducibility of human cortical organoids reveals consistent cell type composition and architecture. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.28.550873. [PMID: 37546772 PMCID: PMC10402155 DOI: 10.1101/2023.07.28.550873] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Background Reproducibility of human cortical organoid (hCO) phenotypes remains a concern for modeling neurodevelopmental disorders. While guided hCO protocols reproducibly generate cortical cell types in multiple cell lines at one site, variability across sites using a harmonized protocol has not yet been evaluated. We present an hCO cross-site reproducibility study examining multiple phenotypes. Methods Three independent research groups generated hCOs from one induced pluripotent stem cell (iPSC) line using a harmonized miniaturized spinning bioreactor protocol. scRNA-seq, 3D fluorescent imaging, phase contrast imaging, qPCR, and flow cytometry were used to characterize the 3 month differentiations across sites. Results In all sites, hCOs were mostly cortical progenitor and neuronal cell types in reproducible proportions with moderate to high fidelity to the in vivo brain that were consistently organized in cortical wall-like buds. Cross-site differences were detected in hCO size and morphology. Differential gene expression showed differences in metabolism and cellular stress across sites. Although iPSC culture conditions were consistent and iPSCs remained undifferentiated, primed stem cell marker expression prior to differentiation correlated with cell type proportions in hCOs. Conclusions We identified hCO phenotypes that are reproducible across sites using a harmonized differentiation protocol. Previously described limitations of hCO models were also reproduced including off-target differentiations, necrotic cores, and cellular stress. Improving our understanding of how stem cell states influence early hCO cell types may increase reliability of hCO differentiations. Cross-site reproducibility of hCO cell type proportions and organization lays the foundation for future collaborative prospective meta-analytic studies modeling neurodevelopmental disorders in hCOs.
Collapse
Affiliation(s)
- Madison R Glass
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Elisa A Waxman
- Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Satoshi Yamashita
- Center for Neuroscience Research, Children's National Hospital, Washington, DC
| | - Michael Lafferty
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Alvaro Beltran
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Tala Farah
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Niyanta K Patel
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Nana Matoba
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Sara Ahmed
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Mary Srivastava
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Emma Drake
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Liam T Davis
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Meghana Yeturi
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Kexin Sun
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Michael I Love
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Departments of Pediatrics, and Pharmacology & Physiology, School of Medicine and Health Sciences, The George Washington University, Washington, DC
| | - Kazue Hashimoto-Torii
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA
| | - Deborah L French
- Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA
| | - Jason L Stein
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| |
Collapse
|
37
|
Aghayev M, Arias-Alvarado A, Ilchenko S, Lepp J, Scott I, Chen YR, Zhang GF, Tsai TH, Kasumov T. A high-fat diet increases hepatic mitochondrial turnover through restricted acetylation in a NAFLD mouse model. Am J Physiol Endocrinol Metab 2023; 325:E83-E98. [PMID: 37224468 PMCID: PMC10312330 DOI: 10.1152/ajpendo.00310.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 05/15/2023] [Accepted: 05/16/2023] [Indexed: 05/26/2023]
Abstract
Lysine acetylation of proteins has emerged as a key posttranslational modification (PTM) that regulates mitochondrial metabolism. Acetylation may regulate energy metabolism by inhibiting and affecting the stability of metabolic enzymes and oxidative phosphorylation (OxPhos) subunits. Although protein turnover can be easily measured, due to the low abundance of modified proteins, it has been difficult to evaluate the effect of acetylation on the stability of proteins in vivo. We applied 2H2O-metabolic labeling coupled with immunoaffinity and high-resolution mass spectrometry method to measure the stability of acetylated proteins in mouse liver based on their turnover rates. As a proof-of-concept, we assessed the consequence of high-fat diet (HFD)-induced altered acetylation in protein turnover in LDL receptor-deficient (LDLR-/-) mice susceptible to diet-induced nonalcoholic fatty liver disease (NAFLD). HFD feeding for 12 wk led to steatosis, the early stage of NAFLD. A significant reduction in acetylation of hepatic proteins was observed in NAFLD mice, based on immunoblot analysis and label-free quantification with mass spectrometry. Compared with control mice on a normal diet, NAFLD mice had overall increased turnover rates of hepatic proteins, including mitochondrial metabolic enzymes (0.159 ± 0.079 vs. 0.132 ± 0.068 day-1), suggesting their reduced stability. Also, acetylated proteins had slower turnover rates (increased stability) than native proteins in both groups (0.096 ± 0.056 vs. 0.170 ± 0.059 day-1 in control, and 0.111 ± 0.050 vs. 0.208 ± 0.074 day-1 in NAFLD). Furthermore, association analysis revealed a relationship between the HFD-induced decrease in acetylation and increased turnover rates for hepatic proteins in NAFLD mice. These changes were associated with increased expressions of the hepatic mitochondrial transcriptional factor (TFAM) and complex II subunit without any changes to other OxPhos proteins, suggesting that enhanced mitochondrial biogenesis prevented restricted acetylation-mediated depletion of mitochondrial proteins. We conclude that decreased acetylation of mitochondrial proteins may contribute to adaptive improved hepatic mitochondrial function in the early stages of NAFLD.NEW & NOTEWORTHY This is the first method to quantify acetylome dynamics in vivo. This method revealed acetylation-mediated altered hepatic mitochondrial protein turnover in response to a high-fat diet in a mouse model of NAFLD.
Collapse
Affiliation(s)
- Mirjavid Aghayev
- Department of Pharmaceutical Sciences, College of Pharmacy, Northeast Ohio Medical University, Rootstown, Ohio, United States
| | - Andrea Arias-Alvarado
- Department of Pharmaceutical Sciences, College of Pharmacy, Northeast Ohio Medical University, Rootstown, Ohio, United States
| | - Sergei Ilchenko
- Department of Pharmaceutical Sciences, College of Pharmacy, Northeast Ohio Medical University, Rootstown, Ohio, United States
| | - Josephine Lepp
- Department of Pharmaceutical Sciences, College of Pharmacy, Northeast Ohio Medical University, Rootstown, Ohio, United States
| | - Iain Scott
- Cardiology Division, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, United States
| | - Yeong-Renn Chen
- Department of Integrative Medical Sciences, College of Medicine, Northeast Ohio Medical University, Rootstown, Ohio, United States
| | - Guo-Fang Zhang
- Division of Endocrinology, Metabolism and Nutrition, Duke Molecular Physiology Institute, Duke University, Durham North Carolina, United States
- Department of Medicine, Duke University, Durham North Carolina, United States
| | - Tsung-Heng Tsai
- Department of Mathematical Sciences, Kent State University, Kent, Ohio, United States
| | - Takhar Kasumov
- Department of Pharmaceutical Sciences, College of Pharmacy, Northeast Ohio Medical University, Rootstown, Ohio, United States
| |
Collapse
|
38
|
Natri HM, Del Azodi CB, Peter L, Taylor CJ, Chugh S, Kendle R, Chung MI, Flaherty DK, Matlock BK, Calvi CL, Blackwell TS, Ware LB, Bacchetta M, Walia R, Shaver CM, Kropski JA, McCarthy DJ, Banovich NE. Cell type-specific and disease-associated eQTL in the human lung. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.17.533161. [PMID: 36993211 PMCID: PMC10055257 DOI: 10.1101/2023.03.17.533161] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Common genetic variants confer substantial risk for chronic lung diseases, including pulmonary fibrosis (PF). Defining the genetic control of gene expression in a cell-type-specific and context-dependent manner is critical for understanding the mechanisms through which genetic variation influences complex traits and disease pathobiology. To this end, we performed single-cell RNA-sequencing of lung tissue from 67 PF and 49 unaffected donors. Employing a pseudo-bulk approach, we mapped expression quantitative trait loci (eQTL) across 38 cell types, observing both shared and cell type-specific regulatory effects. Further, we identified disease-interaction eQTL and demonstrated that this class of associations is more likely to be cell-type specific and linked to cellular dysregulation in PF. Finally, we connected PF risk variants to their regulatory targets in disease-relevant cell types. These results indicate that cellular context determines the impact of genetic variation on gene expression, and implicates context-specific eQTL as key regulators of lung homeostasis and disease.
Collapse
|
39
|
Kentistou KA, Kaisinger LR, Stankovic S, Vaudel M, de Oliveira EM, Messina A, Walters RG, Liu X, Busch AS, Helgason H, Thompson DJ, Santon F, Petricek KM, Zouaghi Y, Huang-Doran I, Gudbjartsson DF, Bratland E, Lin K, Gardner EJ, Zhao Y, Jia R, Terao C, Riggan M, Bolla MK, Yazdanpanah M, Yazdanpanah N, Bradfield JP, Broer L, Campbell A, Chasman DI, Cousminer DL, Franceschini N, Franke LH, Girotto G, He C, Järvelin MR, Joshi PK, Kamatani Y, Karlsson R, Luan J, Lunetta KL, Mägi R, Mangino M, Medland SE, Meisinger C, Noordam R, Nutile T, Concas MP, Polašek O, Porcu E, Ring SM, Sala C, Smith AV, Tanaka T, van der Most PJ, Vitart V, Wang CA, Willemsen G, Zygmunt M, Ahearn TU, Andrulis IL, Anton-Culver H, Antoniou AC, Auer PL, Barnes CLK, Beckmann MW, Berrington A, Bogdanova NV, Bojesen SE, Brenner H, Buring JE, Canzian F, Chang-Claude J, Couch FJ, Cox A, Crisponi L, Czene K, Daly MB, Demerath EW, Dennis J, Devilee P, Vivo ID, Dörk T, Dunning AM, Dwek M, Eriksson JG, Fasching PA, Fernandez-Rhodes L, Ferreli L, Fletcher O, Gago-Dominguez M, García-Closas M, García-Sáenz JA, González-Neira A, Grallert H, Guénel P, Haiman CA, Hall P, Hamann U, Hakonarson H, Hart RJ, Hickey M, Hooning MJ, Hoppe R, Hopper JL, Hottenga JJ, Hu FB, Hübner H, Hunter DJ, Jernström H, John EM, Karasik D, Khusnutdinova EK, Kristensen VN, Lacey JV, Lambrechts D, Launer LJ, Lind PA, Lindblom A, Magnusson PKE, Mannermaa A, McCarthy MI, Meitinger T, Menni C, Michailidou K, Millwood IY, Milne RL, Montgomery GW, Nevanlinna H, Nolte IM, Nyholt DR, Obi N, O’Brien KM, Offit K, Oldehinkel AJ, Ostrowski SR, Palotie A, Pedersen OB, Peters A, Pianigiani G, Plaseska-Karanfilska D, Pouta A, Pozarickij A, Radice P, Rennert G, Rosendaal FR, Ruggiero D, Saloustros E, Sandler DP, Schipf S, Schmidt CO, Schmidt MK, Small K, Spedicati B, Stampfer M, Stone J, Tamimi RM, Teras LR, Tikkanen E, Turman C, Vachon CM, Wang Q, Winqvist R, Wolk A, Zemel BS, Zheng W, van Dijk KW, Alizadeh BZ, Bandinelli S, Boerwinkle E, Boomsma DI, Ciullo M, Chenevix-Trench G, Cucca F, Esko T, Gieger C, Grant SFA, Gudnason V, Hayward C, Kolčić I, Kraft P, Lawlor DA, Martin NG, Nøhr EA, Pedersen NL, Pennell CE, Ridker PM, Robino A, Snieder H, Sovio U, Spector TD, Stöckl D, Sudlow C, Timpson NJ, Toniolo D, Uitterlinden A, Ulivi S, Völzke H, Wareham NJ, Widen E, Wilson JF, Pharoah PDP, Li L, Easton DF, Njølstad P, Sulem P, Murabito JM, Murray A, Manousaki D, Juul A, Erikstrup C, Stefansson K, Horikoshi M, Chen Z, Farooqi IS, Pitteloud N, Johansson S, Day FR, Perry JRB, Ong KK. Understanding the genetic complexity of puberty timing across the allele frequency spectrum. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.06.14.23291322. [PMID: 37503126 PMCID: PMC10371120 DOI: 10.1101/2023.06.14.23291322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Pubertal timing varies considerably and has been associated with a range of health outcomes in later life. To elucidate the underlying biological mechanisms, we performed multi-ancestry genetic analyses in ~800,000 women, identifying 1,080 independent signals associated with age at menarche. Collectively these loci explained 11% of the trait variance in an independent sample, with women at the top and bottom 1% of polygenic risk exhibiting a ~11 and ~14-fold higher risk of delayed and precocious pubertal development, respectively. These common variant analyses were supported by exome sequence analysis of ~220,000 women, identifying several genes, including rare loss of function variants in ZNF483 which abolished the impact of polygenic risk. Next, we implicated 660 genes in pubertal development using a combination of in silico variant-to-gene mapping approaches and integration with dynamic gene expression data from mouse embryonic GnRH neurons. This included an uncharacterized G-protein coupled receptor GPR83, which we demonstrate amplifies signaling of MC3R, a key sensor of nutritional status. Finally, we identified several genes, including ovary-expressed genes involved in DNA damage response that co-localize with signals associated with menopause timing, leading us to hypothesize that the ovarian reserve might signal centrally to trigger puberty. Collectively these findings extend our understanding of the biological complexity of puberty timing and highlight body size dependent and independent mechanisms that potentially link reproductive timing to later life disease.
Collapse
Affiliation(s)
- Katherine A Kentistou
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Box 285 Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Lena R Kaisinger
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Box 285 Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Stasa Stankovic
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Box 285 Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Marc Vaudel
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, NO-5020, Bergen, Norway
- Department of Genetics and Bioinformatics, Health Data and Digitalization, Norwegian Institute of Public Health, NO-0213, Oslo, Norway
| | - Edson M de Oliveira
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-MRC Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, UK
| | - Andrea Messina
- Division of Endocrinology, Diabetology, and Metabolism, Lausanne University Hospital, 1011 Lausanne, Switzerland
| | - Robin G Walters
- Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, UK
- MRC Population Health Research Unit, University of Oxford, Oxford OX3 7LF, UK
| | - Xiaoxi Liu
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Alexander S Busch
- Department of General Pediatrics, University of Münster, Münster, Germany
- Deptartment of Growth and Reproduction, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Hannes Helgason
- deCODE Genetics/Amgen, Inc., Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Deborah J Thompson
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Federico Santon
- Division of Endocrinology, Diabetology, and Metabolism, Lausanne University Hospital, 1011 Lausanne, Switzerland
| | - Konstantin M Petricek
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pharmacology, Berlin, Germany
| | - Yassine Zouaghi
- Division of Endocrinology, Diabetology, and Metabolism, Lausanne University Hospital, 1011 Lausanne, Switzerland
| | - Isabel Huang-Doran
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-MRC Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, UK
| | - Daniel F Gudbjartsson
- deCODE Genetics/Amgen, Inc., Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Eirik Bratland
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, NO-5020, Bergen, Norway
- Department of Medical Genetics, Haukeland University Hospital, NO-5021, Bergen, Norway
| | - Kuang Lin
- Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, UK
| | - Eugene J Gardner
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Box 285 Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Yajie Zhao
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Box 285 Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Raina Jia
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Box 285 Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Clinical Research Center, Shizuoka General Hospital, Shizuoka, Japan
- The Department of Applied Genetics, The School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Margie Riggan
- Department of Gynecology, Duke University Medical Center, Durham, North Carolina, USA
| | - Manjeet K Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Mojgan Yazdanpanah
- Research Center of the Sainte-Justine University Hospital, University of Montreal, Montreal, Quebec, Canada
| | - Nahid Yazdanpanah
- Research Center of the Sainte-Justine University Hospital, University of Montreal, Montreal, Quebec, Canada
| | - Jonath P Bradfield
- Quantinuum Research, Wayne, PA, USA
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Linda Broer
- Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, UK
| | - Daniel I Chasman
- Division of Preventive Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02215, USA
| | - Diana L Cousminer
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Nora Franceschini
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Lude H Franke
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Giorgia Girotto
- Institute for Maternal and Child Health – IRCCS ‘‘Burlo Garofolo”, Trieste, Italy
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | - Chunyan He
- Department of Epidemiology and Biostatistics, Department of Big Data in Health Science, School of Public Health, Zhejiang University School of Medicine, Hangzhou 310058, China
- Departments of Medical Oncology and Hematology, Sir Runrun Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310016, China
| | - Marjo-Riitta Järvelin
- Department of Epidemiology and Biostatistics, MRC Health Protection Agency (HPA) Centre for Environment and Health, School of Public Health, Imperial College London, UK
- Institute of Health Sciences, P.O.Box 5000, FI-90014 University of Oulu, Finland
- Biocenter Oulu, P.O.Box 5000, Aapistie 5A, FI-90014 University of Oulu, Finland
- Unit of Primary Care, Oulu University Hospital, Kajaanintie 50, P.O.Box 20, FI-90220 Oulu, 90029 OYS, Finland
- Department of Children and Young People and Families, National Institute for Health and Welfare, Aapistie 1, Box 310, FI-90101 Oulu, Finland
| | - Peter K Joshi
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Teviot Place, Edinburgh EH8 9AG, Scotland
| | - Yoichiro Kamatani
- Laboratory of Complex Trait Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Robert Karlsson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Jian’an Luan
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Box 285 Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Kathryn L Lunetta
- Boston University School of Public Health, Department of Biostatistics. Boston, Massachusetts 02118, USA
- NHLBI’s and Boston University’s Framingham Heart Study, Framingham, Massachusetts 01702-5827, USA
| | - Reedik Mägi
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Massimo Mangino
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, UK
- NIHR Biomedical Research Centre at Guy’s and St. Thomas’ Foundation Trust, London, UK
| | - Sarah E Medland
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- School of Psychology, University of Queensland, Brisbane, Queensland, Australia
- Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - Christa Meisinger
- Epidemiology, Medical Faculty, University of Augsburg, University Hospital of Augsburg, Augsburg, Germany
| | - Raymond Noordam
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, The Netherlands
| | - Teresa Nutile
- Institute of Genetics and Biophysics “A. Buzzati-Traverso”, CNR, Naples, Italy
| | - Maria Pina Concas
- Institute for Maternal and Child Health – IRCCS ‘‘Burlo Garofolo”, Trieste, Italy
| | - Ozren Polašek
- University of Split School of Medicine, Split, Croatia
- Algebra University College, Zagreb, Croatia
| | - Eleonora Porcu
- Institute of Genetics and Biomedical Research, National Research Council, Cagliari, Sardinia 09042, Italy
- University of Sassari, Department of Biomedical Sciences, Sassari, Sassari 07100, Italy
| | - Susan M Ring
- MRC Integrative Epidemiology Unit at the University of Bristol, UK
- Population Health Science, Bristol Medical School, University of Bristol, UK
| | - Cinzia Sala
- Division of Genetics and Cell Biology, San Raffele Hospital, Milano, Italy
| | - Albert V Smith
- Icelandic Heart Association, 201 Kopavogur, Iceland
- Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
| | - Toshiko Tanaka
- National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | - Peter J van der Most
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, The Netherlands
| | - Veronique Vitart
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Carol A Wang
- School of Medicine and Public Health, University of Newcastle, Newcastle, New South Wales 2308, Australia
- Hunter Medical Research Institute, Newcastle, New South Wales 2305, Australia
| | - Gonneke Willemsen
- Dept of Biological Psychology, Vrije Universiteit, Amsterdam; Amsterdam Public Health (APH) research institute, The Netherlands
| | - Marek Zygmunt
- Clinic of Gynaecology and Obstetrics, University Medicine Greifswald, Germany
| | - Thomas U Ahearn
- Division of Cancer Epidemiology and Genetics National Cancer Institute, National Institutes of Health, Department of Health and Human Services Bethesda, MD, USA
| | - Irene L Andrulis
- Fred A. Litwin Center for Cancer Genetics Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital Toronto, Ontario, Canada
- Department of Molecular Genetics University of Toronto Toronto, Ontario, Canada
| | - Hoda Anton-Culver
- Department of Medicine, Genetic Epidemiology Research Institute University of California Irvine Irvine, CA, USA
| | - Antonis C Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Paul L Auer
- Division of Biostatistics, Institute for Health and Equity, and Cancer Center Medical College of Wisconsin Milwaukee, WI, USA
| | - Catriona LK Barnes
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Teviot Place, Edinburgh EH8 9AG, Scotland
| | - Matthias W Beckmann
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander University Erlangen-Nuremberg, University Hospital Erlangen, Erlangen, Germany
| | - Amy Berrington
- Division of Genetics and Epidemiology The Institute of Cancer Research, London, UK
| | - Natalia V Bogdanova
- Department of Radiation Oncology, Hannover Medical School, Hannover, Germany
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
- N.N. Alexandrov Research Institute of Oncology and Medical Radiology, Minsk, Belarus
| | - Stig E Bojesen
- Copenhagen General Population Study, Herlev and Gentofte Hospital Copenhagen University Hospital, Herlev, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital Copenhagen University Hospital, Herlev, Denmark
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- German Cancer Consortium (DKTK) German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Julie E Buring
- Division of Preventive Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02215, USA
| | - Federico Canzian
- Genomic Epidemiology Group German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology German Cancer Research Center (DKFZ), Heidelberg, Germany
- Cancer Epidemiology Group, University Cancer Center Hamburg (UCCH) University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Fergus J Couch
- Department of Laboratory Medicine and Pathology Mayo Clinic Rochester, MN, USA
| | - Angela Cox
- Sheffield Institute for Nucleic Acids (SInFoNiA), Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK
| | - Laura Crisponi
- Institute of Genetics and Biomedical Research, National Research Council, Cagliari, Sardinia 09042, Italy
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Mary B Daly
- Department of Clinical Genetics Fox Chase Cancer Center Philadelphia, PA, USA
| | - Ellen W Demerath
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, USA
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Peter Devilee
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Immaculata De Vivo
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Miriam Dwek
- School of Life Sciences, University of Westminster, London, UK
| | - Johan G Eriksson
- Department of General Practice and Primary Healthcare, University of Helsinki, Helsinki University Hospital, Helsinki, Finland
| | - Peter A Fasching
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander University Erlangen-Nuremberg, University Hospital Erlangen, Erlangen, Germany
| | | | - Liana Ferreli
- Institute of Genetics and Biomedical Research, National Research Council, Cagliari, Sardinia 09042, Italy
| | - Olivia Fletcher
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Manuela Gago-Dominguez
- Genomic Medicine Group, International Cancer Genetics and Epidemiology Group Fundación Pública Galega de Medicina Xenómica, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago, SERGAS Santiago de Compostela, Spain
| | - Montserrat García-Closas
- Division of Cancer Epidemiology and Genetics National Cancer Institute, National Institutes of Health, Department of Health and Human Services Bethesda, MD, USA
| | - José A García-Sáenz
- Medical Oncology Department, Hospital Clínico San Carlos Instituto de Investigación Sanitaria San Carlos (IdISSC), Centro Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Anna González-Neira
- Human Genotyping Unit-CeGen, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Harald Grallert
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München–German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München–German Research Center for Environmental Health, Neuherberg, Germany
| | - Pascal Guénel
- Team “Exposome and Heredity”, CESP, Gustave Roussy INSERM, University Paris-Saclay, UVSQ Villejuif, France
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Oncology, Södersjukhuset, Stockholm, Sweden
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hakon Hakonarson
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Division of Pulmonary Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Roger J Hart
- Division of Obstetrics and Gynaecology, University of Western Australia, Western Australia, Australia
| | - Martha Hickey
- Department of Obstetrics and Gynaecology at the University of Melbourne and The Royal Women’s Hospital, Victoria, Australia
| | - Maartje J Hooning
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Reiner Hoppe
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany
- University of Tübingen, Tübingen, Germany
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne Melbourne, Victoria, Australia
| | - Jouke-Jan Hottenga
- Dept of Biological Psychology, Vrije Universiteit, Amsterdam; Amsterdam Public Health (APH) research institute, The Netherlands
| | - Frank B Hu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health School of Public Health, Boston, Massachusetts 02115, USA
| | - Hanna Hübner
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander University Erlangen-Nuremberg, University Hospital Erlangen, Erlangen, Germany
| | - David J Hunter
- Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, UK
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
| | - ABCTB Investigators
- Australian Breast Cancer Tissue Bank, Westmead Institute for Medical Research, University of Sydney, Sydney, New South Wales, Australia
| | - Helena Jernström
- Oncology, Department of Clinical Sciences in Lund, Lund University, Lund, Sweden
| | - Esther M John
- Department of Epidemiology and Population Health, Stanford University School of Medicine Stanford, CA, USA
- Department of Medicine, Division of Oncology Stanford Cancer Institute, Stanford University School of Medicine Stanford, CA, USA
| | - David Karasik
- Hebrew SeniorLife Institute for Aging Research, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Elza K Khusnutdinova
- Institute of Biochemistry and Genetics of the Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, Russia
- Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia
| | - Vessela N Kristensen
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - James V Lacey
- Department of Computational and Quantitative Medicine, City of Hope Duarte, CA, USA
- City of Hope Comprehensive Cancer Center, City of Hope Duarte, CA, USA
| | - Diether Lambrechts
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Center for Cancer Biology, VIB, Leuven, Belgium
| | - Lenore J Launer
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, Intramural Research Program, National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - Penelope A Lind
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
- School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Patrik KE Magnusson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Arto Mannermaa
- Translational Cancer Research Area, University of Eastern Finland, Kuopio, Finland
- Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Kuopio, Finland
| | - Mark I McCarthy
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology, & Metabolism, University of Oxford, Churchill Hospital, Oxford OX3 7LJ, UK
- NIHR Oxford Biomedical Research Centre, Churchill Hospital, OX3 7LE Oxford, UK
| | - Thomas Meitinger
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
| | - Cristina Menni
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, UK
| | - Kyriaki Michailidou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
- Biostatistics Unit, The Cyprus Institute of Neurology & Genetics, Nicosia, Cyprus
| | - Iona Y Millwood
- Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, UK
- MRC Population Health Research Unit, University of Oxford, Oxford OX3 7LF, UK
| | - Roger L Milne
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne Melbourne, Victoria, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
| | - Grant W Montgomery
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Ilja M Nolte
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Dale R Nyholt
- School of Biomedical Sciences, Faculty of Health, Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Nadia Obi
- Institute for Medical Biometry and Epidemiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Katie M O’Brien
- Epidemiology Branch National Institute of Environmental Health Sciences, NIH Research Triangle Park, NC, USA
| | - Kenneth Offit
- Clinical Genetics Research Lab, Department of Cancer Biology and Genetics Memorial Sloan Kettering Cancer Center New York, NY, USA
- Clinical Genetics Service, Department of Medicine Memorial Sloan Kettering Cancer Center New York, NY, USA
| | - Albertine J Oldehinkel
- Interdisciplinary Center Psychopathology and Emotion Regulation, University Medical Center Groningen, University of Groningen, The Netherlands
| | - Sisse R Ostrowski
- Department of Clinical Immunology, Rigshospitalet - University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of health and medical sciences, University of Copenhagen, Denmark
| | - Aarno Palotie
- Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
- Analytic and Translational Genetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Ole B Pedersen
- Department of Clinical Medicine, Faculty of health and medical sciences, University of Copenhagen, Denmark
- Department of Clinical Immunology, Zealand University Hospital, Køge, Denmark
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München–German Research Center for Environmental Health, Neuherberg, Germany
- Institute for Medical Information Processing, Biometry and Epidemiology - IBE, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Giulia Pianigiani
- Institute for Maternal and Child Health – IRCCS ‘‘Burlo Garofolo”, Trieste, Italy
| | - Dijana Plaseska-Karanfilska
- Research Centre for Genetic Engineering and Biotechnology “Georgi D. Efremov” MASA Skopje Republic of North Macedonia
| | - Anneli Pouta
- National Institute for Health and Welfare, Finland
| | - Alfred Pozarickij
- Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, UK
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Research Fondazione IRCCS, Istituto Nazionale dei Tumori (INT), Milan, Italy
| | - Gad Rennert
- Clalit National Cancer Control Center, Carmel Medical Center and Technion, Faculty of Medicine, Haifa, Israel
| | - Frits R Rosendaal
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Daniela Ruggiero
- Institute of Genetics and Biophysics “A. Buzzati-Traverso”, CNR, Naples, Italy
- IRCCS Neuromed, Pozzilli, Isernia, Italy
| | | | - Dale P Sandler
- Epidemiology Branch National Institute of Environmental Health Sciences, NIH Research Triangle Park, NC, USA
| | - Sabine Schipf
- Institute for Community Medicine, University Medicine Greifswald, Germany
| | - Carsten O Schmidt
- Institute for Community Medicine, University Medicine Greifswald, Germany
| | - Marjanka K Schmidt
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Division of Psychosocial Research and Epidemiology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek hospital, Amsterdam, The Netherlands
| | - Kerrin Small
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, UK
| | - Beatrice Spedicati
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | - Meir Stampfer
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Jennifer Stone
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne Melbourne, Victoria, Australia
- Genetic Epidemiology Group, School of Population and Global Health, University of Western Australia Perth, Western Australia, Australia
| | - Rulla M Tamimi
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
- Department of Population Health Sciences Weill Cornell Medicine New York, NY, USA
| | - Lauren R Teras
- Department of Population Science American Cancer Society Atlanta, GA, USA
| | - Emmi Tikkanen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Public Health Genomics Unit, Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland
| | - Constance Turman
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Celine M Vachon
- Department of Quantitative Health Sciences, Division of Epidemiology Mayo Clinic Rochester, MN, USA
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Robert Winqvist
- Laboratory of Cancer Genetics and Tumor Biology, Translational Medicine Research Unit, Biocenter Oulu, University of Oulu, Oulu, Finland
- Laboratory of Cancer Genetics and Tumor Biology, Northern Finland Laboratory Centre Oulu, Oulu, Finland
| | - Alicja Wolk
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Babette S Zemel
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Division of Gastroenterology, Hepatology and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center Vanderbilt University School of Medicine Nashville, TN, USA
| | - Ko W van Dijk
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
- Department of Internal Medicine, Division of Endocrinology, Leiden University Medical Center, Leiden, The Netherlands
| | - Behrooz Z Alizadeh
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Eric Boerwinkle
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Dorret I Boomsma
- Dept of Biological Psychology, Vrije Universiteit, Amsterdam; Amsterdam Public Health (APH) research institute, The Netherlands
- Amsterdam Reproduction & Development research institute, Amsterdam, The Netherlands
| | - Marina Ciullo
- Institute of Genetics and Biophysics “A. Buzzati-Traverso”, CNR, Naples, Italy
- IRCCS Neuromed, Pozzilli, Isernia, Italy
| | | | - Francesco Cucca
- Institute of Genetics and Biomedical Research, National Research Council, Cagliari, Sardinia 09042, Italy
- University of Sassari, Department of Biomedical Sciences, Sassari, Sassari 07100, Italy
| | - Tõnu Esko
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Christian Gieger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München–German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München–German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Struan FA Grant
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Division of Endocrinology and Diabetes, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Vilmundur Gudnason
- Icelandic Heart Association, 201 Kopavogur, Iceland
- Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Ivana Kolčić
- University of Split School of Medicine, Split, Croatia
- Algebra University College, Zagreb, Croatia
| | - Peter Kraft
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Deborah A Lawlor
- MRC Integrative Epidemiology Unit at the University of Bristol, UK
- Population Health Science, Bristol Medical School, University of Bristol, UK
| | - Nicholas G Martin
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Ellen A Nøhr
- Institute of Clinical Research, University of Southern Denmark, Department of Obstetrics & Gynecology, Odense University Hospital, Denmark
| | - Nancy L Pedersen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Craig E Pennell
- School of Medicine and Public Health, University of Newcastle, Newcastle, New South Wales 2308, Australia
- Hunter Medical Research Institute, Newcastle, New South Wales 2305, Australia
- Department of Maternity and Gynaecology, John Hunter Hospital, Newcastle, New South Wales 2305, Australia
| | - Paul M Ridker
- Division of Preventive Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02215, USA
| | - Antonietta Robino
- Institute for Maternal and Child Health – IRCCS ‘‘Burlo Garofolo”, Trieste, Italy
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Ulla Sovio
- Department of Epidemiology and Biostatistics, MRC Health Protection Agency (HPA) Centre for Environment and Health, School of Public Health, Imperial College London, UK
- Department of Obstetrics and Gynaecology, University of Cambridge, Cambridge, UK
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, UK
| | - Doris Stöckl
- Gesundheitsamt Fürstenfeldbruck, Regierung von Oberbayern, Fürstenfeldbruck, Germany
| | - Cathie Sudlow
- Centre for Genomic and Experimental Medicine, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, UK
- Centre for Medical Informatics, Usher Institute, University of Edinburgh
| | - Nic J Timpson
- MRC Integrative Epidemiology Unit at the University of Bristol, UK
- Population Health Science, Bristol Medical School, University of Bristol, UK
| | - Daniela Toniolo
- Division of Genetics and Cell Biology, San Raffele Hospital, Milano, Italy
| | - André Uitterlinden
- Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
| | - Sheila Ulivi
- Institute for Maternal and Child Health – IRCCS ‘‘Burlo Garofolo”, Trieste, Italy
| | - Henry Völzke
- Institute for Community Medicine, University Medicine Greifswald, Germany
| | - Nicholas J Wareham
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Box 285 Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Elisabeth Widen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - James F Wilson
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Teviot Place, Edinburgh EH8 9AG, Scotland
| | | | | | | | | | | | | | - Paul DP Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Liming Li
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
- Center for Public Health and Epidemic Preparedness and Response, Peking University, Beijing, China
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Pål Njølstad
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, NO-5020, Bergen, Norway
- Department of Pediatrics and Adolescents, Haukeland University Hospital, NO-5021, Bergen, Norway
| | | | - Joanne M Murabito
- NHLBI’s and Boston University’s Framingham Heart Study, Framingham, Massachusetts 01702-5827, USA
- Boston University Chobanian & Avedisian School of Medicine, Department of Medicine, Section of General Internal Medicine, Boston, MA 02118, USA
| | - Anna Murray
- Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, RILD Level 3, Royal Devon & Exeter Hospital, Barrack Road, Exeter, EX2 5DW, UK
| | - Despoina Manousaki
- Research Center of the Sainte-Justine University Hospital, University of Montreal, Montreal, Quebec, Canada
- Department of Pediatrics, University of Montreal, Montreal, Canada
- Department of Biochemistry and Molecular Medicine, University of Montreal, Montreal, Canada
| | - Anders Juul
- Department of Growth and Reproduction, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
- International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC), Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Christian Erikstrup
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Kari Stefansson
- deCODE Genetics/Amgen, Inc., Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
| | - Momoko Horikoshi
- Laboratory for Genomics of Diabetes and Metabolism, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Zhengming Chen
- Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, UK
- MRC Population Health Research Unit, University of Oxford, Oxford OX3 7LF, UK
| | - I Sadaf Farooqi
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-MRC Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, UK
| | - Nelly Pitteloud
- Division of Endocrinology, Diabetology, and Metabolism, Lausanne University Hospital, 1011 Lausanne, Switzerland
- Faculty of Biology and Medicine, University of Lausanne, Lausanne 1005, Switzerland
| | - Stefan Johansson
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, NO-5020, Bergen, Norway
- Department of Medical Genetics, Haukeland University Hospital, NO-5021, Bergen, Norway
| | - Felix R Day
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Box 285 Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - John RB Perry
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Box 285 Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
- Metabolic Research Laboratory, Wellcome-MRC Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK
| | - Ken K Ong
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Box 285 Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK
| |
Collapse
|
40
|
Weiß E, Hennig T, Graßl P, Djakovic L, Whisnant AW, Jürges CS, Koller F, Kluge M, Erhard F, Dölken L, Friedel CC. HSV-1 Infection Induces a Downstream Shift of Promoter-Proximal Pausing for Host Genes. J Virol 2023; 97:e0038123. [PMID: 37093003 PMCID: PMC10231138 DOI: 10.1128/jvi.00381-23] [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: 03/10/2023] [Accepted: 04/03/2023] [Indexed: 04/25/2023] Open
Abstract
Herpes simplex virus 1 (HSV-1) infection exerts a profound shutoff of host gene expression at multiple levels. Recently, HSV-1 infection was reported to also impact promoter-proximal RNA polymerase II (Pol II) pausing, a key step in the eukaryotic transcription cycle, with decreased and increased Pol II pausing observed for activated and repressed genes, respectively. Here, we demonstrate that HSV-1 infection induces more complex alterations in promoter-proximal pausing than previously suspected for the vast majority of cellular genes. While pausing is generally retained, it is shifted to more downstream and less well-positioned sites for most host genes. The downstream shift of Pol II pausing was established between 1.5 and 3 h of infection, remained stable until at least 6 hours postinfection, and was observed in the absence of ICP22. The shift in Pol II pausing does not result from alternative de novo transcription initiation at downstream sites or read-in transcription originating from disruption of transcription termination of upstream genes. The use of downstream secondary pause sites associated with +1 nucleosomes was previously observed upon negative elongation factor (NELF) depletion. However, downstream shifts of Pol II pausing in HSV-1 infection were much more pronounced than observed upon NELF depletion. Thus, our study reveals a novel aspect in which HSV-1 infection fundamentally reshapes host transcriptional processes, providing new insights into the regulation of promoter-proximal Pol II pausing in eukaryotic cells. IMPORTANCE This study provides a genome-wide analysis of changes in promoter-proximal polymerase II (Pol II) pausing on host genes induced by HSV-1 infection. It shows that standard measures of pausing, i.e., pausing indices, do not properly capture the complex and unsuspected alterations in Pol II pausing occurring in HSV-1 infection. Instead of a reduction of pausing with increased elongation, as suggested by pausing index analysis, HSV-1 infection leads to a shift of pausing to downstream and less well-positioned sites than in uninfected cells for the majority of host genes. Thus, HSV-1 infection fundamentally reshapes a key regulatory step at the beginning of the host transcriptional cycle on a genome-wide scale.
Collapse
Affiliation(s)
- Elena Weiß
- Institute of Informatics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Thomas Hennig
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Pilar Graßl
- Institute of Informatics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Lara Djakovic
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Adam W. Whisnant
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Christopher S. Jürges
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Franziska Koller
- Institute of Informatics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Michael Kluge
- Institute of Informatics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Florian Erhard
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Lars Dölken
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Würzburg, Germany
| | - Caroline C. Friedel
- Institute of Informatics, Ludwig-Maximilians-Universität München, Munich, Germany
| |
Collapse
|
41
|
Pollo SMJ, Leon-Coria A, Liu H, Cruces-Gonzalez D, Finney CAM, Wasmuth JD. Transcriptional patterns of sexual dimorphism and in host developmental programs in the model parasitic nematode Heligmosomoides bakeri. Parasit Vectors 2023; 16:171. [PMID: 37246221 DOI: 10.1186/s13071-023-05785-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 04/24/2023] [Indexed: 05/30/2023] Open
Abstract
BACKGROUND Heligmosomoides bakeri (often mistaken for Heligmosomoides polygyrus) is a promising model for parasitic nematodes with the key advantage of being amenable to study and manipulation within a controlled laboratory environment. While draft genome sequences are available for this worm, which allow for comparative genomic analyses between nematodes, there is a notable lack of information on its gene expression. METHODS We generated biologically replicated RNA-seq datasets from samples taken throughout the parasitic life of H. bakeri. RNA from tissue-dwelling and lumen-dwelling worms, collected under a dissection microscope, was sequenced on an Illumina platform. RESULTS We find extensive transcriptional sexual dimorphism throughout the fourth larval and adult stages of this parasite and identify alternative splicing, glycosylation, and ubiquitination as particularly important processes for establishing and/or maintaining sex-specific gene expression in this species. We find sex-linked differences in transcription related to aging and oxidative and osmotic stress responses. We observe a starvation-like signature among transcripts whose expression is consistently upregulated in males, which may reflect a higher energy expenditure by male worms. We detect evidence of increased importance for anaerobic respiration among the adult worms, which coincides with the parasite's migration into the physiologically hypoxic environment of the intestinal lumen. Furthermore, we hypothesize that oxygen concentration may be an important driver of the worms encysting in the intestinal mucosa as larvae, which not only fully exposes the worms to their host's immune system but also shapes many of the interactions between the host and parasite. We find stage- and sex-specific variation in the expression of immunomodulatory genes and in anthelmintic targets. CONCLUSIONS We examine how different the male and female worms are at the molecular level and describe major developmental events that occur in the worm, which extend our understanding of the interactions between this parasite and its host. In addition to generating new hypotheses for follow-up experiments into the worm's behavior, physiology, and metabolism, our datasets enable future more in-depth comparisons between nematodes to better define the utility of H. bakeri as a model for parasitic nematodes in general.
Collapse
Affiliation(s)
- Stephen M J Pollo
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
- Host-Parasite Interactions Research Training Network, University of Calgary, Calgary, AB, Canada
| | - Aralia Leon-Coria
- Host-Parasite Interactions Research Training Network, University of Calgary, Calgary, AB, Canada
- Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, AB, Canada
| | - Hongrui Liu
- Host-Parasite Interactions Research Training Network, University of Calgary, Calgary, AB, Canada
- Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, AB, Canada
| | - David Cruces-Gonzalez
- Host-Parasite Interactions Research Training Network, University of Calgary, Calgary, AB, Canada
- Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, AB, Canada
| | - Constance A M Finney
- Host-Parasite Interactions Research Training Network, University of Calgary, Calgary, AB, Canada
- Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, AB, Canada
| | - James D Wasmuth
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada.
- Host-Parasite Interactions Research Training Network, University of Calgary, Calgary, AB, Canada.
| |
Collapse
|
42
|
Chung HY, Wickel J, Hahn N, Mein N, Schwarzbrunn M, Koch P, Ceanga M, Haselmann H, Baade-Büttner C, von Stackelberg N, Hempel N, Schmidl L, Groth M, Andreas N, Götze J, Coldewey SM, Bauer M, Mawrin C, Dargvainiene J, Leypoldt F, Steinke S, Wang ZQ, Hust M, Geis C. Microglia mediate neurocognitive deficits by eliminating C1q-tagged synapses in sepsis-associated encephalopathy. SCIENCE ADVANCES 2023; 9:eabq7806. [PMID: 37235660 DOI: 10.1126/sciadv.abq7806] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 04/20/2023] [Indexed: 05/28/2023]
Abstract
Sepsis-associated encephalopathy (SAE) is a severe and frequent complication of sepsis causing delirium, coma, and long-term cognitive dysfunction. We identified microglia and C1q complement activation in hippocampal autopsy tissue of patients with sepsis and increased C1q-mediated synaptic pruning in a murine polymicrobial sepsis model. Unbiased transcriptomics of hippocampal tissue and isolated microglia derived from septic mice revealed an involvement of the innate immune system, complement activation, and up-regulation of lysosomal pathways during SAE in parallel to neuronal and synaptic damage. Microglial engulfment of C1q-tagged synapses could be prevented by stereotactic intrahippocampal injection of a specific C1q-blocking antibody. Pharmacologically targeting microglia by PLX5622, a CSF1-R inhibitor, reduced C1q levels and the number of C1q-tagged synapses, protected from neuronal damage and synapse loss, and improved neurocognitive outcome. Thus, we identified complement-dependent synaptic pruning by microglia as a crucial pathomechanism for the development of neuronal defects during SAE.
Collapse
Affiliation(s)
- Ha-Yeun Chung
- Section of Translational Neuroimmunology, Department of Neurology, Jena University Hospital, Jena 07747, Germany
- Center for Sepsis Control and Care, Jena University Hospital, Jena 07747, Germany
| | - Jonathan Wickel
- Section of Translational Neuroimmunology, Department of Neurology, Jena University Hospital, Jena 07747, Germany
- Center for Sepsis Control and Care, Jena University Hospital, Jena 07747, Germany
| | - Nina Hahn
- Section of Translational Neuroimmunology, Department of Neurology, Jena University Hospital, Jena 07747, Germany
- Center for Sepsis Control and Care, Jena University Hospital, Jena 07747, Germany
| | - Nils Mein
- Section of Translational Neuroimmunology, Department of Neurology, Jena University Hospital, Jena 07747, Germany
| | - Meike Schwarzbrunn
- Section of Translational Neuroimmunology, Department of Neurology, Jena University Hospital, Jena 07747, Germany
| | - Philipp Koch
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena 07745, Germany
| | - Mihai Ceanga
- Section of Translational Neuroimmunology, Department of Neurology, Jena University Hospital, Jena 07747, Germany
| | - Holger Haselmann
- Section of Translational Neuroimmunology, Department of Neurology, Jena University Hospital, Jena 07747, Germany
| | - Carolin Baade-Büttner
- Section of Translational Neuroimmunology, Department of Neurology, Jena University Hospital, Jena 07747, Germany
| | - Nikolai von Stackelberg
- Section of Translational Neuroimmunology, Department of Neurology, Jena University Hospital, Jena 07747, Germany
| | - Nina Hempel
- Section of Translational Neuroimmunology, Department of Neurology, Jena University Hospital, Jena 07747, Germany
| | - Lars Schmidl
- Section of Translational Neuroimmunology, Department of Neurology, Jena University Hospital, Jena 07747, Germany
| | - Marco Groth
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena 07745, Germany
| | - Nico Andreas
- Institute of Immunology, Jena University Hospital, Jena 07743, Germany
| | - Juliane Götze
- Department of Anaesthesiology and Intensive Care Medicine, Jena University Hospital, Jena 07747, Germany
- Septomics Research Center, Jena University Hospital, Jena 07745, Germany
| | - Sina M Coldewey
- Center for Sepsis Control and Care, Jena University Hospital, Jena 07747, Germany
- Department of Anaesthesiology and Intensive Care Medicine, Jena University Hospital, Jena 07747, Germany
- Septomics Research Center, Jena University Hospital, Jena 07745, Germany
| | - Michael Bauer
- Center for Sepsis Control and Care, Jena University Hospital, Jena 07747, Germany
- Department of Anaesthesiology and Intensive Care Medicine, Jena University Hospital, Jena 07747, Germany
| | - Christian Mawrin
- Department of Neuropathology, University of Magdeburg, Magdeburg, Germany
- Section of Pathology, Institute of Forensic Medicine, Jena University Hospital, Jena 07749, Germany
| | | | - Frank Leypoldt
- Neuroimmunology, Institute of Clinical Chemistry, UKSH, Kiel/Lübeck, Germany
- Department of Neurology, Christian-Albrechts University, Kiel 24105, Germany
| | - Stephan Steinke
- Department Medical Biotechnology, Institute of Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Zhao-Qi Wang
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena 07745, Germany
- Faculty of Biological Sciences, Friedrich Schiller University, Jena 07745, Germany
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Michael Hust
- Department Medical Biotechnology, Institute of Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Christian Geis
- Section of Translational Neuroimmunology, Department of Neurology, Jena University Hospital, Jena 07747, Germany
- Center for Sepsis Control and Care, Jena University Hospital, Jena 07747, Germany
| |
Collapse
|
43
|
Zhang FL, Li WD, Zhang G, Zhang M, Liu ZJ, Zhu KX, Liu QC, Zhang SE, Shen W, Zhang XF. Identification of unique transcriptomic signatures through integrated multispecies comparative analysis and WGCNA in bovine oocyte development. BMC Genomics 2023; 24:265. [PMID: 37202739 DOI: 10.1186/s12864-023-09362-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 05/06/2023] [Indexed: 05/20/2023] Open
Abstract
BACKGROUND Cattle (Bos taurus) are a major large livestock, however, compared with other species, the transcriptional specificity of bovine oocyte development has not been emphasised. RESULTS To reveal the unique transcriptional signatures of bovine oocyte development, we used integrated multispecies comparative analysis and weighted gene co-expression network analysis (WGCNA) to perform bioinformatic analysis of the germinal follicle (GV) and second meiosis (MII) gene expression profile from cattle, sheep, pigs and mice. We found that the expression levels of most genes were down-regulated from GV to MII in all species. Next, the multispecies comparative analysis showed more genes involved in the regulation of cAMP signalling during bovine oocyte development. Moreover, the green module identified by WGCNA was closely related to bovine oocyte development. Finally, integrated multispecies comparative analysis and WGCNA picked up 61 bovine-specific signature genes that participate in metabolic regulation and steroid hormone biosynthesis. CONCLUSION In a short, this study provides new insights into the regulation of cattle oocyte development from a cross-species comparison.
Collapse
Affiliation(s)
- Fa-Li Zhang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, 266100, China
- College of Life Sciences, Key Laboratory of Animal Reproduction and Biotechnology in Universities of Shandong, Qingdao Agricultural University, Qingdao, 266109, China
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, 271018, China
| | - Wei-Dong Li
- Advanced Medical Research Institute, Shandong University, Jinan, Shandong, China
| | - Geng Zhang
- College of Life Sciences, Key Laboratory of Animal Reproduction and Biotechnology in Universities of Shandong, Qingdao Agricultural University, Qingdao, 266109, China
| | - Min Zhang
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, 271018, China
| | - Zhao-Jun Liu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ke-Xin Zhu
- College of Life Sciences, Key Laboratory of Animal Reproduction and Biotechnology in Universities of Shandong, Qingdao Agricultural University, Qingdao, 266109, China
| | - Qing-Chun Liu
- College of Life Sciences, Key Laboratory of Animal Reproduction and Biotechnology in Universities of Shandong, Qingdao Agricultural University, Qingdao, 266109, China
| | - Shu-Er Zhang
- Animal Husbandry General Station of Shandong Province, Jinan, 250010, China
| | - Wei Shen
- College of Life Sciences, Key Laboratory of Animal Reproduction and Biotechnology in Universities of Shandong, Qingdao Agricultural University, Qingdao, 266109, China
| | - Xi-Feng Zhang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, 266100, China.
- Qingdao Longming Cattle Industry Co., Ltd, Qingdao, China.
| |
Collapse
|
44
|
Mansouri S, Pessoni AM, Rivera AM, Tamminga CA, Parise E, Turecki G, Nestler EJ, Chen TH, Labonté B. Transcriptional dissection of symptomatic profiles across the brain of men and women with depression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.21.537733. [PMID: 37131585 PMCID: PMC10153251 DOI: 10.1101/2023.04.21.537733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Major depressive disorder (MDD) is one of the most important causes of disability worldwide. While recent work provides insights into the molecular alterations in the brain of patients with MDD, whether these molecular signatures can be associated with the expression of specific symptom domains in males and females remains unclear. Here, we identified sex-specific gene modules associated with the expression of MDD, combining differential gene expression and co-expression network analyses in six cortical and subcortical brain regions. Our results show varying levels of network homology between males and females across brain regions, although the association between these structures and the expression of MDD remains highly sex-specific. We refined these associations to several symptom domains and identified transcriptional signatures associated with distinct functional pathways, including GABAergic and glutamatergic neurotransmission, metabolic processes, and intracellular signal transduction, across brain regions associated with distinct symptomatic profiles in a sex-specific fashion. In most cases, these associations were specific to males or to females with MDD, although a subset of gene modules associated with common symptomatic features in both sexes was also identified. Together, our findings suggest that the expression of distinct MDD symptom domains is associated with sex-specific transcriptional structures across brain regions.
Collapse
|
45
|
Resnick JD, Beer MA, Pekosz A. Early transcriptional responses of human nasal epithelial cells to infection with Influenza A and SARS-CoV-2 virus differ and are influenced by physiological temperature. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.07.531609. [PMID: 36945583 PMCID: PMC10028862 DOI: 10.1101/2023.03.07.531609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Influenza A (IAV) and SARS-CoV-2 (SCV2) viruses represent an ongoing threat to public health. Both viruses target the respiratory tract, which consists of a gradient of cell types, receptor expression, and temperature. Environmental temperature has been an un-derstudied contributor to infection susceptibility and understanding its impact on host responses to infection could help uncover new insights into severe disease risk factors. As the nasal passageways are the initial site of respiratory virus infection, in this study we investigated the effect of temperature on host responses in human nasal epithelial cells (hNECs) utilizing IAV and SCV2 in vitro infection models. We demonstrate that temperature affects SCV2, but not IAV, viral replicative fitness and that SCV2 infected cultures are slower to mount an infection-induced response, likely due to suppression by the virus. Additionally, we show that that temperature not only changes the basal transcriptomic landscape of epithelial cells, but that it also impacts the response to infection. The induction of interferon and other innate immune responses were not drastically affected by temperature, suggesting that while the baseline antiviral response at different temperatures remains consistent, there may be metabolic or signaling changes that affect how well the cultures are able to adapt to new pressures such as infection. Finally, we show that hNECs respond differently to IAV and SCV2 infection in ways that give insight into how the virus is able to manipulate the cell to allow for replication and release. Taken together, these data give new insight into the innate immune response to respiratory infections and can assist in identifying new treatment strategies for respiratory infections.
Collapse
Affiliation(s)
- Jessica D Resnick
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- McKusick- Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Michael A Beer
- McKusick- Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Andrew Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| |
Collapse
|
46
|
Inoue K, Bostan H, Browne MR, Bevis OF, Bortner CD, Moore SA, Stence AA, Martin NP, Chen SH, Burkholder AB, Li JL, Shaw ND. DUX4 double whammy: The transcription factor that causes a rare muscular dystrophy also kills the precursors of the human nose. SCIENCE ADVANCES 2023; 9:eabq7744. [PMID: 36800423 PMCID: PMC9937577 DOI: 10.1126/sciadv.abq7744] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 01/12/2023] [Indexed: 05/19/2023]
Abstract
SMCHD1 mutations cause congenital arhinia (absent nose) and a muscular dystrophy called FSHD2. In FSHD2, loss of SMCHD1 repressive activity causes expression of double homeobox 4 (DUX4) in muscle tissue, where it is toxic. Studies of arhinia patients suggest a primary defect in nasal placode cells (human nose progenitors). Here, we show that upon SMCHD1 ablation, DUX4 becomes derepressed in H9 human embryonic stem cells (hESCs) as they differentiate toward a placode cell fate, triggering cell death. Arhinia and FSHD2 patient-derived induced pluripotent stem cells (iPSCs) express DUX4 when converted to placode cells and demonstrate variable degrees of cell death, suggesting an environmental disease modifier. HSV-1 may be one such modifier as herpesvirus infection amplifies DUX4 expression in SMCHD1 KO hESC and patient iPSC. These studies suggest that arhinia, like FSHD2, is due to compromised SMCHD1 repressive activity in a cell-specific context and provide evidence for an environmental modifier.
Collapse
Affiliation(s)
- Kaoru Inoue
- Pediatric Neuroendocrinology Group, Clinical Research Branch, National Institute of Environmental Health Sciences (NIEHS), Research Triangle Park, NC, USA
| | - Hamed Bostan
- Integrative Bioinformatics, NIEHS, Research Triangle Park, NC, USA
| | - MaKenna R. Browne
- Pediatric Neuroendocrinology Group, Clinical Research Branch, National Institute of Environmental Health Sciences (NIEHS), Research Triangle Park, NC, USA
| | - Owen F. Bevis
- Pediatric Neuroendocrinology Group, Clinical Research Branch, National Institute of Environmental Health Sciences (NIEHS), Research Triangle Park, NC, USA
| | - Carl D. Bortner
- Signal Transduction Laboratory, NIEHS, Research Triangle Park, NC, USA
| | - Steven A. Moore
- Department of Pathology, University of Iowa Carver College of Medicine and Senator Paul D. Wellstone Muscular Dystrophy Specialized Research Center, Iowa City, IA, USA
| | - Aaron A. Stence
- University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | | | - Shih-Heng Chen
- Viral Vector Core, NIEHS, Research Triangle Park, NC, USA
| | | | - Jian-Liang Li
- Integrative Bioinformatics, NIEHS, Research Triangle Park, NC, USA
| | - Natalie D. Shaw
- Pediatric Neuroendocrinology Group, Clinical Research Branch, National Institute of Environmental Health Sciences (NIEHS), Research Triangle Park, NC, USA
| |
Collapse
|
47
|
Hu H, Burrow MF, Leung WK. Proteomic profile of in situ acquired pellicle on tooth and restorative material surfaces. J Dent 2023; 129:104389. [PMID: 36526084 DOI: 10.1016/j.jdent.2022.104389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/08/2022] [Accepted: 12/10/2022] [Indexed: 12/15/2022] Open
Abstract
OBJECTIVES To evaluate and compare the proteomic profile of acquired pellicle on smooth bovine tooth and tooth-coloured restorative materials, including resin composite (RC), glass ionomer cement (GIC), and casein phosphopeptide-amorphous calcium phosphate modified GIC (CPP-ACP GIC). METHODS Two-hour in situ pellicles on tooth/materials specimens mounted in oral appliances worn by ten healthy adults were investigated. Pellicle proteins and corresponding unstimulated whole saliva were quantitatively analysed through liquid chromatography-tandem mass spectrometry. RESULTS Significantly higher amounts of protein were adsorbed onto tooth surface than restorative materials tested (4.11 ± 0.69 vs. 2.54 ± 0.38/2.98 ± 0.80/3.01 ± 0.37 µg, RC/GIC/CPP-ACP GIC). From the ten participants, 1,444 (487-1,086/person), 1,454 (645-1,051/person), 1,731 (454-1,475/person), or 1,597 (423-1,261/person) pellicle proteins were detected at least once on bovine tooth, RC, GIC, or CPP-ACP GIC, respectively, and with 1,072 (304-793/person) salivary proteins identified. Comparative quantification revealed minor differences between tooth and restorative materials pellicle profiles. High inter-individual variations in pellicle protein composition were demonstrated. Compared to the salivary protein profile, 214/57 proteins showed significantly increased/decreased abundance in pellicle formed on at least one substrate (fold change > 3.325/fold change < 0.301). Gene Ontology enrichment analysis showed some pellicle proteins detected with increased affinity to tooth/material surface were identified as being related to "calcium-dependent protein binding" or "cell-cell adhesion mediator activity". CONCLUSION Similar protein quantity and composition was observed in 2 h in situ pellicles formed on different smooth restorative material surfaces. The proteomic profile of pellicles appeared distinct from that of the corresponding unstimulated whole saliva. CLINICAL SIGNIFICANCE Host backgrounds appeared more influential on the proteomic profile of the in situ acquired pellicle than the underlying substrate characteristics among systemically and orally healthy adults. Pellicle proteins preferentially adsorbed on tooth/materials were putatively associated with calcium ion homeostasis or host-microbiota interaction.
Collapse
Affiliation(s)
- Hongying Hu
- Faculty of Dentistry, The University of Hong Kong, 34 Hospital Road, Sai Ying Pun, Hong Kong SAR, China
| | - Michael Francis Burrow
- Faculty of Dentistry, The University of Hong Kong, 34 Hospital Road, Sai Ying Pun, Hong Kong SAR, China
| | - Wai Keung Leung
- Faculty of Dentistry, The University of Hong Kong, 34 Hospital Road, Sai Ying Pun, Hong Kong SAR, China.
| |
Collapse
|
48
|
Jackson R, Rajadhyaksha EV, Loeffler RS, Flores CE, Van Doorslaer K. Characterization of 3D organotypic epithelial tissues reveals tonsil-specific differences in tonic interferon signaling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.19.524743. [PMID: 36711548 PMCID: PMC9882319 DOI: 10.1101/2023.01.19.524743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
Three-dimensional (3D) culturing techniques can recapitulate the stratified nature of multicellular epithelial tissues. Organotypic 3D epithelial tissue culture methods have several applications, including the study of tissue development and function, drug discovery and toxicity testing, host-pathogen interactions, and the development of tissue-engineered constructs for use in regenerative medicine. We grew 3D organotypic epithelial tissues from foreskin, cervix, and tonsil-derived primary cells and characterized the transcriptome of these in vitro tissue equivalents. Using the same 3D culturing method, all three tissues yielded stratified squamous epithelium, validated histologically using basal and superficial epithelial cell markers. The goal of this study was to use RNA-seq to compare gene expression patterns in these three types of epithelial tissues to gain a better understanding of the molecular mechanisms underlying their function and identify potential therapeutic targets for various diseases. Functional profiling by over-representation and gene set enrichment analysis revealed tissue-specific differences: i.e. , cutaneous homeostasis and lipid metabolism in foreskin, extracellular matrix remodeling in cervix, and baseline innate immune differences in tonsil. Specifically, tonsillar epithelia may play an active role in shaping the immune microenvironment of the tonsil balancing inflammation and immune responses in the face of constant exposure to microbial insults. Overall, these data serve as a resource, with gene sets made available for the research community to explore, and as a foundation for understanding the epithelial heterogeneity and how it may impact their in vitro use. An online resource is available to investigate these data ( https://viz.datascience.arizona.edu/3DEpiEx/ ).
Collapse
Affiliation(s)
- Robert Jackson
- School of Animal and Comparative Biomedical Sciences, College of Agriculture and Life Sciences, University of Arizona, Tucson, AZ, USA
- BIO5 Institute, University of Arizona, Tucson, AZ, USA
| | - Esha V Rajadhyaksha
- College of Medicine and College of Science, University of Arizona, Tucson, AZ, USA
| | - Reid S Loeffler
- Biosystems Engineering, College of Agriculture and Life Sciences; College of Engineering, University of Arizona, Tucson, AZ, USA
| | - Caitlyn E Flores
- School of Animal and Comparative Biomedical Sciences, College of Agriculture and Life Sciences, University of Arizona, Tucson, AZ, USA
| | - Koenraad Van Doorslaer
- School of Animal and Comparative Biomedical Sciences, College of Agriculture and Life Sciences, University of Arizona, Tucson, AZ, USA
- BIO5 Institute, University of Arizona, Tucson, AZ, USA
- Department of Immunobiology; Cancer Biology Graduate Interdisciplinary Program; Genetics Graduate Interdisciplinary Program; and University of Arizona Cancer Center, University of Arizona, Tucson, AZ USA
| |
Collapse
|
49
|
Genomic heterozygosity is associated with parasite abundance, but the effects are not mediated by host condition. Evol Ecol 2023; 37:75-96. [PMID: 36568713 PMCID: PMC9666582 DOI: 10.1007/s10682-022-10175-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 03/17/2022] [Indexed: 12/27/2022]
Abstract
Whether, when, and how genetic diversity buffers individuals and populations against infectious disease risk is a critical and open question for understanding wildlife disease and zoonotic disease risk. Several, but not all, studies have found negative relationships between infection and heterozygosity in wildlife. Since they can host multiple zoonotic infections, we sampled a population of wild deer mice (Peromyscus maniculatus), sequenced their genomes, and examined their fecal samples for coccidia and nematode eggs. We analyzed coccidia infection status, abundance, and coinfection status in relation to per-locus and per-individual measures of heterozygosity, as well as identified SNPs associated with infection status. Since heterozygosity might affect host condition, and condition is known to affect immunity, it was included as a co-variate in the per-individual analyses and as response variable in relation to heterozygosity. Not only did coccidia-infected individuals have lower levels of genome-wide per-locus diversity across all metrics, but we found an inverse relationship between genomic diversity and severity of coccidia infection. We also found weaker evidence that coinfected individuals had lower levels of private allelic variation than all other groups. In the per-individual analyses, relationships between heterozygosity and infection were marginal but followed the same negative trends. Condition was negatively correlated with infection, but was not associated with heterozygosity, suggesting that effects of heterozygosity on infection were not mediated by host condition in this system. Association tests identified multiple loci involved in the inflammatory response, with a particular role for NF-κB signaling, supporting previous work on the genetic basis of coccidia resistance. Taken together, we find that increased genome-wide neutral diversity, the presence of specific genetic variants, and improved condition positively impact infection status. Our results underscore the importance of considering host genomic variation as a buffer against infection, especially in systems that can harbor zoonotic diseases. Supplementary Information The online version contains supplementary material available at 10.1007/s10682-022-10175-8.
Collapse
|
50
|
D’Arcy C, Bass O, Junk P, Sevrin T, Oliviero G, Wynne K, Halasz M, Kiel C. Disease-Gene Networks of Skin Pigmentation Disorders and Reconstruction of Protein-Protein Interaction Networks. BIOENGINEERING (BASEL, SWITZERLAND) 2022; 10:bioengineering10010013. [PMID: 36671585 PMCID: PMC9854651 DOI: 10.3390/bioengineering10010013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 12/17/2022] [Accepted: 12/18/2022] [Indexed: 12/24/2022]
Abstract
Melanin, a light and free radical absorbing pigment, is produced in melanocyte cells that are found in skin, but also in hair follicles, eyes, the inner ear, heart, brain and other organs. Melanin synthesis is the result of a complex network of signaling and metabolic reactions. It therefore comes as no surprise that mutations in many of the genes involved are associated with various types of pigmentation diseases and phenotypes ('pigmentation genes'). Here, we used bioinformatics tools to first reconstruct gene-disease/phenotype associations for all pigmentation genes. Next, we reconstructed protein-protein interaction (PPI) networks centered around pigmentation gene products ('pigmentation proteins') and supplemented the PPI networks with protein expression information obtained by mass spectrometry in a panel of melanoma cell lines (both pigment producing and non-pigment producing cells). The analysis provides a systems network representation of all genes/ proteins centered around pigmentation and melanin biosynthesis pathways ('pigmentation network map'). Our work will enable the pigmentation research community to experimentally test new hypothesis arising from the pigmentation network map and to identify new targets for drug discovery.
Collapse
Affiliation(s)
- Cian D’Arcy
- Systems Biology Ireland and UCD Charles Institute of Dermatology, School of Medicine, University College Dublin, Belfield, D04 V1W8 Dublin, Ireland
| | - Olivia Bass
- Systems Biology Ireland and UCD Charles Institute of Dermatology, School of Medicine, University College Dublin, Belfield, D04 V1W8 Dublin, Ireland
| | - Philipp Junk
- Systems Biology Ireland and UCD Charles Institute of Dermatology, School of Medicine, University College Dublin, Belfield, D04 V1W8 Dublin, Ireland
| | - Thomas Sevrin
- Systems Biology Ireland and UCD Charles Institute of Dermatology, School of Medicine, University College Dublin, Belfield, D04 V1W8 Dublin, Ireland
| | - Giorgio Oliviero
- Systems Biology Ireland, School of Medicine, University College Dublin, Belfield, D04 V1W8 Dublin, Ireland
| | - Kieran Wynne
- Systems Biology Ireland, School of Medicine, and Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, D04 V1W8 Dublin, Ireland
| | - Melinda Halasz
- Systems Biology Ireland, School of Medicine, and Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, D04 V1W8 Dublin, Ireland
| | - Christina Kiel
- Systems Biology Ireland and UCD Charles Institute of Dermatology, School of Medicine, University College Dublin, Belfield, D04 V1W8 Dublin, Ireland
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Correspondence:
| |
Collapse
|