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Zhang S, Wang R, Zhang L, Birchler JA, Sun L. Inverse and Proportional Trans Modulation of Gene Expression in Human Aneuploidies. Genes (Basel) 2024; 15:637. [PMID: 38790266 PMCID: PMC11121296 DOI: 10.3390/genes15050637] [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: 04/19/2024] [Revised: 05/15/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024] Open
Abstract
Genomic imbalance in aneuploidy is often detrimental to organisms. To gain insight into the molecular basis of aneuploidies in humans, we analyzed transcriptome data from several autosomal and sex chromosome aneuploidies. The results showed that in human aneuploid cells, genes located on unvaried chromosomes are inversely or proportionally trans-modulated, while a subset of genes on the varied chromosomes are compensated. Less genome-wide modulation is found for sex chromosome aneuploidy compared with autosomal aneuploidy due to X inactivation and the retention of dosage sensitive regulators on both sex chromosomes to limit the effective dosage change. We also found that lncRNA and mRNA can have different responses to aneuploidy. Furthermore, we analyzed the relationship between dosage-sensitive transcription factors and their targets, which illustrated the modulations and indicates genomic imbalance is related to stoichiometric changes in components of gene regulatory complexes.In summary, this study demonstrates the existence of trans-acting effects and compensation mechanisms in human aneuploidies and contributes to our understanding of gene expression regulation in unbalanced genomes and disease states.
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Affiliation(s)
- Shuai Zhang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; (S.Z.); (R.W.); (L.Z.)
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Ruixue Wang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; (S.Z.); (R.W.); (L.Z.)
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Ludan Zhang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; (S.Z.); (R.W.); (L.Z.)
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - James A. Birchler
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Lin Sun
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; (S.Z.); (R.W.); (L.Z.)
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing 100875, China
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Luan W, Cheng H, Xie H, Liu H, Wang Y, Wang S, Ye X, Zhu H, Tang F, Li Y, Chang X. PRKDC-Mediated NHEJ May Play a Crucial Role in Aneuploidy of Chromosome 8-Driven Progression of Ovarian Cancer. Int J Mol Sci 2024; 25:4825. [PMID: 38732044 PMCID: PMC11084440 DOI: 10.3390/ijms25094825] [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: 02/08/2024] [Revised: 04/15/2024] [Accepted: 04/20/2024] [Indexed: 05/13/2024] Open
Abstract
High malignancy is a prominent characteristic of epithelial ovarian cancer (EOC), emphasizing the necessity for further elucidation of the potential mechanisms underlying cancer progression. Aneuploidy and copy number variation (CNV) partially contribute to the heightened malignancy observed in EOC; however, the precise features of aneuploidy and their underlying molecular patterns, as well as the relationship between CNV and aneuploidy in EOC, remain unclear. In this study, we employed single-cell sequencing data along with The Cancer Genome Atlas (TCGA) to investigate aneuploidy and CNV in EOC. The technique of fluorescence in situ hybridization (FISH) was employed using specific probes. The copy number variation within the genomic region of chromosome 8 (42754568-47889815) was assessed and utilized as a representative measure for the ploidy status of individual cells in chromosome 8. Differential expression analysis was performed between different subgroups based on chromosome 8 ploidy. Gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), protein-protein interaction (PPI), and hub-gene analyses were subsequently utilized to identify crucial genes involved. By classifying enriched tumor cells into distinct subtypes based on chromosome 8 ploidy combined with TCGA data integration, we identified key genes driving chromosome 8 aneuploidy in EOC, revealing that PRKDC gene involvement through the mediated non-homologous end-joining pathway may play a pivotal role in disease progression. Further validation through analysis of the GEO and TCGA database and survival assessment, considering both mRNA expression levels and CNV status of PRKDC, has confirmed its involvement in the progression of EOC. Further functional analysis revealed an upregulation of PRKDC in both ovarian EOC cells and tissues, with its expression showing a significant correlation with the extent of copy number variation (CNV) on chromosome 8. Taken together, CNV amplification and aneuploidy of chromosome 8 are important characteristics of EOC. PRKDC and the mediated NHEJ pathway may play a crucial role in driving aneuploidy on chromosome 8 during the progression of EOC.
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Affiliation(s)
- Wenqing Luan
- Department of Obstetrics and Gynecology, Peking University People’s Hospital, School of Life Sciences, Biomedical Pioneering Innovation Center, Peking University, Beijing 100044, China; (W.L.); (H.C.); (H.X.); (H.L.); (Y.W.); (S.W.); (X.Y.); (H.Z.); (F.T.)
- Center of Gynecologic Oncology, Peking University People’s Hospital, Beijing 100044, China
| | - Hongyan Cheng
- Department of Obstetrics and Gynecology, Peking University People’s Hospital, School of Life Sciences, Biomedical Pioneering Innovation Center, Peking University, Beijing 100044, China; (W.L.); (H.C.); (H.X.); (H.L.); (Y.W.); (S.W.); (X.Y.); (H.Z.); (F.T.)
- Center of Gynecologic Oncology, Peking University People’s Hospital, Beijing 100044, China
| | - Haoling Xie
- Department of Obstetrics and Gynecology, Peking University People’s Hospital, School of Life Sciences, Biomedical Pioneering Innovation Center, Peking University, Beijing 100044, China; (W.L.); (H.C.); (H.X.); (H.L.); (Y.W.); (S.W.); (X.Y.); (H.Z.); (F.T.)
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing 100871, China
| | - Huiping Liu
- Department of Obstetrics and Gynecology, Peking University People’s Hospital, School of Life Sciences, Biomedical Pioneering Innovation Center, Peking University, Beijing 100044, China; (W.L.); (H.C.); (H.X.); (H.L.); (Y.W.); (S.W.); (X.Y.); (H.Z.); (F.T.)
- Center of Gynecologic Oncology, Peking University People’s Hospital, Beijing 100044, China
| | - Yicheng Wang
- Department of Obstetrics and Gynecology, Peking University People’s Hospital, School of Life Sciences, Biomedical Pioneering Innovation Center, Peking University, Beijing 100044, China; (W.L.); (H.C.); (H.X.); (H.L.); (Y.W.); (S.W.); (X.Y.); (H.Z.); (F.T.)
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing 100871, China
| | - Shang Wang
- Department of Obstetrics and Gynecology, Peking University People’s Hospital, School of Life Sciences, Biomedical Pioneering Innovation Center, Peking University, Beijing 100044, China; (W.L.); (H.C.); (H.X.); (H.L.); (Y.W.); (S.W.); (X.Y.); (H.Z.); (F.T.)
- Center of Gynecologic Oncology, Peking University People’s Hospital, Beijing 100044, China
| | - Xue Ye
- Department of Obstetrics and Gynecology, Peking University People’s Hospital, School of Life Sciences, Biomedical Pioneering Innovation Center, Peking University, Beijing 100044, China; (W.L.); (H.C.); (H.X.); (H.L.); (Y.W.); (S.W.); (X.Y.); (H.Z.); (F.T.)
- Center of Gynecologic Oncology, Peking University People’s Hospital, Beijing 100044, China
| | - Honglan Zhu
- Department of Obstetrics and Gynecology, Peking University People’s Hospital, School of Life Sciences, Biomedical Pioneering Innovation Center, Peking University, Beijing 100044, China; (W.L.); (H.C.); (H.X.); (H.L.); (Y.W.); (S.W.); (X.Y.); (H.Z.); (F.T.)
- Center of Gynecologic Oncology, Peking University People’s Hospital, Beijing 100044, China
| | - Fuchou Tang
- Department of Obstetrics and Gynecology, Peking University People’s Hospital, School of Life Sciences, Biomedical Pioneering Innovation Center, Peking University, Beijing 100044, China; (W.L.); (H.C.); (H.X.); (H.L.); (Y.W.); (S.W.); (X.Y.); (H.Z.); (F.T.)
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing 100871, China
| | - Yi Li
- Department of Obstetrics and Gynecology, Peking University People’s Hospital, School of Life Sciences, Biomedical Pioneering Innovation Center, Peking University, Beijing 100044, China; (W.L.); (H.C.); (H.X.); (H.L.); (Y.W.); (S.W.); (X.Y.); (H.Z.); (F.T.)
- Center of Gynecologic Oncology, Peking University People’s Hospital, Beijing 100044, China
| | - Xiaohong Chang
- Department of Obstetrics and Gynecology, Peking University People’s Hospital, School of Life Sciences, Biomedical Pioneering Innovation Center, Peking University, Beijing 100044, China; (W.L.); (H.C.); (H.X.); (H.L.); (Y.W.); (S.W.); (X.Y.); (H.Z.); (F.T.)
- Center of Gynecologic Oncology, Peking University People’s Hospital, Beijing 100044, China
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Zhang S, Wang R, Zhu X, Zhang L, Liu X, Sun L. Characteristics and expression of lncRNA and transposable elements in Drosophila aneuploidy. iScience 2023; 26:108494. [PMID: 38125016 PMCID: PMC10730892 DOI: 10.1016/j.isci.2023.108494] [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: 07/02/2023] [Revised: 09/28/2023] [Accepted: 11/16/2023] [Indexed: 12/23/2023] Open
Abstract
Aneuploidy can globally affect the expression of the whole genome, which is detrimental to organisms. Dosage-sensitive regulators usually have multiple intermolecular interactions, and changes in their stoichiometry are responsible for the dysregulation of the regulatory network. Currently, studies on noncoding genes in aneuploidy are relatively rare. We studied the characteristics and expression profiles of long noncoding RNAs (lncRNAs) and transposable elements (TEs) in aneuploid Drosophila. It is found that lncRNAs and TEs are affected by genomic imbalance and appear to be more sensitive to an inverse dosage effect than mRNAs. Several dosage-sensitive lncRNAs and TEs were detected for their expression patterns during embryogenesis, and their biological functions in the ovary and testes were investigated using tissue-specific RNAi. This study advances our understanding of the noncoding sequences in imbalanced genomes and provides a novel perspective for the study of aneuploidy-related human diseases such as cancer.
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Affiliation(s)
- Shuai Zhang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Ruixue Wang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Xilin Zhu
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Ludan Zhang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Xinyu Liu
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Lin Sun
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Science, Beijing Normal University, Beijing 100875, China
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4
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Liu X, Yan R, Liu H, Zhang S, Wang R, Zhang B, Sun L. Genome-Wide Expression Analysis of Long Noncoding RNAs and Their Target Genes in Metafemale Drosophila. Int J Mol Sci 2023; 24:ijms24098381. [PMID: 37176087 PMCID: PMC10179461 DOI: 10.3390/ijms24098381] [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: 03/07/2023] [Revised: 04/28/2023] [Accepted: 05/04/2023] [Indexed: 05/15/2023] Open
Abstract
Aneuploidy is usually more detrimental than altered ploidy of the entire set of chromosomes. To explore the regulatory mechanism of gene expression in aneuploidy, we analyzed the transcriptome sequencing data of metafemale Drosophila. The results showed that most genes on the X chromosome undergo dosage compensation, while the genes on the autosomal chromosomes mainly present inverse dosage effects. Furthermore, long noncoding RNAs (lncRNAs) have been identified as key regulators of gene expression, and they are more sensitive to dosage changes than mRNAs. We analyzed differentially expressed mRNAs (DEGs) and differentially expressed lncRNAs (DELs) in metafemale Drosophila and performed functional enrichment analyses of DEGs and the target genes of DELs, and we found that they are involved in several important biological processes. By constructing lncRNA-mRNA interaction networks and calculating the maximal clique centrality (MCC) value of each node in the network, we also identified two key candidate lncRNAs (CR43940 and CR42765), and two of their target genes, Sin3A and MED1, were identified as inverse dosage modulators. These results suggest that lncRNAs play an important role in the regulation of genomic imbalances. This study may deepen the understanding of the gene expression regulatory mechanisms in aneuploidy from the perspective of lncRNAs.
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Affiliation(s)
- Xinyu Liu
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Ran Yan
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Haosheng Liu
- State Key Laboratory of Earth Surface Process and Resource Ecology, College of Life Sciences, Beijing Normal University, Beijing 100875, China
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Shuai Zhang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Ruixue Wang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Bowen Zhang
- State Key Laboratory of Earth Surface Process and Resource Ecology, College of Life Sciences, Beijing Normal University, Beijing 100875, China
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Lin Sun
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Science, Beijing Normal University, Beijing 100875, China
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Shi X, Yang H, Chen C, Hou J, Ji T, Cheng J, Birchler JA. Dosage-sensitive miRNAs trigger modulation of gene expression during genomic imbalance in maize. Nat Commun 2022; 13:3014. [PMID: 35641525 PMCID: PMC9156689 DOI: 10.1038/s41467-022-30704-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 05/13/2022] [Indexed: 11/09/2022] Open
Abstract
The genomic imbalance caused by varying the dosage of individual chromosomes or chromosomal segments (aneuploidy) has more detrimental effects than altering the dosage of complete chromosome sets (ploidy). Previous analysis of maize (Zea mays) aneuploids revealed global modulation of gene expression both on the varied chromosome (cis) and the remainder of the genome (trans). However, little is known regarding the role of microRNAs (miRNAs) under genomic imbalance. Here, we report the impact of aneuploidy and polyploidy on the expression of miRNAs. In general, cis miRNAs in aneuploids present a predominant gene-dosage effect, whereas trans miRNAs trend toward the inverse level, although other types of responses including dosage compensation, increased effect, and decreased effect also occur. By contrast, polyploids show less differential miRNA expression than aneuploids. Significant correlations between expression levels of miRNAs and their targets are identified in aneuploids, indicating the regulatory role of miRNAs on gene expression triggered by genomic imbalance.
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Affiliation(s)
- Xiaowen Shi
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.,Division of Biological Sciences, University of Missouri, Columbia, MO, USA
| | - Hua Yang
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA
| | - Chen Chen
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA
| | - Jie Hou
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA
| | - Tieming Ji
- Department of Statistics, University of Missouri, Columbia, MO, USA
| | - Jianlin Cheng
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA
| | - James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA.
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