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Gonzalez TL, Willson BE, Wang ET, Taylor KD, Novoa A, Swarna A, Ortiz JC, Zeno GJ, Jefferies CA, Lawrenson K, Rotter JI, Chen YDI, Williams J, Cui J, Goodarzi MO, Pisarska MD. Sexually dimorphic DNA methylation and gene expression patterns in human first trimester placenta. Biol Sex Differ 2024; 15:63. [PMID: 39152463 PMCID: PMC11328442 DOI: 10.1186/s13293-024-00629-9] [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: 01/19/2024] [Accepted: 06/19/2024] [Indexed: 08/19/2024] Open
Abstract
BACKGROUND Fetal sex and placental development impact pregnancy outcomes and fetal-maternal health, but the critical timepoint of placenta establishment in first trimester is understudied in human pregnancies. METHODS Pregnant subjects were recruited in late first trimester (weeks 10-14) at time of chorionic villus sampling, a prenatal diagnostic test. Leftover placenta tissue was collected and stored until birth outcomes were known, then DNA and RNA were isolated from singleton, normal karyotype pregnancies resulting in live births. DNA methylation was measured with the Illumina Infinium MethylationEPIC BeadChip array (n = 56). Differential methylation analysis compared 25 females versus 31 males using a generalized linear model on 743,461 autosomal probes. Gene expression sex differences were analyzed with RNA-sequencing (n = 74). An integrated analysis was performed using linear regression to correlate gene expression and DNA methylation in 51 overlapping placentas. RESULTS Methylation analysis identified 151 differentially methylated probes (DMPs) significant at false discovery rate < 0.05, including 89 (59%) hypermethylated in females. Probe cg17612569 (GABPA, ATP5J) was the most significant CpG site, hypermethylated in males. There were 11 differentially methylated regions affected by fetal sex, with transcription factors ZNF300 and ZNF311 most significantly hypermethylated in males and females, respectively. RNA-sequencing identified 152 genes significantly sexually dimorphic at false discovery rate < 0.05. The 151 DMPs were associated with 18 genes with gene downregulation (P < 0.05) in the direction of hypermethylation, including 2 genes significant at false discovery rate < 0.05 (ZNF300 and CUB and Sushi multiple domains 1, CSMD1). Both genes, as well as Family With Sequence Similarity 228 Member A (FAM228A), showed significant correlation between DNA methylation and sexually dimorphic gene expression, though FAM228A DNA methylation was less sexually dimorphic. Comparison with other sex differences studies found that cg17612569 is male-hypermethylated across gestation in placenta and in human blood up to adulthood. CONCLUSIONS Overall, sex dimorphic differential methylation with associated differential gene expression in the first trimester placenta is small, but there remain significant genes that may be regulated through methylation leading to differences in the first trimester placenta.
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Affiliation(s)
- Tania L Gonzalez
- Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, 8635 West 3rd Street, Suite 160, Los Angeles, CA, 90048, USA
| | - Bryn E Willson
- Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, 8635 West 3rd Street, Suite 160, Los Angeles, CA, 90048, USA
| | - Erica T Wang
- Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, 8635 West 3rd Street, Suite 160, Los Angeles, CA, 90048, USA
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Allynson Novoa
- Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, 8635 West 3rd Street, Suite 160, Los Angeles, CA, 90048, USA
| | - Akhila Swarna
- Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, 8635 West 3rd Street, Suite 160, Los Angeles, CA, 90048, USA
| | - Juanita C Ortiz
- Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, 8635 West 3rd Street, Suite 160, Los Angeles, CA, 90048, USA
| | - Gianna J Zeno
- Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, 8635 West 3rd Street, Suite 160, Los Angeles, CA, 90048, USA
| | - Caroline A Jefferies
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Division of Rheumatology, Department of Medicine, Kao Autoimmune Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Kate Lawrenson
- Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, 8635 West 3rd Street, Suite 160, Los Angeles, CA, 90048, USA
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - John Williams
- Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, 8635 West 3rd Street, Suite 160, Los Angeles, CA, 90048, USA
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jinrui Cui
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Mark O Goodarzi
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Margareta D Pisarska
- Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, 8635 West 3rd Street, Suite 160, Los Angeles, CA, 90048, USA.
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
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de Klein N, Tsai EA, Vochteloo M, Baird D, Huang Y, Chen CY, van Dam S, Oelen R, Deelen P, Bakker OB, El Garwany O, Ouyang Z, Marshall EE, Zavodszky MI, van Rheenen W, Bakker MK, Veldink J, Gaunt TR, Runz H, Franke L, Westra HJ. Brain expression quantitative trait locus and network analyses reveal downstream effects and putative drivers for brain-related diseases. Nat Genet 2023; 55:377-388. [PMID: 36823318 PMCID: PMC10011140 DOI: 10.1038/s41588-023-01300-6] [Citation(s) in RCA: 54] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 01/17/2023] [Indexed: 02/25/2023]
Abstract
Identification of therapeutic targets from genome-wide association studies (GWAS) requires insights into downstream functional consequences. We harmonized 8,613 RNA-sequencing samples from 14 brain datasets to create the MetaBrain resource and performed cis- and trans-expression quantitative trait locus (eQTL) meta-analyses in multiple brain region- and ancestry-specific datasets (n ≤ 2,759). Many of the 16,169 cortex cis-eQTLs were tissue-dependent when compared with blood cis-eQTLs. We inferred brain cell types for 3,549 cis-eQTLs by interaction analysis. We prioritized 186 cis-eQTLs for 31 brain-related traits using Mendelian randomization and co-localization including 40 cis-eQTLs with an inferred cell type, such as a neuron-specific cis-eQTL (CYP24A1) for multiple sclerosis. We further describe 737 trans-eQTLs for 526 unique variants and 108 unique genes. We used brain-specific gene-co-regulation networks to link GWAS loci and prioritize additional genes for five central nervous system diseases. This study represents a valuable resource for post-GWAS research on central nervous system diseases.
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Affiliation(s)
- Niek de Klein
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Wellcome Sanger Institute, Hinxton, UK
| | - Ellen A Tsai
- Translational Biology, Research and Development, Biogen Inc., Cambridge, MA, USA
| | - Martijn Vochteloo
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Institute for Life Science and Technology, Hanze University of Applied Sciences, Groningen, The Netherlands
- Oncode Institute, Groningen, The Netherlands
| | - Denis Baird
- Translational Biology, Research and Development, Biogen Inc., Cambridge, MA, USA
| | - Yunfeng Huang
- Translational Biology, Research and Development, Biogen Inc., Cambridge, MA, USA
| | - Chia-Yen Chen
- Translational Biology, Research and Development, Biogen Inc., Cambridge, MA, USA
| | - Sipko van Dam
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Ancora Health, Groningen, The Netherlands
| | - Roy Oelen
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Oncode Institute, Groningen, The Netherlands
| | - Patrick Deelen
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Oncode Institute, Groningen, The Netherlands
| | - Olivier B Bakker
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Wellcome Sanger Institute, Hinxton, UK
| | - Omar El Garwany
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Wellcome Sanger Institute, Hinxton, UK
| | | | - Eric E Marshall
- Translational Biology, Research and Development, Biogen Inc., Cambridge, MA, USA
| | - Maria I Zavodszky
- Translational Biology, Research and Development, Biogen Inc., Cambridge, MA, USA
| | - Wouter van Rheenen
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Mark K Bakker
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Jan Veldink
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Tom R Gaunt
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, UK
| | - Heiko Runz
- Translational Biology, Research and Development, Biogen Inc., Cambridge, MA, USA.
| | - Lude Franke
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
- Oncode Institute, Groningen, The Netherlands.
| | - Harm-Jan Westra
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
- Oncode Institute, Groningen, The Netherlands.
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Shan L, Lu Y, Song Y, Zhu X, Xiang CC, Zuo ED, Cheng X. Identification of Nine M6A-Related Long Noncoding RNAs as Prognostic Signatures Associated with Oxidative Stress in Oral Cancer Based on Data from The Cancer Genome Atlas. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:9529814. [PMID: 35910847 PMCID: PMC9337974 DOI: 10.1155/2022/9529814] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 06/12/2022] [Accepted: 06/29/2022] [Indexed: 11/18/2022]
Abstract
Objective Although the expression of long noncoding RNAs (lncRNAs) and N6-methyladenosine (M6A) is correlated with different tumors, it remains unclear how M6A-related lncRNA functioning affects the initiation and progression of oral squamous cell carcinoma (OSCC). Materials and Methods Gene expression and clinical data were retrieved from The Cancer Genome Atlas. The prognostic value of M6A-related lncRNAs was determined using univariate Cox regression analyses. Gene set enrichment analysis of OSCC patient clusters revealed the pathways that elucidate the mechanism. Furthermore, a risk-based model was established. The difference in the overall survival (OS) between groups, including low-/high-risk groups, was determined by Kaplan-Meier analysis. Relationships among immune cells, clusters, clinicopathological characteristics, and risk scores were explored. Results Among 1,080 M6A-related lncRNAs, 36 were prognosis-related. Patients with OSCC were divided into two clusters. T stage and the pathological grade were noticeably lower in cluster 2 than in cluster 1. Epithelial-mesenchymal transition showed greater enrichment in cluster 1. Nine hub M6A-related lncRNAs were identified for the model of risk score for predicting OSCC prognosis. The OS was longer in patients with a low-risk score than in patients with a high-risk score. The risk score was an independent prognostic factor of OSCC and was associated with the infiltration of different immune cells. T stages and the American Joint Committee on Cancer (AJCC) stages were more advanced in the high-risk score group than in the low-risk score group. Finally, expression correlation analysis showed that the risk score is associated with the expression of oxidative stress markers. Conclusion M6A-related lncRNAs play an important role in OSCC progression. Immune cell infiltration was related to the risk score model in OSCC and could accurately predict OSCC prognosis.
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Affiliation(s)
- Li Shan
- Department of Hematology and Oncology, Soochow University Affiliated Taicang Hospital (the First People's Hospital of Taicang), Jiangsu 215400, China
| | - Ye Lu
- Suzhou Medical College of Soochow University/Soochow University Affiliated Taicang Hospital, China
| | - Yihua Song
- Department of Stomatology Affiliated Hospital of Nantong University, Nantong University, Nantong, Jiangsu, China
| | - Xiaoli Zhu
- Department of Hematology and Oncology, Soochow University Affiliated Taicang Hospital (the First People's Hospital of Taicang), Jiangsu 215400, China
| | - Cheng-Cheng Xiang
- Department of Hematology and Oncology, Soochow University Affiliated Taicang Hospital (the First People's Hospital of Taicang), Jiangsu 215400, China
| | - Er-Dong Zuo
- Department of Hematology and Oncology, Soochow University Affiliated Taicang Hospital (the First People's Hospital of Taicang), Jiangsu 215400, China
| | - Xu Cheng
- Department of Hematology and Oncology, Soochow University Affiliated Taicang Hospital (the First People's Hospital of Taicang), Jiangsu 215400, China
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Xiong J, Wu L, Huang L, Wu C, Liu Z, Deng W, Ma S, Zhou Z, Yu H, Cao K. LncRNA FOXP4-AS1 Promotes Progression of Ewing Sarcoma and Is Associated With Immune Infiltrates. Front Oncol 2021; 11:718876. [PMID: 34765540 PMCID: PMC8577041 DOI: 10.3389/fonc.2021.718876] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 10/05/2021] [Indexed: 12/25/2022] Open
Abstract
Ewing sarcoma (ES) is a highly malignant primary bone tumor with poor prognosis. Studies have shown that abnormal expression of lncRNA influences the prognosis of tumor patients. Herein, we established that FOXP4-AS1 was up-regulated in ES and this correlated with poor prognosis. Further analysis illustrated that FOXP4-AS1 down-regulation repression growth, migration, along with invasion of ES. On the contrary, up-regulation of FOXP4-AS1 promoted the growth, migration, as well as invasion of ES. To explore the mechanism of FOXP4-AS1, Spearman correlation analysis was carried out to determine genes that were remarkably linked to FOXP4-AS1 expression. The potential functions and pathways involving FOXP4-AS1 were identified by GO analysis, Hallmark gene set enrichment analysis, GSEA, and GSVA. The subcellular fractionation results illustrated that FOXP4-AS1 was primarily located in the cytoplasm of ES cells. Then a ceRNA network of FOXP4-AS1 was constructed. Analysis of the ceRNA network and GSEA yielded two candidate mRNAs for FOXP4-AS1. Results of the combined survival analysis led us to speculate that FOXP4-AS1 may affect the expression of TMPO by sponging miR-298, thereby regulating the malignant phenotype of ES. Finally, we found that FOXP4-AS1 may modulates the tumor immune microenvironment in an extracellular vesicle-mediated manner. In summary, FOXP4-AS1 correlates with poor prognosis of ES. It promotes the growth, migration, as well as invasion of ES cells and may modulate the tumor immune microenvironment.
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Affiliation(s)
- Jiachao Xiong
- The Orthopedics Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, China.,Department of Orthopedics, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Liang Wu
- The Orthopedics Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Lu Huang
- Child Health Department of the Maternal and Children Health Hospital of Jiangxi Province, Nanchang, China
| | - Chunyang Wu
- The Orthopedics Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zhiming Liu
- The Orthopedics Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Wenqiang Deng
- The Orthopedics Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Shengbiao Ma
- The Orthopedics Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zhenhai Zhou
- The Orthopedics Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Honggui Yu
- The Orthopedics Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Kai Cao
- The Orthopedics Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, China
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