1
|
Key J, Gispert S, Koornneef L, Sleddens-Linkels E, Kohli A, Torres-Odio S, Koepf G, Amr S, Reichlmeir M, Harter PN, West AP, Münch C, Baarends WM, Auburger G. CLPP Depletion Causes Diplotene Arrest; Underlying Testis Mitochondrial Dysfunction Occurs with Accumulation of Perrault Proteins ERAL1, PEO1, and HARS2. Cells 2022; 12:52. [PMID: 36611846 PMCID: PMC9818230 DOI: 10.3390/cells12010052] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/13/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022] Open
Abstract
Human Perrault syndrome (PRLTS) is autosomal, recessively inherited, and characterized by ovarian insufficiency with hearing loss. Among the genetic causes are mutations of matrix peptidase CLPP, which trigger additional azoospermia. Here, we analyzed the impact of CLPP deficiency on male mouse meiosis stages. Histology, immunocytology, different OMICS and biochemical approaches, and RT-qPCR were employed in CLPP-null mouse testis. Meiotic chromosome pairing and synapsis proceeded normally. However, the foci number of the crossover marker MLH1 was slightly reduced, and foci persisted in diplotene, most likely due to premature desynapsis, associated with an accumulation of the DNA damage marker γH2AX. No meiotic M-phase cells were detected. Proteome profiles identified strong deficits of proteins involved in male meiotic prophase (HSPA2, SHCBP1L, DMRT7, and HSF5), versus an accumulation of AURKAIP1. Histone H3 cleavage, mtDNA extrusion, and cGAMP increase suggested innate immunity activation. However, the deletion of downstream STING/IFNAR failed to alleviate pathology. As markers of underlying mitochondrial pathology, we observed an accumulation of PRLTS proteins ERAL1, PEO1, and HARS2. We propose that the loss of CLPP leads to the extrusion of mitochondrial nucleotide-binding proteins to cytosol and nucleus, affecting late meiotic prophase progression, and causing cell death prior to M-phase entry. This phenotype is more severe than in mito-mice or mutator-mice.
Collapse
Affiliation(s)
- Jana Key
- Experimental Neurology, Medical Faculty, Goethe University, 60590 Frankfurt am Main, Germany
| | - Suzana Gispert
- Experimental Neurology, Medical Faculty, Goethe University, 60590 Frankfurt am Main, Germany
| | - Lieke Koornneef
- Department of Developmental Biology, Erasmus Medical Center, 3015 GD Rotterdam, The Netherlands
- Oncode Institute, Erasmus Medical Center, 3015 GD Rotterdam, The Netherlands
| | - Esther Sleddens-Linkels
- Department of Developmental Biology, Erasmus Medical Center, 3015 GD Rotterdam, The Netherlands
| | - Aneesha Kohli
- Institute of Biochemistry II, Goethe University Medical School, 60590 Frankfurt am Main, Germany
| | - Sylvia Torres-Odio
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Health Science Center, Texas A&M University, Bryan, TX 77807, USA
| | - Gabriele Koepf
- Experimental Neurology, Medical Faculty, Goethe University, 60590 Frankfurt am Main, Germany
| | - Shady Amr
- Institute of Biochemistry II, Goethe University Medical School, 60590 Frankfurt am Main, Germany
| | - Marina Reichlmeir
- Experimental Neurology, Medical Faculty, Goethe University, 60590 Frankfurt am Main, Germany
| | - Patrick N. Harter
- Institute of Neurology (Edinger-Institute), University Hospital Frankfurt, Goethe University, Heinrich-Hoffmann-Strasse 7, 60528 Frankfurt am Main, Germany
| | - Andrew Phillip West
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Health Science Center, Texas A&M University, Bryan, TX 77807, USA
| | - Christian Münch
- Institute of Biochemistry II, Goethe University Medical School, 60590 Frankfurt am Main, Germany
- Frankfurt Cancer Institute, 60590 Frankfurt am Main, Germany
- Cardio-Pulmonary Institute, 35392 Gießen, Germany
| | - Willy M. Baarends
- Department of Developmental Biology, Erasmus Medical Center, 3015 GD Rotterdam, The Netherlands
| | - Georg Auburger
- Experimental Neurology, Medical Faculty, Goethe University, 60590 Frankfurt am Main, Germany
| |
Collapse
|
2
|
Zhu X, Liu Y, Xu J, Cheng Z, Yu Y, Chu M, Lu X, Yuan W. miR-608 rs4919510 Polymorphism May Affect Susceptibility to Colorectal Cancer by Upregulating MRPL43 Expression. DNA Cell Biol 2020; 39:2017-2027. [PMID: 33147064 DOI: 10.1089/dna.2020.5689] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
There are many studies on the association between miR-608 rs4919510 polymorphism and susceptibility to colorectal cancer (CRC). However, the role of rs4919510 in CRC development and its underlying mechanism remain unclear. We first evaluated the gene that may be regulated by the variation of rs4919510 through a two-stage expression quantitative trait loci analysis and then compared the expression of that identified gene in CRC tissues and adjacent nontumor tissues. Next, methyl thiazolyl tetrazolium (MTT) assay, transwell assay, and flow cytometry analyses were performed to investigate the in vitro capacity of cell proliferation, migration, invasion, apoptosis, and cell cycle of CRC cells, respectively. Finally, through bioinformatics prediction, we contrasted the regulatory network and identified microRNAs (miRNAs) and long noncoding RNAs (lncRNAs) that could regulate the obtained gene. We found that the variant G allele of rs4919510 located in miR-608 was associated with a potentially increased expression of MRPL43 in colon tissues (p = 0.065). Moreover, the results of functional experiments suggested that knockdown of the MRPL43 gene could inhibit the growth of the CRC HCT-116 cell line and promote apoptosis. Additionally, the cell cycle of CRC HCT-116 cell line was significantly arrested at the G2 phase. Next, we obtained a competing endogenous RNA regulatory network of MRPL43 with 17 pairs of miRNAs-lncRNAs by bioinformatics prediction, out of which, survival analysis indicated that different expression levels of miR-193b-3p (p = 0.0269) and miR-194-3p (p = 0.0113) were associated with overall survival in CRC patients. The rs4919510 variant G allele in miR-608 may increase the proliferation, invasion, and migration ability and decrease the apoptosis of CRC HCT-116 cell line by upregulating the expression of MRPL43, ultimately may affect the risk of CRC. Moreover, miR-193b-3p and miR-194-3p that target MRPL43 may serve as potential predictive biomarkers of CRC survival.
Collapse
Affiliation(s)
- Xiaoqi Zhu
- Department of Epidemiology, School of Public Health, Nantong University, Nantong, China
| | - Yichen Liu
- Department of Epidemiology, School of Public Health, Nantong University, Nantong, China
| | - Jingsheng Xu
- Department of Epidemiology, School of Public Health, Nantong University, Nantong, China
| | - Zhounan Cheng
- Department of Epidemiology, School of Public Health, Nantong University, Nantong, China
| | - Yuhui Yu
- Department of Epidemiology, School of Public Health, Nantong University, Nantong, China
| | - Minjie Chu
- Department of Epidemiology, School of Public Health, Nantong University, Nantong, China
| | - Xiao Lu
- Department of Oncology, Changshu No. 1 People's Hospital, Suzhou, China
| | - Weiyan Yuan
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Nantong, China
| |
Collapse
|
3
|
Li D, Lin C, Li N, Du Y, Yang C, Bai Y, Feng Z, Su C, Wu R, Song S, Yan P, Chen M, Jain A, Huang L, Zhang Y, Li X. PLAGL2 and POFUT1 are regulated by an evolutionarily conserved bidirectional promoter and are collaboratively involved in colorectal cancer by maintaining stemness. EBioMedicine 2019; 45:124-138. [PMID: 31279780 PMCID: PMC6642334 DOI: 10.1016/j.ebiom.2019.06.051] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 06/25/2019] [Accepted: 06/26/2019] [Indexed: 02/07/2023] Open
Abstract
Background Our previous study revealed that PLAGL2 or POFUT1 can promote tumorigenesis and maintain significant positive correlations in colorectal cancer (CRC). However, the mechanism leading to the co-expression and the underlying functional and biological implications remain unclear. Methods Clinical tumor tissues and TCGA dataset were utilized to analyze the co-expression of PLAGL2 and POFUT1. Luciferase reporter assays, specially made bidirectional promoter vectors and ectopic expression of 3’UTR were employed to study the mechanisms of co-expression. In vitro and in vivo assays were performed to further confirm the oncogenic function of both. The sphere formation assay, immunofluorescence, Western blot and qRT-PCR were performed to investigate the effect of both genes in colorectal cancer stem cells (CSCs). Findings PLAGL2 and POFUT1 maintained co-expression in CRC (r = 0.91, p < .0001). An evolutionarily conserved bidirectional promoter, rather than post-transcriptional regulation by competing endogenous RNAs, caused the co-expression of PLAGL2 and POFUT1 in CRC. The bidirectional gene pair PLAGL2/POFUT1 was subverted in CRC and acted synergistically to promote colorectal tumorigenesis by maintaining stemness of colorectal cancer stem cells through the Wnt and Notch pathways. Finally, PLAGL2 and POFUT1 share transcription factor binding sites, and introducing mutations into promoter regions with shared transcription regulatory elements led to a decrease in the PLAGL2/POFUT1 promoter activity in both directions. Interpretation Our team identified for the first time a bidirectional promoter pair oncogene, PLAGL2-POFUT1, in CRC. The two genes synergistically promote the progression of CRC and affect the characteristics of CSCs, which can offer promising intervention targets for clinicians and researchers. Fund National Nature Science Foundation of China, the Hunan province projects of Postgraduate Independent Exploration and Innovation of Central South University.
Collapse
Affiliation(s)
- Daojiang Li
- Department of gastroenterological surgery, The Third XiangYa Hospital of Central South University, Changsha, Hunan 410013, China; Department of Colorectal and Anal Surgery of Zhongnan Hospital of Wuhan University, Wuhan 430071, Hubei Province, China
| | - Changwei Lin
- Department of gastroenterological surgery, The Third XiangYa Hospital of Central South University, Changsha, Hunan 410013, China
| | - Nanpeng Li
- Department of gastroenterological surgery, The Third XiangYa Hospital of Central South University, Changsha, Hunan 410013, China
| | - Yuheng Du
- Department of gastroenterological surgery, The Third XiangYa Hospital of Central South University, Changsha, Hunan 410013, China
| | - Chunxing Yang
- Department of gastroenterological surgery, The Third XiangYa Hospital of Central South University, Changsha, Hunan 410013, China
| | - Yang Bai
- Department of gastroenterological surgery, The Third XiangYa Hospital of Central South University, Changsha, Hunan 410013, China
| | - Zhicai Feng
- Department of Burns and Plastic Surgery, the 3rd Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Chen Su
- Department of gastroenterological surgery, The Third XiangYa Hospital of Central South University, Changsha, Hunan 410013, China
| | - Runliu Wu
- Department of gastroenterological surgery, The Third XiangYa Hospital of Central South University, Changsha, Hunan 410013, China
| | - Shenglei Song
- Department of gastroenterological surgery, The Third XiangYa Hospital of Central South University, Changsha, Hunan 410013, China
| | - Peicheng Yan
- Department of gastroenterological surgery, The Third XiangYa Hospital of Central South University, Changsha, Hunan 410013, China
| | - Miao Chen
- Department of gastroenterological surgery, The Third XiangYa Hospital of Central South University, Changsha, Hunan 410013, China
| | - Arad Jain
- College of Arts and Science, University of Virginia, Charlottesville, Virginia 22904, United States of America
| | - Lihua Huang
- Center for Experimental Medicine, The Third XiangYa Hospital of Central South University, Changsha, Hunan 410013, China
| | - Yi Zhang
- Department of gastroenterological surgery, The Third XiangYa Hospital of Central South University, Changsha, Hunan 410013, China
| | - Xiaorong Li
- Department of gastroenterological surgery, The Third XiangYa Hospital of Central South University, Changsha, Hunan 410013, China; Center for Experimental Medicine, The Third XiangYa Hospital of Central South University, Changsha, Hunan 410013, China.
| |
Collapse
|
4
|
Meersseman C, Letaief R, Léjard V, Rebours E, Guillocheau G, Esquerré D, Djari A, Chamberlain A, Vander Jagt C, Klopp C, Boussaha M, Renand G, Maftah A, Petit D, Rocha D. Genetic variability of the activity of bidirectional promoters: a pilot study in bovine muscle. DNA Res 2017; 24:221-233. [PMID: 28338730 PMCID: PMC5499805 DOI: 10.1093/dnares/dsx004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 01/24/2017] [Indexed: 11/25/2022] Open
Abstract
Bidirectional promoters are regulatory regions co-regulating the expression of two neighbouring genes organized in a head-to-head orientation. In recent years, these regulatory regions have been studied in many organisms; however, no investigation to date has been done to analyse the genetic variation of the activity of this type of promoter regions. In our study, we conducted an investigation to first identify bidirectional promoters sharing genes expressed in bovine Longissimus thoracis and then to find genetic variants affecting the activity of some of these bidirectional promoters. Combining bovine gene information and expression data obtained using RNA-Seq, we identified 120 putative bidirectional promoters active in bovine muscle. We experimentally validated in vitro 16 of these bidirectional promoters. Finally, using gene expression and whole-genome genotyping data, we explored the variability of the activity in muscle of the identified bidirectional promoters and discovered genetic variants affecting their activity. We found that the expression level of 77 genes is correlated with the activity of 12 bidirectional promoters. We also identified 57 single nucleotide polymorphisms associated with the activity of 5 bidirectional promoters. To our knowledge, our study is the first analysis in any species of the genetic variability of the activity of bidirectional promoters.
Collapse
Affiliation(s)
- Cédric Meersseman
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.,GMA, INRA, Université de Limoges, 87060 Limoges, France
| | - Rabia Letaief
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Véronique Léjard
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Emmanuelle Rebours
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Gabriel Guillocheau
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Diane Esquerré
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, 31326 Castanet Tolosan, France
| | - Anis Djari
- SIGENAE, UR 875, INRA, 31362 Castanet-Tolosan, France
| | - Amanda Chamberlain
- Dairy Futures Cooperative Research Centre, AgriBio, Bundoora, Victoria, Australia.,AgriBio, Department of Economic Development, Jobs, Transport & Resources, Victoria, Australia
| | - Christy Vander Jagt
- Dairy Futures Cooperative Research Centre, AgriBio, Bundoora, Victoria, Australia.,AgriBio, Department of Economic Development, Jobs, Transport & Resources, Victoria, Australia
| | | | - Mekki Boussaha
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Gilles Renand
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | | | - Daniel Petit
- GMA, INRA, Université de Limoges, 87060 Limoges, France
| | - Dominique Rocha
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| |
Collapse
|
5
|
Wang R, Yan Y, Zhu M, Yang M, Zhou F, Chen H, Lin Y. Isolation and Functional Characterization of Bidirectional Promoters in Rice. FRONTIERS IN PLANT SCIENCE 2016; 7:766. [PMID: 27303432 PMCID: PMC4885881 DOI: 10.3389/fpls.2016.00766] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Accepted: 05/17/2016] [Indexed: 05/19/2023]
Abstract
Bidirectional promoters, which show great application potential in genetic improvement of plants, have aroused great research interest recently. However, most bidirectional promoters were cloned individually in the studies of single genes. Here, we initiatively combined RNA-seq data and cDNA microarray data to discover the potential bidirectional promoters in rice genome. Based on the expression level and correlation of each adjacent and oppositely transcribed gene pair, we selected four candidate gene pairs. Then, the intergenic region between each pair was isolated and cloned into a dual reporter vector pDX2181 for functional identification. GUS and GFP assays of the transgenic plants indicated that all the intergenic regions showed bidirectional expression activity in various tissues. Through 5' and 3' deletion analysis on one of the above bidirectional promoters, we identified the enhancing region which sharply increased its bidirectional expression efficiency and the essential regions respectively responsible for its 5' and 3' basic expression activity. The bidirectional arrangement of the four gene pairs in six gramineous plants was also analyzed, showing the conserved characteristics of the four bidirectional promoters identified in our study. In addition, two novel cis-sequences conserved in the four bidirectional promoters were discovered by bioinformatic identification. Our study proposes a feasible method for selecting, cloning, and functionally identifying bidirectional promoters as well as for discovering their bidirectional regulatory regions and conserved sequences in rice.
Collapse
Affiliation(s)
- Rui Wang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural UniversityWuhan, China
| | - Yan Yan
- Chinese Academy of Tropical Agricultural SciencesHainan, China
| | - Menglin Zhu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural UniversityWuhan, China
| | - Mei Yang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural UniversityWuhan, China
| | - Fei Zhou
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural UniversityWuhan, China
| | - Hao Chen
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural UniversityWuhan, China
| | - Yongjun Lin
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural UniversityWuhan, China
- *Correspondence: Yongjun Lin
| |
Collapse
|