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Zeng Y, Hoshino Y, Susami K, Honda S, Minami N, Ikeda S. Evaluating histone modification analysis of individual preimplantation embryos. BMC Genomics 2024; 25:75. [PMID: 38238676 PMCID: PMC10795292 DOI: 10.1186/s12864-024-09984-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 01/06/2024] [Indexed: 01/22/2024] Open
Abstract
BACKGROUND We previously reported a modification of the CUT&Tag method (NTU-CAT) that allows genome-wide histone modification analysis in individual preimplantation embryos. In the present study, NTU-CAT was further simplified by taking advantage of the Well-of-the-Well (WOW) system, which enables the processing of multiple embryos in a shorter time with less reagent and cell loss during the procedure (WOW-CUT&Tag, WOW-CAT). RESULTS WOW-CAT allowed histone modification profiling from not only a single blastocyst but also from a portion of it. WOW-CAT generated similar H3K4me3 profiles as NTU-CAT, but they were closer to the profiles produced by chromatin immunoprecipitation-sequencing, such as a valley-like trend and relatively lower false positive rates, indicating that WOW-CAT may attenuate the bias of Tn5 transposase to cut open chromatin regions. Simultaneous WOW-CAT of two halves of single blastocysts was conducted to analyze two different histone modifications (H3K4me3 and H3K27ac) within the same embryo. Furthermore, trophectoderm cells were biopsied and subjected to WOW-CAT in anticipation of preimplantation diagnosis of histone modifications. WOW-CAT allowed the monitoring of epigenetic modifications in the main body of the embryo. For example, analysis of H3K4me3 modifications of XIST and DDX3Y in trophectoderm biopsies could be used to sex embryos in combination with quantitative PCR, but without the need for deep sequencing. CONCLUSIONS These results suggest the applicability of WOW-CAT for flexible epigenetic analysis of individual embryos in preimplantation epigenetic diagnosis.
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Affiliation(s)
- Yiren Zeng
- Laboratory of Reproductive Biology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Yoichiro Hoshino
- Laboratory of Reproductive Biology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Kazuki Susami
- Laboratory of Reproductive Biology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Shinnosuke Honda
- Laboratory of Reproductive Biology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Naojiro Minami
- Laboratory of Reproductive Biology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Shuntaro Ikeda
- Laboratory of Reproductive Biology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan.
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Park SI, Cho SM, Atsumi S, Kawada M, Shibuya M, Lee JY, Kim JY, Kwon HJ. NDUFA12 as a Functional Target of the Anticancer Compound Ertredin in Human Hepatoma Cells As Revealed by Label-Free Chemical Proteomics. J Proteome Res 2024; 23:130-141. [PMID: 38104258 DOI: 10.1021/acs.jproteome.3c00471] [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] [Indexed: 12/19/2023]
Abstract
Many attempts have been made to develop new agents that target EGFR mutants or regulate downstream factors in various cancers. Cell-based screening showed that a natural small molecule, Ertredin, inhibited the growth of EGFRvIII mutant cancer cells. Previous studies have shown that Ertredin effectively inhibits anchorage-independent 3D growth of sphere-forming cells transfected with EGFRvIII mutant cDNA. However, the underlying mechanism remains unclear. In this study, we investigated the target protein of Ertredin by combining drug affinity-responsive target stability (DARTS) assays with liquid chromatography-mass spectrometry using label-free Ertredin as a bait and HepG2 cell lysates as a proteome pool. NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 (NDUFA12) was identified as an Ertredin-binding protein that was responsible for its biological activity. The interaction between NDUFA12 and Ertredin was validated by DARTS and cellular thermal shift assays. In addition, the genetic knockdown of the identified target, NDUFA12, was shown to suppress cell proliferation. NDUFA12 was identified as a biologically relevant target protein of Ertredin that is responsible for its antitumor activity, and these results provide insights into the role of NDUFA12 as a downstream factor in EGFRvIII mutants.
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Affiliation(s)
- Se In Park
- Chemical Genomics Leader Research Laboratory, Department of Biotechnology College of Life Science & Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Sung Min Cho
- Chemical Genomics Leader Research Laboratory, Department of Biotechnology College of Life Science & Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Sonoko Atsumi
- Laboratory of Oncology, Institute of Microbial Chemistry, 3-14-23 Kamiosaki, Shinagawa-ku 141-0021, Tokyo, Japan
| | - Manabu Kawada
- Laboratory of Oncology, Institute of Microbial Chemistry, 3-14-23 Kamiosaki, Shinagawa-ku 141-0021, Tokyo, Japan
| | - Masabumi Shibuya
- Institute of Physiology and Medicine, Jobu University, Takasaki-shi, Gunma 370-1393, Japan
| | - Ju Yeon Lee
- Research Center of Bioconvergence Analysis, Korea Basic Science Institute, Ochang 28119, Korea
- Critical Diseases Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| | - Jin Young Kim
- Research Center of Bioconvergence Analysis, Korea Basic Science Institute, Ochang 28119, Korea
- Critical Diseases Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| | - Ho Jeong Kwon
- Chemical Genomics Leader Research Laboratory, Department of Biotechnology College of Life Science & Biotechnology, Yonsei University, Seoul 03722, Korea
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Herrera-Luis E, Rosa-Baez C, Huntsman S, Eng C, Beckman KB, LeNoir MA, Rodriguez-Santana JR, Villar J, Laprise C, Borrell LN, Ziv E, Burchard EG, Pino-Yanes M. Novel insights into the whole-blood DNA methylome of asthma in ethnically diverse children and youth. Eur Respir J 2023; 62:2300714. [PMID: 37802634 PMCID: PMC10841414 DOI: 10.1183/13993003.00714-2023] [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: 10/03/2022] [Accepted: 08/20/2023] [Indexed: 10/10/2023]
Abstract
BACKGROUND The epigenetic mechanisms of asthma remain largely understudied in African Americans and Hispanics/Latinos, two populations disproportionately affected by asthma. We aimed to identify markers, regions and processes with differential patterns of DNA methylation (DNAm) in whole blood by asthma status in ethnically diverse children and youth, and to assess their functional consequences. METHODS DNAm levels were profiled with the Infinium MethylationEPIC or HumanMethylation450 BeadChip arrays among 1226 African Americans or Hispanics/Latinos and assessed for differential methylation per asthma status at the CpG and region (differentially methylated region (DMR)) level. Novel associations were validated in blood and/or nasal epithelium from ethnically diverse children and youth. The functional and biological implications of the markers identified were investigated by combining epigenomics with transcriptomics from study participants. RESULTS 128 CpGs and 196 DMRs were differentially methylated after multiple testing corrections, including 92.3% and 92.8% novel associations, respectively. 41 CpGs were replicated in other Hispanics/Latinos, prioritising cg17647904 (NCOR2) and cg16412914 (AXIN1) as asthma DNAm markers. Significant DNAm markers were enriched in previous associations for asthma, fractional exhaled nitric oxide, bacterial infections, immune regulation or eosinophilia. Functional annotation highlighted epigenetically regulated gene networks involved in corticosteroid response, host defence and immune regulation. Several implicated genes are targets for approved or experimental drugs, including TNNC1 and NDUFA12. Many differentially methylated loci previously associated with asthma were validated in our study. CONCLUSIONS We report novel whole-blood DNAm markers for asthma underlying key processes of the disease pathophysiology and confirm the transferability of previous asthma DNAm associations to ethnically diverse populations.
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Affiliation(s)
- Esther Herrera-Luis
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna (ULL), La Laguna, Spain
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Carlos Rosa-Baez
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna (ULL), La Laguna, Spain
| | - Scott Huntsman
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Celeste Eng
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | | | - Michael A LeNoir
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna (ULL), La Laguna, Spain
- Bay Area Pediatrics, Oakland, CA, USA
| | - Jose R Rodriguez-Santana
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna (ULL), La Laguna, Spain
- Centro de Neumología Pediátrica, San Juan, Puerto Rico
| | - Jesús Villar
- Multidisciplinary Organ Dysfunction Evaluation Research Network, Research Unit, Hospital Universitario Dr. Negrín, Las Palmas de Gran Canaria, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Li Ka Shing Knowledge Institute at St Michael's Hospital, Toronto, ON, Canada
| | - Catherine Laprise
- Département des Sciences Fondamentales, Université du Québec à Chicoutimi, Saguenay, QC, Canada
- Centre Intersectoriel en Santé Durable, Université du Québec à Chicoutimi, Saguenay, QC, Canada
| | - Luisa N Borrell
- Department of Epidemiology and Biostatistics, Graduate School of Public Health and Health Policy, City University of New York, New York, NY, USA
| | - Elad Ziv
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Division of General Internal Medicine, Department of Medicine and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Esteban G Burchard
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Division of General Internal Medicine, Department of Medicine and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Instituto de Tecnologías Biomédicas, Universidad de La Laguna (ULL), La Laguna, Spain
| | - Maria Pino-Yanes
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna (ULL), La Laguna, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Instituto de Tecnologías Biomédicas, Universidad de La Laguna (ULL), La Laguna, Spain
- These authors contributed equally as senior authors
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Zheng Z, Zhang L, Zhao C, Xiong H, Li J. Identification of differentially expressed proteins in heart of mouse death from smother based on label-free proteomics. Leg Med (Tokyo) 2023; 65:102302. [PMID: 37549592 DOI: 10.1016/j.legalmed.2023.102302] [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: 05/31/2023] [Revised: 07/18/2023] [Accepted: 07/28/2023] [Indexed: 08/09/2023]
Abstract
Identification of mechanical asphyxia deaths without obvious injuries is a difficult problem for forensic medicine. This study aimed to identify molecular biological markers to predict death from mechanical asphyxia (smother). We established a smother model of mice by over the head with plastic bag tightly until the mice died and applied label-free proteomic technology to identify differentially expressed proteins (DEPs) in heart. A total of 3307 proteins were quantified, and a Fold Change (FC) > 1.2 (or <1/1.2) and Q value < 0.05 were considered as DEPs. Through comparative analysis, we identified 606 DEPs compared to the control group, comprising 219 upregulated and 387 downregulated proteins. Bioinformatics analysis (MCODE analysis) showed that the candidate proteins were mainly involved in regulation of ribosome function, myocardial contraction and calcium regulation, regulation of coagulation and regulation of mitochondrial oxidative respiration. Seven of these proteins were validated using parallel reaction monitoring (PRM), including fibrinogen alpha chain (FIBA), fibrinogen gamma chain (FIBG), Calsequestrin-2 (CASQ2), NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 (NDUAB), NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 (NDUA3), NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 (NDUAD) and Rab7 (RAB7A). CASQ2 and FIBG were further validated by immunohistochemistry. In conclusion, our results may provide some auxiliary indices for identifying the death from mechanical asphyxia.
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Affiliation(s)
- Zhe Zheng
- Department of Basic Medicine and Forensic Medicine, Henan University of Science and Technology, Luoyang, Henan 471023, China; Department of Forensic Medicine, Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Li Zhang
- Department of Basic Medicine, Chongqing College of Traditional Chinese Medicine, Chongqing 402760, China
| | - Congcong Zhao
- Department of Forensic Medicine, Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Hongli Xiong
- Department of Forensic Medicine, Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Jianbo Li
- Department of Forensic Medicine, Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China.
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Chang X, Xu Y, Cheng L, Yi K, Gu X, Luo Z, Zhang J, Wang J, Geng F. Quantitative proteomic analysis of cattle-yak and yak longissimus thoracis provides insights into the differential mechanisms of meat quality. Food Res Int 2023; 173:113253. [PMID: 37803567 DOI: 10.1016/j.foodres.2023.113253] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 07/05/2023] [Accepted: 07/06/2023] [Indexed: 10/08/2023]
Abstract
In this study, proteins of cattle-yak longissimus thoracis (CYLT) and yak longissimus thoracis (YLT) were compared using tandem mass tag-labeled quantitative proteomic analysis. A total of 157 proteins were screened as differentially abundant proteins (DAPs) derived from 1551 quantitative proteins. Bioinformatics analysis revealed that the upregulated DAPs in CYLT were mainly involved in energy metabolism, oxidative stress, muscle fiber structure, and extracellular matrix (ECM), while the downregulated DAPs were mainly involved in energy metabolism and ECM function. The upregulated myoglobin, downregulation of NADH dehydrogenase, and upregulation of cytochrome oxidase indicated that CYLT initiates compensatory regulation in response to hypoxic high-altitude environments. Two differentially abundant myosins and five collagens suggested that CYLT and YLT may have distinct differences in the assembly structure of muscle fibers and connective tissue. These differences in energy metabolism and muscle structure will inevitably affect the postmortem physiology of "muscle to meat" and consequently the meat qualities. Therefore, our results will provide important clues to gain insight into the potential causes of meat quality differences between cattle-yak and yak based on high-altitude response.
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Affiliation(s)
- Xinping Chang
- Meat Processing Key Laboratory of Sichuan Province, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China
| | - Yisha Xu
- Meat Processing Key Laboratory of Sichuan Province, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China.
| | - Lei Cheng
- School of Food and Health, Beijing Technology & Business University (BTBU), Beijing 100048, China.
| | - Kaige Yi
- Provincial and Ministerial Co-Founded Collaborative Innovation Center for R & D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Tibet Agricultural and Animal Husbandry University, Linzhi 860000, China; College of Food Science, Tibet Agricultural and Animal Husbandry University, Linzhi 860000, China
| | - Xuedong Gu
- Provincial and Ministerial Co-Founded Collaborative Innovation Center for R & D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Tibet Agricultural and Animal Husbandry University, Linzhi 860000, China; College of Food Science, Tibet Agricultural and Animal Husbandry University, Linzhi 860000, China
| | - Zhang Luo
- Provincial and Ministerial Co-Founded Collaborative Innovation Center for R & D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Tibet Agricultural and Animal Husbandry University, Linzhi 860000, China; College of Food Science, Tibet Agricultural and Animal Husbandry University, Linzhi 860000, China.
| | - Jiamin Zhang
- Meat Processing Key Laboratory of Sichuan Province, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China
| | - Jinqiu Wang
- Meat Processing Key Laboratory of Sichuan Province, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China
| | - Fang Geng
- Meat Processing Key Laboratory of Sichuan Province, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China.
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6
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Gao Y, Long Q, Yang H, Hu Y, Xu Y, Tang C, Gu C, Yong S. Transcriptomics and metabolomics study in mouse kidney of the molecular mechanism underlying energy metabolism response to hypoxic stress in highland areas. Exp Ther Med 2023; 26:533. [PMID: 37869643 PMCID: PMC10587886 DOI: 10.3892/etm.2023.12232] [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: 05/15/2023] [Accepted: 08/25/2023] [Indexed: 10/24/2023] Open
Abstract
Exposure to hypoxia disrupts energy metabolism and induces inflammation. However, the pathways and mechanisms underlying energy metabolism disorders caused by hypoxic conditions remain unclear. In the present study, a hypoxic animal model was created and transcriptomic and non-targeted metabolomics techniques were applied to further investigate the pathways and mechanisms of hypoxia exposure that disrupt energy metabolism. Transcriptome results showed that 3,007 genes were significantly differentially expressed under hypoxic exposure, and Gene Ontology annotation analysis and Kyoto Encyclopaedia of Genes and Genomes (KEGG) enrichment analysis showed that the differentially expressed genes (DEGs) were mainly involved in energy metabolism and were significantly enriched in the tricarboxylic acid (TCA) cycle and oxidative phosphorylation (OXPHOS) pathway. The DEGs IDH3A, SUCLA2, and MDH2 in the TCA cycle and the DEGs NDUFA3, NDUFS7, UQCRC1, CYC1 and UQCRFS1 in the OXPHOS pathway were validated using mRNA and protein expression, and the results showed downregulation. The results of non-targeted metabolomics showed that 365 significant differential metabolites were identified under plateau hypoxia stress. KEGG enrichment analysis showed that the differential metabolites were mainly enriched in metabolic processes, such as energy, nucleotide and amino acid metabolism. Hypoxia exposure disrupted the TCA cycle and reduced the synthesis of amino acids and nucleotides by decreasing the concentration of cis-aconitate, α-ketoglutarate, NADH, NADPH and that of most amino acids, purines, and pyrimidines. Bioinformatics analysis was used to identify inflammatory genes related to hypoxia exposure and some of them were selected for verification. It was shown that the mRNA and protein expression levels of IL1B, IL12B, S100A8 and S100A9 in kidney tissues were upregulated under hypoxic exposure. The results suggest that hypoxia exposure inhibits the TCA cycle and the OXPHOS signalling pathway by inhibiting IDH3A, SUCLA2, MDH2, NDUFFA3, NDUFS7, UQCRC1, CYC1 and UQCRFS1, thereby suppressing energy metabolism, inducing amino acid and nucleotide deficiency and promoting inflammation, ultimately leading to kidney damage.
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Affiliation(s)
- Yujie Gao
- Department of Basic Medicine, School of Medicine, Qinghai University, Xining, Qinghai 810016, P.R. China
| | - Qifu Long
- Department of Basic Medicine, School of Medicine, Qinghai University, Xining, Qinghai 810016, P.R. China
| | - Hui Yang
- Department of Basic Medicine, School of Medicine, Qinghai University, Xining, Qinghai 810016, P.R. China
| | - Ying Hu
- Department of Basic Medicine, School of Medicine, Qinghai University, Xining, Qinghai 810016, P.R. China
| | - Yuzhen Xu
- Department of Basic Medicine, School of Medicine, Qinghai University, Xining, Qinghai 810016, P.R. China
| | - Chaoqun Tang
- Department of Basic Medicine, School of Medicine, Qinghai University, Xining, Qinghai 810016, P.R. China
| | - Cunlin Gu
- Department of Basic Medicine, School of Medicine, Qinghai University, Xining, Qinghai 810016, P.R. China
| | - Sheng Yong
- Department of Basic Medicine, School of Medicine, Qinghai University, Xining, Qinghai 810016, P.R. China
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Cao MC, Ryan B, Wu J, Curtis MA, Faull RLM, Dragunow M, Scotter EL. A panel of TDP-43-regulated splicing events verifies loss of TDP-43 function in amyotrophic lateral sclerosis brain tissue. Neurobiol Dis 2023; 185:106245. [PMID: 37527763 DOI: 10.1016/j.nbd.2023.106245] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/13/2023] [Accepted: 07/28/2023] [Indexed: 08/03/2023] Open
Abstract
TDP-43 dysfunction is a molecular hallmark of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). A major hypothesis of TDP-43 dysfunction in disease is the loss of normal nuclear function, resulting in impaired RNA regulation and the emergence of cryptic exons. Cryptic exons and differential exon usage are emerging as promising markers of lost TDP-43 function in addition to revealing biological pathways involved in neurodegeneration in ALS/FTD. In this brief report, we identified markers of TDP-43 loss of function by depleting TARDBP from post-mortem human brain pericytes, a manipulable in vitro primary human brain cell model, and identifying differential exon usage events with bulk RNA-sequencing analysis. We present these data in an interactive database (https://www.scotterlab.auckland.ac.nz/research-themes/tdp43-lof-db-v2/) together with seven other TDP-43-depletion datasets we meta-analysed previously, for user analysis of differential expression and splicing signatures. Differential exon usage events that were validated by qPCR were then compiled into a 'differential exon usage panel' with other well-established TDP-43 loss-of-function exon markers. This differential exon usage panel was investigated in ALS and control motor cortex tissue to verify whether, and to what extent, TDP-43 loss of function occurs in ALS. We find that profiles of TDP-43-regulated cryptic exons, changed exon usage and changed 3' UTR usage discriminate ALS brain tissue from controls, verifying that TDP-43 loss of function occurs in ALS. We propose that TDP-43-regulated splicing events that occur in brain tissue will have promise as predictors of disease.
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Affiliation(s)
- Maize C Cao
- Department of Pharmacology, University of Auckland, New Zealand; Centre for Brain Research, University of Auckland, New Zealand.
| | - Brigid Ryan
- Department of Anatomy and Medical Imaging, University of Auckland, New Zealand; Centre for Brain Research, University of Auckland, New Zealand.
| | - Jane Wu
- Department of Anatomy and Medical Imaging, University of Auckland, New Zealand; Centre for Brain Research, University of Auckland, New Zealand.
| | - Maurice A Curtis
- Department of Anatomy and Medical Imaging, University of Auckland, New Zealand; Centre for Brain Research, University of Auckland, New Zealand.
| | - Richard L M Faull
- Department of Anatomy and Medical Imaging, University of Auckland, New Zealand; Centre for Brain Research, University of Auckland, New Zealand.
| | - Mike Dragunow
- Department of Pharmacology, University of Auckland, New Zealand; Centre for Brain Research, University of Auckland, New Zealand.
| | - Emma L Scotter
- School of Biological Sciences, University of Auckland, New Zealand; Centre for Brain Research, University of Auckland, New Zealand.
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8
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Zhao L, Gao J, Chen G, Huang C, Kong W, Feng Y, Zhen G. Mitochondria dysfunction in airway epithelial cells is associated with type 2-low asthma. Front Genet 2023; 14:1186317. [PMID: 37152983 PMCID: PMC10160377 DOI: 10.3389/fgene.2023.1186317] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 04/10/2023] [Indexed: 05/09/2023] Open
Abstract
Background: Type 2 (T2)-low asthma can be severe and corticosteroid-resistant. Airway epithelial cells play a pivotal role in the development of asthma, and mitochondria dysfunction is involved in the pathogenesis of asthma. However, the role of epithelial mitochondria dysfunction in T2-low asthma remains unknown. Methods: Differentially expressed genes (DEGs) were identified using gene expression omnibus (GEO) dataset GSE4302, which is originated from airway epithelial brushings from T2-high (n = 22) and T2-low asthma patients (n = 20). Gene set enrichment analysis (GSEA) was implemented to analyze the potential biological pathway involved between T2-low and T2-high asthma. T2-low asthma related genes were identified using weighted gene co-expression network analysis (WGCNA). The mitochondria-related genes (Mito-RGs) were referred to the Molecular Signatures Database (MSigDB). T2-low asthma related mitochondria (T2-low-Mito) DEGs were obtained by intersecting the DEGs, T2-low asthma related genes, and Mito-RGs. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) was performed to further explore the potential function of the T2-low-Mito DEGs. In addition, the hub genes were further identified by protein-protein interaction (PPI), and the expressions of hub genes were verified in another GEO dataset GSE67472 and bronchial brushings from patients recruited at Tongji Hospital. Results: Six hundred and ninety-two DEGs, including 107 downregulated genes and 585 upregulated genes were identified in airway epithelial brushings from T2-high and T2-low asthma patients included in GSE4302 dataset. GSEA showed that mitochondrial ATP synthesis coupled electron transport is involved in T2-low asthma. Nine hundred and four T2-low asthma related genes were identified using WGCNA. Twenty-two T2-low-Mito DEGs were obtained by intersecting the DEGs, T2-low asthma and Mito-RGs. The GO enrichment analysis of the T2-low-Mito DEGs showed significant enrichment of mitochondrial respiratory chain complex assembly, and respiratory electron transport chain. PPI network was constructed using 22 T2-low-Mito DEGs, and five hub genes, ATP5G1, UQCR10, NDUFA3, TIMM10, and NDUFAB1, were identified. Moreover, the expression of these hub genes was validated in another GEO dataset, and our cohort of asthma patients. Conclusion: This study suggests that mitochondria dysfunction contributes to T2-low asthma.
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Affiliation(s)
- Lu Zhao
- Division of Respiratory and Critical Care Medicine, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Respiratory Diseases, National Health Commission of People’s Republic of China, Wuhan, China
| | - Jiali Gao
- Division of Respiratory and Critical Care Medicine, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Respiratory Diseases, National Health Commission of People’s Republic of China, Wuhan, China
| | - Gongqi Chen
- Division of Respiratory and Critical Care Medicine, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Respiratory Diseases, National Health Commission of People’s Republic of China, Wuhan, China
| | - Chunli Huang
- Division of Respiratory and Critical Care Medicine, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Respiratory Diseases, National Health Commission of People’s Republic of China, Wuhan, China
| | - Weiqiang Kong
- Division of Respiratory and Critical Care Medicine, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Respiratory Diseases, National Health Commission of People’s Republic of China, Wuhan, China
| | - Yuchen Feng
- Division of Respiratory and Critical Care Medicine, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Respiratory Diseases, National Health Commission of People’s Republic of China, Wuhan, China
- *Correspondence: Yuchen Feng, ; Guohua Zhen,
| | - Guohua Zhen
- Division of Respiratory and Critical Care Medicine, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Respiratory Diseases, National Health Commission of People’s Republic of China, Wuhan, China
- *Correspondence: Yuchen Feng, ; Guohua Zhen,
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Zhang Y, Wen R, Bao J, Gong Y, Wang X. Mancozeb induces nephrotoxicity by impairing the oxidative phosphorylation pathway: A transcriptome study. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 249:114471. [PMID: 38321686 DOI: 10.1016/j.ecoenv.2022.114471] [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: 09/26/2022] [Revised: 12/19/2022] [Accepted: 12/23/2022] [Indexed: 02/08/2024]
Abstract
This study analyzed the mechanism underlying mancozeb (MCZ)-induced kidney injury by detecting kidney function indicators, combined with transcriptome and metabolome sequencing. Twenty mice were randomly assigned into two groups (control and MCZ groups) to explore the MCZ-induced kidney toxicity. The control group was gavaged with 0.2 mL of deionized water, and the MCZ group with 0.2 mL of 100 mg/kg MCZ for 30 days. The kidney structure of the MCZ group was damaged, with slight hyaline degeneration in the kidney tubular epithelial envelope. The creatinine (CRE) and uric acid (UA) were significantly increased in the MCZ group than in the control group. Moreover, the reactive oxygen species (ROS) significantly accumulated in the MCZ group kidneys. Compared to the control group, superoxide dismutase (SOD) and glutathione peroxidase (GSH-PX) were significantly decreased in the MCZ group, while the MDA content was substantially increased. The differentially expressed genes (DEGs) in the MCZ group were mainly enriched in the oxidative phosphorylation pathway. Besides, in the MCZ group, ndufs1 and ndufab1 genes were significantly up-regulated, while cox5b, ndufa5, and ndufa6 genes were significantly down-regulated, consistent with the PCR verification results. The metabolomic analysis identified cGMP-PKG signaling pathway of MCZ-induced nephrotoxicity, with Guanosine monophosphate and Adenosine 5'-monophosphate as the main altered metabolites. These results indicated that MCZ impairs the mice kidneys by obstructing the oxidative phosphorylation pathway, which increases oxidative stress in the kidneys, resulting in kidney injury.
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Affiliation(s)
- Yan Zhang
- College of Traditional Chinese Veterinary Medicine, Hebei Agricultural University, Baoding 071001, China
| | - Ran Wen
- College of Traditional Chinese Veterinary Medicine, Hebei Agricultural University, Baoding 071001, China
| | - Jialu Bao
- College of Traditional Chinese Veterinary Medicine, Hebei Agricultural University, Baoding 071001, China
| | - Yinglan Gong
- College of Traditional Chinese Veterinary Medicine, Hebei Agricultural University, Baoding 071001, China
| | - Xiaodan Wang
- College of Traditional Chinese Veterinary Medicine, Hebei Agricultural University, Baoding 071001, China.
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10
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A 69 kb Deletion in chr19q13.42 including PRPF31 Gene in a Chinese Family Affected with Autosomal Dominant Retinitis Pigmentosa. J Clin Med 2022; 11:jcm11226682. [PMID: 36431159 PMCID: PMC9695658 DOI: 10.3390/jcm11226682] [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: 08/10/2022] [Revised: 10/20/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022] Open
Abstract
We aimed to identify the genetic cause of autosomal dominant retinitis pigmentosa (adRP) and characterize the underlying molecular mechanisms of incomplete penetrance in a Chinese family affected with adRP. All enrolled family members underwent ophthalmic examinations. Whole-genome sequencing (WGS), multiplex ligation-dependent probe amplification (MLPA), linkage analysis and haplotype construction were performed in all participants. RNA-seq was performed to analyze the regulating mechanism of incomplete penetrance among affected patients, mutation carriers and healthy controls. In the studied family, 14 individuals carried a novel heterozygous large deletion of 69 kilobase (kb) in 19q13.42 encompassing exon 1 of the PRPF31 gene and five upstream genes: TFPT, OSCAR, NDUFA3, TARM1, and VSTM1. Three family members were sequenced and diagnosed as non-penetrant carriers (NPCs). RNA-seq showed significant differential expression of genes in deletion between mutation carriers and healthy control. The RP11 pedigree in this study was the largest pedigree compared to other reported RP11 pedigrees with large deletions. Early onset in all affected members in this pedigree was considered to be a special phenotype and was firstly reported in a RP11 family for the first time. Differential expression of PRPF31 between affected and unaffected subjects indicates a haploinsufficiency to cause the disease in the family. The other genes with significant differential expression might play a cooperative effect on the penetrance of RP11.
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11
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Westbrook TC, Guan X, Rodansky E, Flores D, Liu CJ, Udager AM, Patel RA, Haffner MC, Hu YM, Sun D, Beer TM, Foye A, Aggarwal R, Quigley DA, Youngren JF, Ryan CJ, Gleave M, Wang Y, Huang J, Coleman I, Morrissey C, Nelson PS, Evans CP, Lara P, Reiter RE, Witte O, Rettig M, Wong CK, Weinstein AS, Uzunangelov V, Stuart JM, Thomas GV, Feng FY, Small EJ, Yates JA, Xia Z, Alumkal JJ. Transcriptional profiling of matched patient biopsies clarifies molecular determinants of enzalutamide-induced lineage plasticity. Nat Commun 2022; 13:5345. [PMID: 36109521 PMCID: PMC9477876 DOI: 10.1038/s41467-022-32701-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 08/11/2022] [Indexed: 11/08/2022] Open
Abstract
The androgen receptor (AR) signaling inhibitor enzalutamide (enza) is one of the principal treatments for metastatic castration-resistant prostate cancer (CRPC). Several emergent enza clinical resistance mechanisms have been described, including lineage plasticity in which the tumors manifest reduced dependency on the AR. To improve our understanding of enza resistance, herein we analyze the transcriptomes of matched biopsies from men with metastatic CRPC obtained prior to treatment and at progression (n = 21). RNA-sequencing analysis demonstrates that enza does not induce marked, sustained changes in the tumor transcriptome in most patients. However, three patients' progression biopsies show evidence of lineage plasticity. The transcription factor E2F1 and pathways linked to tumor stemness are highly activated in baseline biopsies from patients whose tumors undergo lineage plasticity. We find a gene signature enriched in these baseline biopsies that is strongly associated with poor survival in independent patient cohorts and with risk of castration-induced lineage plasticity in patient-derived xenograft models, suggesting that tumors harboring this gene expression program may be at particular risk for resistance mediated by lineage plasticity and poor outcomes.
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Affiliation(s)
- Thomas C Westbrook
- Division of Hematology and Oncology, Department of Internal Medicine, Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Xiangnan Guan
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Eva Rodansky
- Division of Hematology and Oncology, Department of Internal Medicine, Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Diana Flores
- Division of Hematology and Oncology, Department of Internal Medicine, Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Chia Jen Liu
- Department of Pathology, Michigan Center for Translational Pathology, Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Aaron M Udager
- Department of Pathology, Michigan Center for Translational Pathology, Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Radhika A Patel
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Michael C Haffner
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Ya-Mei Hu
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Duanchen Sun
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Tomasz M Beer
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Adam Foye
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Rahul Aggarwal
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - David A Quigley
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Jack F Youngren
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Charles J Ryan
- Masonic Cancer Center, University of Minnesota; Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Martin Gleave
- Department of Urological Sciences and Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada
| | - Yuzhuo Wang
- Department of Urological Sciences and Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada
- Department of Experimental Therapeutics, BC Cancer, University of British Columbia, Vancouver, BC, Canada
| | | | - Ilsa Coleman
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Colm Morrissey
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Peter S Nelson
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Primo Lara
- University of California Davis, Davis, CA, USA
| | | | - Owen Witte
- Department of Microbiology, Immunology, and Molecular Genetics at the David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Matthew Rettig
- University of California Los Angeles, Los Angeles, CA, USA
- VA Greater Los Angeles Healthcare System, Los Angeles, CA, USA
| | - Christopher K Wong
- UC Santa Cruz Genomics Institute and Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Alana S Weinstein
- UC Santa Cruz Genomics Institute and Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Vlado Uzunangelov
- UC Santa Cruz Genomics Institute and Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Josh M Stuart
- UC Santa Cruz Genomics Institute and Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - George V Thomas
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Felix Y Feng
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Departments of Radiation Oncology and Urology, University of California San Francisco, San Francisco, CA, USA
| | - Eric J Small
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Joel A Yates
- Division of Hematology and Oncology, Department of Internal Medicine, Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Zheng Xia
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.
| | - Joshi J Alumkal
- Division of Hematology and Oncology, Department of Internal Medicine, Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.
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12
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Ogawa S, Darhan H, Suzuki K. Genetic and genomic analysis of oxygen consumption in mice. J Anim Breed Genet 2022; 139:596-610. [PMID: 35608337 DOI: 10.1111/jbg.12721] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 05/07/2022] [Indexed: 12/16/2022]
Abstract
We estimated genetic parameters for oxygen consumption (OC), OC per metabolic body weight (OCMBW) and body weight at three through 8 weeks of age in divergently selected mice populations, with an animal model considering maternal genetic, common litter environmental and cytoplasmic inheritance effects. Cytoplasmic inheritance was considered based on maternal lineage information. With respect to OC, estimated direct heritability was moderate (0.32) and the estimated proportion of the variance of cytoplasmic inheritance effects to the phenotypic variance was very low (0.01), implying that causal genes for OC could be located on autosomes. To assess this hypothesis, we attempted to identify possible candidate causal genes through selective signature detection with the results of pooled whole-genome resequencing using pooled DNA samples from high and low OC mice. We made a list of possible candidate causal genes for OC, including those relating to electron transport chain and ATP-binding proteins (Ndufa12, Sdhc, Atp10b, etc.), Prr16 encoding Largen protein, Cry1 encoding a key component of the circadian core oscillator and so on. The results, although careful interpretation must be required, could contribute to elucidate the genetic mechanism of OC, an indicator for maintenance energy requirement, and therefore feed efficiency.
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Affiliation(s)
- Shinichiro Ogawa
- Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, Japan
| | - Hongyu Darhan
- Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, Japan
| | - Keiichi Suzuki
- Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, Japan
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13
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Transcriptome Sequencing Analysis Reveals Dynamic Changes in Major Biological Functions during the Early Development of Clearhead Icefish, Protosalanx chinensis. FISHES 2022. [DOI: 10.3390/fishes7030115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Early development, when many important developmental events occur, is a critical period for fish. However, research on the early development of clearhead icefish is very limited, especially in molecular research. In this study, we aimed to explore the dynamic changes in the biological functions of five key periods in clearhead icefish early development, namely the YL (embryonic), PM (first day after hatching), KK (fourth day after hatching), LC (seventh day after hatching), and SL (tenth day after hatching) stages, through transcriptome sequencing and different analysis strategies. A trend expression analysis and an enrichment analysis revealed that the expression ofgenes encoding G protein-coupled receptors and their ligands, i.e., prss1_2_3, pomc, npy, npb, sst, rln3, crh, gh, and prl that are associated with digestion and feeding regulation gradually increased during early development. In addition, a weighted gene co-expression network analysis (WGCNA) showed that eleven modules were significantly associated with early development, among which nine modules were significantly positively correlated. Through the enrichment analysis and hub gene identification results of these nine modules, it was found that the pathways related to eye, bone, and heart development were significantly enriched in the YL stage, and the ccnd2, seh1l, kdm6a, arf4, and ankrd28 genes that are associated with cell proliferation and differentiation played important roles in these developmental processes; the pak3, dlx3, dgat2, and tas1r1 genes that are associated with jaw and tooth development, TG (triacylglycerol) synthesis, and umami amino acid receptors were identified as hub genes for the PM stage; the pathways associated with aerobic metabolism and unsaturated fatty acid synthesis were significantly enriched in the KK stage, with the foxk, slc13a2_3_5, ndufa5, and lsc2 genes playing important roles; the pathways related to visual perception were significantly enriched in the LC stage; and the bile acid biosynthetic and serine-type peptidase activity pathways were significantly enriched in the SL stage. These results provide a more detailed understanding of the processes of early development of clearhead icefish.
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14
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Magrinelli F, Cali E, Braga VL, Yis U, Tomoum H, Shamseldin H, Raiman J, Kernstock C, Rezende Filho FM, Barsottini OGP, Taylor RW, Østergaard E, Tamim A, Schäferhoff K, Sallum JMF, Zaki MS, Kok F, Bhatia KP, Wissinger B, Sergeant K, Haack TB, Horvath R, Hiz S, Alkuraya FS, Houlden H, Pedroso JL, Maroofian R. Biallelic Loss-of-Function NDUFA12 Variants Cause a Wide Phenotypic Spectrum from Leigh/Leigh-Like Syndrome to Isolated Optic Atrophy. Mov Disord Clin Pract 2022; 9:218-228. [PMID: 35141356 PMCID: PMC8810437 DOI: 10.1002/mdc3.13398] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 11/28/2021] [Accepted: 12/11/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Biallelic loss-of-function NDUFA12 variants have hitherto been linked to mitochondrial complex I deficiency presenting with heterogeneous clinical and radiological features in nine cases only. OBJECTIVES To fully characterize, both phenotypically and genotypically, NDUFA12-related mitochondrial disease. METHODS We collected data from cases identified by screening genetic databases of several laboratories worldwide and systematically reviewed the literature. RESULTS Nine unreported NDUFA12 cases from six pedigrees were identified, with presentation ranging from movement disorder phenotypes (dystonia and/or spasticity) to isolated optic atrophy. MRI showed basal ganglia abnormalities (n = 6), optic atrophy (n = 2), or was unremarkable (n = 1). All carried homozygous truncating NDUFA12 variants, three of which are novel. CONCLUSIONS Our case series expands phenotype-genotype correlations in NDUFA12-associated mitochondrial disease, providing evidence of intra- and inter-familial clinical heterogeneity for the same variant. It confirms NDUFA12 variants should be included in the diagnostic workup of Leigh/Leigh-like syndromes - particularly with dystonia - as well as isolated optic atrophy.
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Affiliation(s)
- Francesca Magrinelli
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of NeurologyUniversity College LondonLondonUnited Kingdom
- Department of Neurosciences, Biomedicine and Movement SciencesUniversity of VeronaVeronaItaly
| | - Elisa Cali
- Department of Neuromuscular DiseasesUCL Queen Square Institute of Neurology, University College LondonLondonUnited Kingdom
| | | | - Uluç Yis
- Division of Pediatric Neurology, Department of PediatricsDokuz Eylül University Faculty of MedicineİzmirTurkey
| | - Hoda Tomoum
- Department of PediatricsAin Shams UniversityCairoEgypt
| | - Hanan Shamseldin
- Department of GeneticsKing Faisal Specialist Hospital and Research CenterRiyadhSaudi Arabia
| | - Julian Raiman
- Department of Inherited Metabolic DiseaseBirmingham Children's HospitalBirminghamUnited Kingdom
| | - Christoph Kernstock
- Center for OphthalmologyInstitute for Ophthalmic Research, University of TübingenTübingenGermany
| | | | | | - Robert W. Taylor
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUnited Kingdom
| | - Elsebet Østergaard
- Department of Clinical GeneticsCopenhagen University Hospital RigshospitaletCopenhagenDenmark
- Department of Clinical MedicineUniversity of CopenhagenCopenhagenDenmark
| | - Abdullah Tamim
- Department of Pediatric NeurologyKing Faisal Specialist Hospital and Research CenterRiyadhSaudi Arabia
| | - Karin Schäferhoff
- Institute of Human Genetics and Applied GenomicsUniversity of TübingenTübingenGermany
| | | | - Maha S. Zaki
- Clinical Genetics Department, Human Genetics and Genome Research InstituteNational Research CentreCairoEgypt
| | - Fernando Kok
- Department of NeurologyUniversidade de São Paulo (USP)São PauloBrazil
- Mendelics Genomic AnalysisSão PauloBrazil
| | - Kailash P. Bhatia
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of NeurologyUniversity College LondonLondonUnited Kingdom
| | - Bernd Wissinger
- Center for OphthalmologyInstitute for Ophthalmic Research, University of TübingenTübingenGermany
| | - Kate Sergeant
- Oxford Genetics LaboratoriesOxford University Hospitals NHS Foundation TrustOxfordUnited Kingdom
| | - Tobias B. Haack
- Institute of Human Genetics and Applied GenomicsUniversity of TübingenTübingenGermany
- Centre for Rare DiseasesUniversity of TübingenTübingenGermany
| | - Rita Horvath
- Department of Clinical NeurosciencesUniversity of Cambridge, John Van Geest Cambridge Centre for Brain RepairCambridgeUnited Kingdom
| | - Semra Hiz
- Division of Pediatric Neurology, Department of PediatricsDokuz Eylül University Faculty of MedicineİzmirTurkey
| | - Fowzan S. Alkuraya
- Department of Translational GenomicsCenter for Genomic Medicine, King Faisal Specialist Hospital and Research CenterRiyadhSaudi Arabia
- Department of Anatomy and Cell BiologyCollege of Medicine, Alfaisal UniversityRiyadhSaudi Arabia
| | - Henry Houlden
- Department of Neuromuscular DiseasesUCL Queen Square Institute of Neurology, University College LondonLondonUnited Kingdom
| | - José Luiz Pedroso
- Department of NeurologyUniversidade Federal de São PauloSão PauloBrazil
| | - Reza Maroofian
- Department of Neuromuscular DiseasesUCL Queen Square Institute of Neurology, University College LondonLondonUnited Kingdom
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15
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Padavannil A, Ayala-Hernandez MG, Castellanos-Silva EA, Letts JA. The Mysterious Multitude: Structural Perspective on the Accessory Subunits of Respiratory Complex I. Front Mol Biosci 2022; 8:798353. [PMID: 35047558 PMCID: PMC8762328 DOI: 10.3389/fmolb.2021.798353] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 11/25/2021] [Indexed: 01/10/2023] Open
Abstract
Complex I (CI) is the largest protein complex in the mitochondrial oxidative phosphorylation electron transport chain of the inner mitochondrial membrane and plays a key role in the transport of electrons from reduced substrates to molecular oxygen. CI is composed of 14 core subunits that are conserved across species and an increasing number of accessory subunits from bacteria to mammals. The fact that adding accessory subunits incurs costs of protein production and import suggests that these subunits play important physiological roles. Accordingly, knockout studies have demonstrated that accessory subunits are essential for CI assembly and function. Furthermore, clinical studies have shown that amino acid substitutions in accessory subunits lead to several debilitating and fatal CI deficiencies. Nevertheless, the specific roles of CI’s accessory subunits have remained mysterious. In this review, we explore the possible roles of each of mammalian CI’s 31 accessory subunits by integrating recent high-resolution CI structures with knockout, assembly, and clinical studies. Thus, we develop a framework of experimentally testable hypotheses for the function of the accessory subunits. We believe that this framework will provide inroads towards the complete understanding of mitochondrial CI physiology and help to develop strategies for the treatment of CI deficiencies.
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Affiliation(s)
- Abhilash Padavannil
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA, United States
| | - Maria G Ayala-Hernandez
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA, United States
| | - Eimy A Castellanos-Silva
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA, United States
| | - James A Letts
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA, United States
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16
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Pan CS, Yan L, Lin SQ, He K, Cui YC, Liu YY, Hu BH, Chang X, Zhao XR, Fan JY, Han JY. QiShenYiQi Pills Attenuates Ischemia/Reperfusion-Induced Cardiac Microvascular Hyperpermeability Implicating Src/Caveolin-1 and RhoA/ROCK/MLC Signaling. Front Physiol 2022; 12:753761. [PMID: 34975519 PMCID: PMC8718710 DOI: 10.3389/fphys.2021.753761] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 11/18/2021] [Indexed: 01/25/2023] Open
Abstract
Aims: Coronary microvascular hyperpermeability is an important contributor to ischemia or reperfusion (I/R) injury. However, the effective strategy for this insult remains limited. This study aimed to explore the protective effect of the compound Chinese medicine QiShenYiQi Pills (QSYQ) against coronary microvascular hyperpermeability after cardiac I/R with focusing on the underlying mechanism. Methods and Results: Male Sprague-Dawley rats under anesthesia were subjected to occlusion of left coronary anterior descending artery followed by reperfusion. QSYQ was administrated 90 min before ischemia initiation. Human cardiac microvascular endothelial cells (HCMECs) underwent hypoxia or reoxygenation (H/R) challenge with QSYQ administrated 1 h prior to hypoxia. QSYQ exhibited effects on attenuating microvascular damage and albumin leakage after I/R injury, showing a role in maintaining endothelial junctions, caveolae, and collagen in basement membrane (BM) of microvessels. Study using HCMECs disclosed that QSYQ protected endothelial barrier from impairment by H/R, attenuating the decline of respiratory chain complex I and ATP synthase, activation of Src/caveolin-1 and increase of RhoA/ROCK/p-MLC, MMP-9, and CTSS. PP2, a Src inhibitor, partially imitated the effect of QSYQ. Conclusions: The QSYQ was able to prevent I/R-induced cardiac microvascular hyperpermeability via a mechanism involving Src/caveolin-1 and RhoA/ROCK/MLC signaling.
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Affiliation(s)
- Chun-Shui Pan
- Tasly Microcirculation Research Center, Peking University Health Science Center, Beijing, China.,Key Laboratory of Microcirculation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Beijing, China.,Key Laboratory of Stasis and Phlegm, State Administration of Traditional Chinese Medicine of the People's Republic of China, Beijing, China.,Department of Integration of Chinese and Western Medicine, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Li Yan
- Tasly Microcirculation Research Center, Peking University Health Science Center, Beijing, China.,Key Laboratory of Microcirculation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Beijing, China.,Key Laboratory of Stasis and Phlegm, State Administration of Traditional Chinese Medicine of the People's Republic of China, Beijing, China.,Department of Integration of Chinese and Western Medicine, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Se-Qi Lin
- Key Laboratory of Modern Preparation of Traditional Chinese Medicine, Ministry of Education, Jiangxi University of Traditional Chinese Medicine, Nanchang, China
| | - Ke He
- Tasly Microcirculation Research Center, Peking University Health Science Center, Beijing, China.,Key Laboratory of Microcirculation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Beijing, China.,Key Laboratory of Stasis and Phlegm, State Administration of Traditional Chinese Medicine of the People's Republic of China, Beijing, China.,Department of Integration of Chinese and Western Medicine, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Yuan-Chen Cui
- Tasly Microcirculation Research Center, Peking University Health Science Center, Beijing, China.,Key Laboratory of Microcirculation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Beijing, China.,Key Laboratory of Stasis and Phlegm, State Administration of Traditional Chinese Medicine of the People's Republic of China, Beijing, China.,Department of Integration of Chinese and Western Medicine, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Yu-Ying Liu
- Tasly Microcirculation Research Center, Peking University Health Science Center, Beijing, China.,Key Laboratory of Microcirculation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Beijing, China.,Key Laboratory of Stasis and Phlegm, State Administration of Traditional Chinese Medicine of the People's Republic of China, Beijing, China.,Department of Integration of Chinese and Western Medicine, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Bai-He Hu
- Tasly Microcirculation Research Center, Peking University Health Science Center, Beijing, China.,Key Laboratory of Microcirculation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Beijing, China.,Key Laboratory of Stasis and Phlegm, State Administration of Traditional Chinese Medicine of the People's Republic of China, Beijing, China.,Department of Integration of Chinese and Western Medicine, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Xin Chang
- Tasly Microcirculation Research Center, Peking University Health Science Center, Beijing, China.,Key Laboratory of Microcirculation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Beijing, China.,Key Laboratory of Stasis and Phlegm, State Administration of Traditional Chinese Medicine of the People's Republic of China, Beijing, China.,Department of Integration of Chinese and Western Medicine, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Xin-Rong Zhao
- Tasly Microcirculation Research Center, Peking University Health Science Center, Beijing, China.,Key Laboratory of Microcirculation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Beijing, China.,Key Laboratory of Stasis and Phlegm, State Administration of Traditional Chinese Medicine of the People's Republic of China, Beijing, China.,Department of Integration of Chinese and Western Medicine, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Jing-Yu Fan
- Tasly Microcirculation Research Center, Peking University Health Science Center, Beijing, China.,Key Laboratory of Microcirculation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Beijing, China.,Department of Integration of Chinese and Western Medicine, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Jing-Yan Han
- Tasly Microcirculation Research Center, Peking University Health Science Center, Beijing, China.,Key Laboratory of Microcirculation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Beijing, China.,Key Laboratory of Stasis and Phlegm, State Administration of Traditional Chinese Medicine of the People's Republic of China, Beijing, China.,Department of Integration of Chinese and Western Medicine, School of Basic Medical Sciences, Peking University, Beijing, China.,State Key Laboratory of Core Technology in Innovative Chinese Medicine, Tianjin, China
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17
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Fadaie Z, Whelan L, Ben-Yosef T, Dockery A, Corradi Z, Gilissen C, Haer-Wigman L, Corominas J, Astuti GDN, de Rooij L, van den Born LI, Klaver CCW, Hoyng CB, Wynne N, Duignan ES, Kenna PF, Cremers FPM, Farrar GJ, Roosing S. Whole genome sequencing and in vitro splice assays reveal genetic causes for inherited retinal diseases. NPJ Genom Med 2021; 6:97. [PMID: 34795310 PMCID: PMC8602293 DOI: 10.1038/s41525-021-00261-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 10/21/2021] [Indexed: 01/08/2023] Open
Abstract
Inherited retinal diseases (IRDs) are a major cause of visual impairment. These clinically heterogeneous disorders are caused by pathogenic variants in more than 270 genes. As 30-40% of cases remain genetically unexplained following conventional genetic testing, we aimed to obtain a genetic diagnosis in an IRD cohort in which the genetic cause was not found using whole-exome sequencing or targeted capture sequencing. We performed whole-genome sequencing (WGS) to identify causative variants in 100 unresolved cases. After initial prioritization, we performed an in-depth interrogation of all noncoding and structural variants in genes when one candidate variant was detected. In addition, functional analysis of putative splice-altering variants was performed using in vitro splice assays. We identified the genetic cause of the disease in 24 patients. Causative coding variants were observed in genes such as ATXN7, CEP78, EYS, FAM161A, and HGSNAT. Gene disrupting structural variants were also detected in ATXN7, PRPF31, and RPGRIP1. In 14 monoallelic cases, we prioritized candidate noncanonical splice sites or deep-intronic variants that were predicted to disrupt the splicing process based on in silico analyses. Of these, seven cases were resolved as they carried pathogenic splice defects. WGS is a powerful tool to identify causative variants residing outside coding regions or heterozygous structural variants. This approach was most efficient in cases with a distinct clinical diagnosis. In addition, in vitro splice assays provide important evidence of the pathogenicity of rare variants.
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Affiliation(s)
- Zeinab Fadaie
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Laura Whelan
- The School of Genetics and Microbiology, Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Tamar Ben-Yosef
- Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Adrian Dockery
- The School of Genetics and Microbiology, Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Zelia Corradi
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lonneke Haer-Wigman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jordi Corominas
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Galuh D N Astuti
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Division of Human Genetics, Center for Biomedical Research (CEBIOR), Faculty of Medicine, Diponegoro University, Semarang, Indonesia
| | - Laura de Rooij
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Caroline C W Klaver
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Carel B Hoyng
- Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Niamh Wynne
- Department of Ophthalmology, Royal Victoria Eye and Ear Hospital, Dublin, Ireland
| | - Emma S Duignan
- Department of Ophthalmology, Royal Victoria Eye and Ear Hospital, Dublin, Ireland
| | - Paul F Kenna
- The School of Genetics and Microbiology, Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
- Department of Ophthalmology, Royal Victoria Eye and Ear Hospital, Dublin, Ireland
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
| | - G Jane Farrar
- The School of Genetics and Microbiology, Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Susanne Roosing
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.
- Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands.
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18
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Kou X, Ding H, Li L, Chao H. Caseinolytic protease P (CLPP) activated by ONC201 inhibits proliferation and promotes apoptosis in human epithelial ovarian cancer cells by inducing mitochondrial dysfunction. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:1463. [PMID: 34734015 PMCID: PMC8506775 DOI: 10.21037/atm-21-4321] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 09/09/2021] [Indexed: 12/23/2022]
Abstract
Background Caseinolytic protease P (CLPP) is a mitochondrial specific protein which has been reported to be related to tumor cell apoptosis. This study aims to explore the roles of CLPP in human epithelial ovarian cancer (EOC). Methods We determined CLPP expression in paracancerous tissues and cancer tissues obtained from 20 EOC patients, and also in 4 EOC cell lines, and one normal ovarian cell line (IOSE-80). We knocked CLPP expression down in SK-OV-3 and A2780 cells and overexpressed it in SW626 and OVcar3 cells. The effect of CLPP expression on cell proliferation, mitochondrial membrane potential, and apoptosis was then assessed by flow cytometry assay. Furthermore, the effect of ONC201 (agonist of CLPP) on the EOC cell lines was also investigated. Results The CLPP expression was markedly down-regulated in EOC cancer tissues, and the Kaplan-Meier Plotter database revealed its low expression was linked to poor prognosis in EOC patients. Low expression of CLPP up-regulated the expression of NADH: ubiquinone oxidoreductase subunit A12 (NDUFA12), succinate dehydrogenase complex flavoprotein subunit A (SDHA), and succinate dehydrogenase complex iron sulfur subunit B (SDHB), which are key members of the mitochondrial respiratory chain, and these up-regulated proteins further led to the increase of mitochondrial membrane potential, cell proliferation promotion and neoplasm metastasis. Conversely, while overexpression of CLPP led to the opposite results, including inducing the decrease of mitochondrial membrane potential and apoptosis. In addition, stimulation with ONC201 enhanced the function of CLPP in SW626 and OVcar3 cells, and silencing of CLPP could neutralize the effect of ONC201. Conclusions Our findings suggest that CLPP mediated mitochondrial dysfunction inhibits the proliferation and migration of EOC cells.
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Affiliation(s)
- Xinxin Kou
- Department of Gynaecology, Cancer Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Hui Ding
- Department of Gynaecology, Cancer Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Lei Li
- Department of Gynaecology, Cancer Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Hongtu Chao
- Department of Gynaecology, Cancer Hospital Affiliated to Zhengzhou University, Zhengzhou, China
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19
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Mellon M, Storti M, Vera-Vives AM, Kramer DM, Alboresi A, Morosinotto T. Inactivation of mitochondrial complex I stimulates chloroplast ATPase in Physcomitrium patens. PLANT PHYSIOLOGY 2021; 187:931-946. [PMID: 34608952 PMCID: PMC8491079 DOI: 10.1093/plphys/kiab276] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 05/18/2021] [Indexed: 06/11/2023]
Abstract
Light is the ultimate source of energy for photosynthetic organisms, but respiration is fundamental for supporting metabolism during the night or in heterotrophic tissues. In this work, we isolated Physcomitrella (Physcomitrium patens) plants with altered respiration by inactivating Complex I (CI) of the mitochondrial electron transport chain by independently targeting on two essential subunits. Inactivation of CI caused a strong growth impairment even in fully autotrophic conditions in tissues where all cells are photosynthetically active, demonstrating that respiration is essential for photosynthesis. CI mutants showed alterations in the stoichiometry of respiratory complexes while the composition of photosynthetic apparatus was substantially unaffected. CI mutants showed altered photosynthesis with high activity of both Photosystems I and II, likely the result of high chloroplast ATPase activity that led to smaller ΔpH formation across thylakoid membranes, decreasing photosynthetic control on cytochrome b6f in CI mutants. These results demonstrate that alteration of respiratory activity directly impacts photosynthesis in P. patens and that metabolic interaction between organelles is essential in their ability to use light energy for growth.
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Affiliation(s)
- Marco Mellon
- Department of Biology, University of Padova, 35121 Padova, Italy
| | - Mattia Storti
- Department of Biology, University of Padova, 35121 Padova, Italy
| | | | - David M. Kramer
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
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20
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Shui JE, Wang W, Liu H, Stepanova A, Liao G, Qian J, Ai X, Ten V, Lu J, Cardoso WV. Prematurity alters the progenitor cell program of the upper respiratory tract of neonates. Sci Rep 2021; 11:10799. [PMID: 34031475 PMCID: PMC8144386 DOI: 10.1038/s41598-021-90093-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 04/29/2021] [Indexed: 11/09/2022] Open
Abstract
The impact of prematurity on human development and neonatal diseases, such as bronchopulmonary dysplasia, has been widely reported. However, little is known about the effects of prematurity on the programs of stem cell self-renewal and differentiation of the upper respiratory epithelium, which is key for adaptation to neonatal life. We developed a minimally invasive methodology for isolation of neonatal basal cells from nasopharyngeal (NP) aspirates and performed functional analysis in organotypic cultures to address this issue. We show that preterm NP progenitors have a markedly distinct molecular signature of abnormal proliferation and mitochondria quality control compared to term progenitors. Preterm progenitors had lower oxygen consumption at baseline and were unable to ramp up consumption to the levels of term cells when challenged. Although they formed a mucociliary epithelium, ciliary function tended to decline in premature cells as they differentiated, compared to term cells. Together, these differences suggested increased sensitivity of preterm progenitors to environmental stressors under non-homeostatic conditions.
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Affiliation(s)
- Jessica E Shui
- Division of Neonatology and Newborn Medicine, Department of Pediatrics, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Wei Wang
- Division of Neonatology and Newborn Medicine, Department of Pediatrics, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Helu Liu
- Columbia Center for Human Development, Pulmonary Allergy & Critical Care Medicine, Department of Medicine, Columbia University Irving Medical Center, 650 West 168th Street, BB 8-812, New York, NY, 10032, USA
| | - Anna Stepanova
- Division of Neonatology, Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Grace Liao
- Columbia Center for Human Development, Pulmonary Allergy & Critical Care Medicine, Department of Medicine, Columbia University Irving Medical Center, 650 West 168th Street, BB 8-812, New York, NY, 10032, USA
- Division of Neonatology, Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Jun Qian
- Columbia Center for Human Development, Pulmonary Allergy & Critical Care Medicine, Department of Medicine, Columbia University Irving Medical Center, 650 West 168th Street, BB 8-812, New York, NY, 10032, USA
| | - Xingbin Ai
- Division of Neonatology and Newborn Medicine, Department of Pediatrics, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Vadim Ten
- Division of Neonatology, Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Jining Lu
- Division of Lung Diseases, NHLBI, NIH, Bethesda, MD, USA
| | - Wellington V Cardoso
- Columbia Center for Human Development, Pulmonary Allergy & Critical Care Medicine, Department of Medicine, Columbia University Irving Medical Center, 650 West 168th Street, BB 8-812, New York, NY, 10032, USA.
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21
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Torraco A, Nasca A, Verrigni D, Pennisi A, Zaki MS, Olivieri G, Assouline Z, Martinelli D, Maroofian R, Rizza T, Di Nottia M, Invernizzi F, Lamantea E, Longo D, Houlden H, Prokisch H, Rötig A, Dionisi-Vici C, Bertini E, Ghezzi D, Carrozzo R, Diodato D. Novel NDUFA12 variants are associated with isolated complex I defect and variable clinical manifestation. Hum Mutat 2021; 42:699-710. [PMID: 33715266 DOI: 10.1002/humu.24195] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 01/27/2021] [Accepted: 03/06/2021] [Indexed: 12/18/2022]
Abstract
Isolated biochemical deficiency of mitochondrial complex I is the most frequent signature among mitochondrial diseases and is associated with a wide variety of clinical symptoms. Leigh syndrome represents the most frequent neuroradiological finding in patients with complex I defect and more than 80 monogenic causes have been involved in the disease. In this report, we describe seven patients from four unrelated families harboring novel NDUFA12 variants, with six of them presenting with Leigh syndrome. Molecular genetic characterization was performed using next-generation sequencing combined with the Sanger method. Biochemical and protein studies were achieved by enzymatic activities, blue native gel electrophoresis, and western blot analysis. All patients displayed novel homozygous mutations in the NDUFA12 gene, leading to the virtual absence of the corresponding protein. Surprisingly, despite the fact that in none of the analyzed patients, NDUFA12 protein was detected, they present a different onset and clinical course of the disease. Our report expands the array of genetic alterations in NDUFA12 and underlines phenotype variability associated with NDUFA12 defect.
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Affiliation(s)
- Alessandra Torraco
- Department of Neurosciences, Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Alessia Nasca
- Diagnostic and Technology Department, Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Daniela Verrigni
- Department of Neurosciences, Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Alessandra Pennisi
- UNITE INSERM U1163 Imagine Institute, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Maha S Zaki
- Human Genetics and Genome Research Division, Clinical Genetics Department, National Research Centre, Cairo, Egypt
| | - Giorgia Olivieri
- Department of Pediatric Subspecialties, Division of Metabolism, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Zahra Assouline
- UNITE INSERM U1163 Imagine Institute, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Diego Martinelli
- Department of Pediatric Subspecialties, Division of Metabolism, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Reza Maroofian
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London, UK
| | - Teresa Rizza
- Department of Neurosciences, Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Michela Di Nottia
- Department of Neurosciences, Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Federica Invernizzi
- Diagnostic and Technology Department, Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Eleonora Lamantea
- Diagnostic and Technology Department, Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Daniela Longo
- Department of Diagnostic Imaging, Unit of Neuroradiology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London, UK
| | - Holger Prokisch
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Human Genetics, Technische Universität München, Munich, Germany
| | - Agnès Rötig
- UNITE INSERM U1163 Imagine Institute, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Carlo Dionisi-Vici
- Department of Pediatric Subspecialties, Division of Metabolism, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Enrico Bertini
- Department of Neurosciences, Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Daniele Ghezzi
- Diagnostic and Technology Department, Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy.,Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Rosalba Carrozzo
- Department of Neurosciences, Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Daria Diodato
- Department of Neurosciences, Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
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22
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Emelyanova L, Bai X, Yan Y, Bosnjak ZJ, Kress D, Warner C, Kroboth S, Rudic T, Kaushik S, Stoeckl E, Ross GR, Rizvi F, Tajik AJ, Jahangir A. Biphasic effect of metformin on human cardiac energetics. Transl Res 2021; 229:5-23. [PMID: 33045408 PMCID: PMC10655614 DOI: 10.1016/j.trsl.2020.10.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 09/30/2020] [Accepted: 10/05/2020] [Indexed: 02/01/2023]
Abstract
Metformin is the first-line medication for treatment of type 2 diabetes and has been shown to reduce heart damage and death. However, mechanisms by which metformin protects human heart remain debated. The aim of the study was to evaluate the cardioprotective effect of metformin on cardiomyocytes derived from human-induced pluripotent stem cells (hiPSC-CMs) and mitochondria isolated from human cardiac tissue. At concentrations ≤2.5 mM, metformin significantly increased oxygen consumption rate (OCR) in the hiPSC-CMs by activating adenosine monophosphate activated protein kinase (AMPK)-dependent signaling and enhancing mitochondrial biogenesis. This effect was abrogated by compound C, an inhibitor of AMPK. At concentrations >5 mM, metformin inhibited the cellular OCR and triggered metabolic reprogramming by enhancing glycolysis and glutaminolysis in the cardiomyocytes. In isolated cardiac mitochondria, metformin did not increase the OCR at any concentrations but inhibited the OCR starting at 1 mM through direct inhibition of electron-transport chain complex I. This was associated with reduction of superoxide production and attenuation of Ca2+-induced mitochondrial permeability transition pore (mPTP) opening in the mitochondria. Thus, in human heart, metformin might improve cardioprotection due to its biphasic effect on mitochondria: at low concentrations, it activates mitochondrial biogenesis via AMPK signaling and increases the OCR; at high concentrations, it inhibits the respiration by directly affecting the activity of complex I, reduces oxidative stress and delays mPTP formation. Moreover, metformin at high concentrations causes metabolic reprogramming by enhancing glycolysis and glutaminolysis. These effects can be a beneficial adjunct to patients with impaired endogenous cardioprotective responses.
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Affiliation(s)
- Larisa Emelyanova
- Center for Integrative Research on Cardiovascular Aging, Advocate Aurora Research Institute, Milwaukee, Wisconsin.
| | - Xiaowen Bai
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Yasheng Yan
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Zeljko J Bosnjak
- Departments of Medicine and Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - David Kress
- Aurora Cardiovascular and Thoracic Services, St. Luke's Medical Center, Advocate Aurora Health Care, Milwaukee, Wisconsin
| | - Catherine Warner
- Center for Integrative Research on Cardiovascular Aging, Advocate Aurora Research Institute, Milwaukee, Wisconsin
| | - Stacie Kroboth
- Aurora Cardiovascular and Thoracic Services, St. Luke's Medical Center, Advocate Aurora Health Care, Milwaukee, Wisconsin
| | - Teodore Rudic
- Center for Integrative Research on Cardiovascular Aging, Advocate Aurora Research Institute, Milwaukee, Wisconsin
| | - Sirisha Kaushik
- Center for Integrative Research on Cardiovascular Aging, Advocate Aurora Research Institute, Milwaukee, Wisconsin
| | - Elizabeth Stoeckl
- Center for Integrative Research on Cardiovascular Aging, Advocate Aurora Research Institute, Milwaukee, Wisconsin
| | - Gracious R Ross
- Center for Integrative Research on Cardiovascular Aging, Advocate Aurora Research Institute, Milwaukee, Wisconsin
| | - Farhan Rizvi
- Center for Integrative Research on Cardiovascular Aging, Advocate Aurora Research Institute, Milwaukee, Wisconsin
| | - A Jamil Tajik
- Aurora Cardiovascular and Thoracic Services, St. Luke's Medical Center, Advocate Aurora Health Care, Milwaukee, Wisconsin
| | - Arshad Jahangir
- Aurora Cardiovascular and Thoracic Services, St. Luke's Medical Center, Advocate Aurora Health Care, Milwaukee, Wisconsin
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23
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Zhang HL, Xu Y, Ju JQ, Pan ZN, Liu JC, Sun SC. Increased Environment-Related Metabolism and Genetic Expression in the In Vitro Matured Mouse Oocytes by Transcriptome Analysis. Front Cell Dev Biol 2021; 9:642010. [PMID: 33681227 PMCID: PMC7928285 DOI: 10.3389/fcell.2021.642010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 01/18/2021] [Indexed: 12/28/2022] Open
Abstract
Infertility in humans at their reproductive age is a world-wide problem. Oocyte in vitro maturation (IVM) is generally used in such cases to acquire the embryo in assisted reproductive technology (ART). However, the differences between an in vivo (IVO) and IVM culture environment in the RNA expression profile in oocytes, remains unclear. In this study, we compared the global RNA transcription pattern of oocytes from in vitro and in vivo maturation. Our results showed that 1,864 genes differentially expressed between the IVO and IVM oocytes. Among these, 1,638 genes were up-regulated, and 226 genes were down-regulated, and these changes were mainly divided into environmental adaption, metabolism, and genetic expression. Our detailed analysis showed that the expression of genes that belonged to metabolism-related processes such as energy metabolism, nucleotide metabolism, and carbohydrate metabolism was changed; and these genes also belonged to organismal systems including environmental adaptation and the circulatory system; moreover, we also found that the relative gene expression of genetic expression processes, such as protein synthesis, modification, and DNA replication and repair were also altered. In conclusion, our data suggests that in vitro maturation of mouse oocyte resulted in metabolism and genetic expression changes due to environmental changes compared with in vivo matured oocytes.
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Affiliation(s)
- Hao-Lin Zhang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yi Xu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Jia-Qian Ju
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Zhen-Nan Pan
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Jing-Cai Liu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Shao-Chen Sun
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
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24
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Ahn M, Oh E, McCown EM, Wang X, Veluthakal R, Thurmond DC. A requirement for PAK1 to support mitochondrial function and maintain cellular redox balance via electron transport chain proteins to prevent β-cell apoptosis. Metabolism 2021; 115:154431. [PMID: 33181191 PMCID: PMC8123936 DOI: 10.1016/j.metabol.2020.154431] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/04/2020] [Accepted: 11/07/2020] [Indexed: 01/05/2023]
Abstract
OBJECTIVE p21 (Cdc42/Rac1) activated Kinase 1 (PAK1) is a candidate susceptibility factor for type 2 diabetes (T2D). PAK1 is depleted in the islets from T2D donors, compared to control individuals. In addition, whole-body PAK1 knock out (PAK1-KO) in mice worsens the T2D-like effects of high-fat diet. The current study tested the effects of modulating PAK1 levels only in β-cells. MATERIALS/METHODS β-cell-specific inducible PAK1 KO (βPAK1-iKO) mice were generated and used with human β-cells and T2D islets to evaluate β-cell function. RESULTS βPAK1-iKO mice exhibited glucose intolerance and elevated β-cell apoptosis, but without peripheral insulin resistance. β-cells from βPAK-iKO mice also contained fewer mitochondria per cell. At the cellular level, human PAK1-deficient β-cells showed blunted glucose-stimulated insulin secretion and reduced mitochondrial function. Mitochondria from human PAK1-deficient β-cells were deficient in the electron transport chain (ETC) subunits CI, CIII, and CIV; NDUFA12, a CI complex protein, was identified as a novel PAK1 binding partner, and was significantly reduced with PAK1 knockdown. PAK1 knockdown disrupted the NAD+/NADH and NADP+/NADPH ratios, and elevated ROS. An imbalance of the redox state due to mitochondrial dysfunction leads to ER stress in β-cells. PAK1 replenishment in the β-cells of T2D human islets ameliorated levels of ER stress markers. CONCLUSIONS These findings support a protective function for PAK1 in β-cells. The results support a new model whereby the PAK1 in the β-cell plays a required role upstream of mitochondrial function, via maintaining ETC protein levels and averting stress-induced β-cell apoptosis to retain healthy functional β-cell mass.
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Affiliation(s)
- Miwon Ahn
- Department of Molecular and Cellular Endocrinology, Diabetes and Metabolism Research Institute and Beckman Research Institute at the City of Hope, Duarte, CA 91010, United States of America
| | - Eunjin Oh
- Department of Molecular and Cellular Endocrinology, Diabetes and Metabolism Research Institute and Beckman Research Institute at the City of Hope, Duarte, CA 91010, United States of America
| | - Erika M McCown
- Department of Molecular and Cellular Endocrinology, Diabetes and Metabolism Research Institute and Beckman Research Institute at the City of Hope, Duarte, CA 91010, United States of America
| | - Xin Wang
- Faculty of Biology, Medicine and Health, University of Manchester, UK
| | - Rajakrishnan Veluthakal
- Department of Molecular and Cellular Endocrinology, Diabetes and Metabolism Research Institute and Beckman Research Institute at the City of Hope, Duarte, CA 91010, United States of America
| | - Debbie C Thurmond
- Department of Molecular and Cellular Endocrinology, Diabetes and Metabolism Research Institute and Beckman Research Institute at the City of Hope, Duarte, CA 91010, United States of America.
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25
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Galperin MY, Wolf YI, Makarova KS, Vera Alvarez R, Landsman D, Koonin EV. COG database update: focus on microbial diversity, model organisms, and widespread pathogens. Nucleic Acids Res 2021; 49:D274-D281. [PMID: 33167031 DOI: 10.1093/nar/gkaa1018] [Citation(s) in RCA: 378] [Impact Index Per Article: 126.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/13/2020] [Accepted: 10/14/2020] [Indexed: 12/20/2022] Open
Abstract
The Clusters of Orthologous Genes (COG) database, also referred to as the Clusters of Orthologous Groups of proteins, was created in 1997 and went through several rounds of updates, most recently, in 2014. The current update, available at https://www.ncbi.nlm.nih.gov/research/COG, substantially expands the scope of the database to include complete genomes of 1187 bacteria and 122 archaea, typically, with a single genome per genus. In addition, the current version of the COGs includes the following new features: (i) the recently deprecated NCBI's gene index (gi) numbers for the encoded proteins are replaced with stable RefSeq or GenBank\ENA\DDBJ coding sequence (CDS) accession numbers; (ii) COG annotations are updated for >200 newly characterized protein families with corresponding references and PDB links, where available; (iii) lists of COGs grouped by pathways and functional systems are added; (iv) 266 new COGs for proteins involved in CRISPR-Cas immunity, sporulation in Firmicutes and photosynthesis in cyanobacteria are included; and (v) the database is made available as a web page, in addition to FTP. The current release includes 4877 COGs. Future plans include further expansion of the COG collection by adding archaeal COGs (arCOGs), splitting the COGs containing multiple paralogs, and continued refinement of COG annotations.
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Affiliation(s)
- Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Roberto Vera Alvarez
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - David Landsman
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
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Dang QCL, Phan DH, Johnson AN, Pasapuleti M, Alkhaldi HA, Zhang F, Vik SB. Analysis of Human Mutations in the Supernumerary Subunits of Complex I. Life (Basel) 2020; 10:life10110296. [PMID: 33233646 PMCID: PMC7699753 DOI: 10.3390/life10110296] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/16/2020] [Accepted: 11/16/2020] [Indexed: 01/02/2023] Open
Abstract
Complex I is the largest member of the electron transport chain in human mitochondria. It comprises 45 subunits and requires at least 15 assembly factors. The subunits can be divided into 14 "core" subunits that carry out oxidation-reduction reactions and proton translocation, as well as 31 additional supernumerary (or accessory) subunits whose functions are less well known. Diminished levels of complex I activity are seen in many mitochondrial disease states. This review seeks to tabulate mutations in the supernumerary subunits of humans that appear to cause disease. Mutations in 20 of the supernumerary subunits have been identified. The mutations were analyzed in light of the tertiary and quaternary structure of human complex I (PDB id = 5xtd). Mutations were found that might disrupt the folding of that subunit or that would weaken binding to another subunit. In some cases, it appeared that no protein was made or, at least, could not be detected. A very common outcome is the lack of assembly of complex I when supernumerary subunits are mutated or missing. We suggest that poor assembly is the result of disrupting the large network of subunit interactions that the supernumerary subunits typically engage in.
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Sweetman E, Kleffmann T, Edgar C, de Lange M, Vallings R, Tate W. A SWATH-MS analysis of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome peripheral blood mononuclear cell proteomes reveals mitochondrial dysfunction. J Transl Med 2020; 18:365. [PMID: 32972442 PMCID: PMC7512220 DOI: 10.1186/s12967-020-02533-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 09/15/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is a serious and complex physical illness that affects all body systems with a multiplicity of symptoms, but key hallmarks of the disease are pervasive fatigue and 'post-exertional malaise', exacerbation after physical and/or mental activity of the intrinsic fatigue and other symptoms that can be highly debilitating and last from days to months. Although the disease can vary widely between individuals, common symptoms also include pain, cognitive deficits, sleep dysfunction, as well as immune, neurological and autonomic symptoms. Typically, it is a very isolating illness socially, carrying a stigma because of the lack of understanding of the cause and pathophysiology. METHODS To gain insight into the pathophysiology of ME/CFS, we examined the proteomes of peripheral blood mononuclear cells (PBMCs) by SWATH-MS analysis in a small well-characterised group of patients and matched controls. A principal component analysis (PCA) was used to stratify groups based on protein abundance patterns, which clearly segregated the majority of the ME/CFS patients (9/11) from the controls. This majority subgroup of ME/CFS patients was then further compared to the control group. RESULTS A total of 60 proteins in the ME/CFS patients were differentially expressed (P < 0.01, Log10 (Fold Change) > 0.2 and < -0.2). Comparison of the PCA selected subgroup of ME/CFS patients (9/11) with controls increased the number of proteins differentially expressed to 99. Of particular relevance to the core symptoms of fatigue and post-exertional malaise experienced in ME/CFS, a proportion of the identified proteins in the ME/CFS groups were involved in mitochondrial function, oxidative phosphorylation, electron transport chain complexes, and redox regulation. A significant number were also involved in previously implicated disturbances in ME/CFS, such as the immune inflammatory response, DNA methylation, apoptosis and proteasome activation. CONCLUSIONS The results from this study support a model of deficient ATP production in ME/CFS, compensated for by upregulation of immediate pathways upstream of Complex V that would suggest an elevation of oxidative stress. This study and others have found evidence of a distinct pathology in ME/CFS that holds promise for developing diagnostic biomarkers.
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Affiliation(s)
- Eiren Sweetman
- Department of Biochemistry, University of Otago, Dunedin, 9016, New Zealand
| | - Torsten Kleffmann
- Department of Biochemistry, University of Otago, Dunedin, 9016, New Zealand
| | - Christina Edgar
- Department of Biochemistry, University of Otago, Dunedin, 9016, New Zealand
| | - Michel de Lange
- Centre for Biostatistics, University of Otago, Dunedin, 9016, New Zealand
| | | | - Warren Tate
- Department of Biochemistry, University of Otago, Dunedin, 9016, New Zealand.
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Liu H, Perumal N, Manicam C, Mercieca K, Prokosch V. Proteomics Reveals the Potential Protective Mechanism of Hydrogen Sulfide on Retinal Ganglion Cells in an Ischemia/Reperfusion Injury Animal Model. Pharmaceuticals (Basel) 2020; 13:ph13090213. [PMID: 32867129 PMCID: PMC7557839 DOI: 10.3390/ph13090213] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 08/24/2020] [Accepted: 08/25/2020] [Indexed: 12/13/2022] Open
Abstract
Glaucoma is the leading cause of irreversible blindness and is characterized by progressive retinal ganglion cell (RGC) degeneration. Hydrogen sulfide (H2S) is a potent neurotransmitter and has been proven to protect RGCs against glaucomatous injury in vitro and in vivo. This study is to provide an overall insight of H2S’s role in glaucoma pathophysiology. Ischemia-reperfusion injury (I/R) was induced in Sprague-Dawley rats (n = 12) by elevating intraocular pressure to 55 mmHg for 60 min. Six of the animals received intravitreal injection of H2S precursor prior to the procedure and the retina was harvested 24 h later. Contralateral eyes were assigned as control. RGCs were quantified and compared within the groups. Retinal proteins were analyzed via label-free mass spectrometry based quantitative proteomics approach. The pathways of the differentially expressed proteins were identified by ingenuity pathway analysis (IPA). H2S significantly improved RGC survival against I/R in vivo (p < 0.001). In total 1115 proteins were identified, 18 key proteins were significantly differentially expressed due to I/R and restored by H2S. Another 11 proteins were differentially expressed following H2S. IPA revealed a significant H2S-mediated activation of pathways related to mitochondrial function, iron homeostasis and vasodilation. This study provides first evidence of the complex role that H2S plays in protecting RGC against I/R.
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Affiliation(s)
- Hanhan Liu
- Experimental and Translational Ophthalmology, University Medical Centre of the Johannes Gutenberg University Mainz, 55131 Mainz, Germany; (H.L.); (N.P.); (C.M.)
| | - Natarajan Perumal
- Experimental and Translational Ophthalmology, University Medical Centre of the Johannes Gutenberg University Mainz, 55131 Mainz, Germany; (H.L.); (N.P.); (C.M.)
| | - Caroline Manicam
- Experimental and Translational Ophthalmology, University Medical Centre of the Johannes Gutenberg University Mainz, 55131 Mainz, Germany; (H.L.); (N.P.); (C.M.)
| | - Karl Mercieca
- Royal Eye Hospital, School of Medicine, University of Manchester, Manchester M13 9WH, UK;
| | - Verena Prokosch
- Department of Ophthalmology, University Medical Centre of the Johannes Gutenberg University Mainz, 55131 Mainz, Germany
- Correspondence: ; Tel.: +49-1703862250
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Bai Y, Carrillo JA, Li Y, He Y, Song J. Diet induced the change of mtDNA copy number and metabolism in Angus cattle. J Anim Sci Biotechnol 2020; 11:84. [PMID: 32699629 PMCID: PMC7372754 DOI: 10.1186/s40104-020-00482-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 06/09/2020] [Indexed: 12/16/2022] Open
Abstract
Background Grass-fed and grain-fed Angus cattle differ in the diet regimes. However, the intricate mechanisms of different beef quality and other phenotypes induced by diet differences are still unclear. Diet affects mitochondrial function and dynamic behavior in response to changes in energy demand and supply. In this study, we examined the mtDNA copy number, mitochondria-related genes expression, and metabolic biomarkers in grass-fed and grain-fed Angus cattle. Results We found that the grass-fed group had a higher mtDNA copy number than the grain-fed group. Among different tissues, the mtDNA copy number was the highest in the liver than muscle, rumen, and spleen. Based on the transcriptome of the four tissues, a lower expression of mtDNA-encoded genes in the grass-fed group compared to the grain-fed group was discovered. For the mitochondria-related nuclear genes, however, most of them were significantly down-regulated in the muscle of the grass-fed group and up-regulated in the other three tissues. In which, COX6A2, POLG2, PPIF, DCN, and NDUFA12, involving in ATP synthesis, mitochondrial replication, transcription, and maintenance, might contribute to the alterations of mtDNA copy number and gene expression. Meanwhile, 40 and 23 metabolic biomarkers were identified in the blood and muscle of the grain-fed group compared to a grass-fed group, respectively. Integrated analysis of the altered metabolites and gene expression revealed the high expression level of MDH1 in the grain-fed group might contribute to the mitochondrial NADH oxidation and spermidine metabolism for adapting the deletion mtDNA copy number. Conclusions Overall, the study may provide further deep insight into the adaptive and regulatory modulations of the mitochondrial function in response to different feeding systems in Angus cattle.
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Affiliation(s)
- Ying Bai
- College of Life Sciences and Food Engineering, Hebei University of Engineering, Handan, 056038 China.,Department of Animal & Avian Sciences, University of Maryland, College Park, MD 20742 USA
| | - José A Carrillo
- Department of Animal & Avian Sciences, University of Maryland, College Park, MD 20742 USA.,Council on Dairy Cattle Breeding, Bowie, MD 20716 USA
| | - Yaokun Li
- Department of Animal & Avian Sciences, University of Maryland, College Park, MD 20742 USA
| | - Yanghua He
- Department of Animal & Avian Sciences, University of Maryland, College Park, MD 20742 USA.,Human Nutrition, Food and Animal Sciences, University of Hawaii at Manoa, Honolulu, HI 96822 USA
| | - Jiuzhou Song
- Department of Animal & Avian Sciences, University of Maryland, College Park, MD 20742 USA
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Wu B, Chen S, Zhuang L, Zeng J. The expression level of COX7C associates with venous thromboembolism in colon cancer patients. Clin Exp Med 2020; 20:527-533. [PMID: 32653968 DOI: 10.1007/s10238-020-00644-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 07/02/2020] [Indexed: 12/13/2022]
Abstract
Venous thromboembolism (VTE) is a common complication of colon cancer. In the present study, we aimed to explore the association of the oncogene COX7C to VTE in colon cancer patients. Samples from 580 patients were examined histologically for VTE and pathological characteristic of cancer. Gene mutation and expression analysis were performed using polymerase chain reaction-based assays to evaluate genes related to VTE, including COX7C. Univariate analysis between clinical pathological factors and VTE was conducted. Logistic regression analysis was performed for the prediction of VTE by pathological factors and gene expressions. Among patients investigated, a total of 56 patients had VTE. COX7C had a significant correlation with VTE (p < 0.001). Despite a correlation between tumor size, invasion depth of tumor, lymph node metastasis, lymph node metastasis, distant metastasis, lymphovascular invasion, histologic type and pathology type, Ki-67, and some other genes, to VTE (p > 0.05), only COX7C expression demonstrated significance in its ability to predict VTE. Here, we show that COX7C upregulation strongly correlates with VTE in colon cancer, which implicates its role as a biomarker and therapeutic target of VTE in colon cancer.
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Affiliation(s)
- Biyu Wu
- Department of Nursing, Quanzhou First Hospital Affiliated To Fujian Medical University, No.250 East Street, Licheng District, Quanzhou, 362000, Fujian, China
| | - Shurong Chen
- Department of Geriatric, Quanzhou First Hospital Affiliated To Fujian Medical University, No.250 East Street, Licheng District, Quanzhou, 362000, Fujian, China
| | - Lihong Zhuang
- Second Department of Gastrointestinal Surgery, Quanzhou First Hospital Affiliated To Fujian Medical University, No.250 East Street, Licheng District, Quanzhou, 362000, Fujian, China
| | - Jingyang Zeng
- Department of Anesthesiology, Quanzhou First Hospital Affiliated To Fujian Medical University, No.250 East Street, Licheng District, Quanzhou, 362000, Fujian, China.
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Mijiritsky E, Gardin C, Ferroni L, Lacza Z, Zavan B. Albumin-impregnated bone granules modulate the interactions between mesenchymal stem cells and monocytes under in vitro inflammatory conditions. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2020; 110:110678. [PMID: 32204105 DOI: 10.1016/j.msec.2020.110678] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 12/22/2019] [Accepted: 01/18/2020] [Indexed: 12/17/2022]
Abstract
Bone regeneration around newly implanted biomaterials is a complex process, which in its early phases involves the interactions between Mesenchymal Stem Cells (MSCs) and immune cells. The response of these cells to the biomaterial depends both on the local microenvironment and on the characteristics of the inserted bone substitute. In this work, bone allografts impregnated with albumin are loaded with a co-culture of human MSCs and monocytes; bone granules without albumin are used for comparison. Co-cultures are contextually treated with pro-inflammatory cytokines to simulate the inflammatory milieu naturally present during the bone regeneration process. As revealed by microscopic images, albumin-impregnated bone granules promote adhesion and interactions between cells populations. Compared to control granules, albumin coating diminishes reactive species production by cells. This reduced oxidative stress may be attributable to antioxidant properties of albumin, and it is also reflected in the mitigated gene expression of mitochondrial electron transport chain complexes, where most intracellular reactive molecules are generated. MSCs-monocytes co-cultured onto albumin-impregnated bone granules additionally release higher amounts of immunomodulatory cytokines and growth factors. In summary, this work demonstrates that impregnation of bone granules with albumin positively modulates the interactions between MSCs and immune cells, consequently influencing their mutual activities and immunomodulatory functions.
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Affiliation(s)
- Eitan Mijiritsky
- Department of Otolaryngology, Head and Neck and Maxillofacial Surgery, Sackler Faculty of Medicine, Tel-Aviv Sourasky Medical Center, 64239 Tel Aviv, Israel
| | - Chiara Gardin
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy; Maria Cecilia Hospital, GVM Care & Research, 48033 Cotignola, Italy.
| | - Letizia Ferroni
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy; Maria Cecilia Hospital, GVM Care & Research, 48033 Cotignola, Italy
| | - Zsombor Lacza
- Institute of Clinical Experimental Research, Semmelweis University, 1094 Budapest, Hungary
| | - Barbara Zavan
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy; Maria Cecilia Hospital, GVM Care & Research, 48033 Cotignola, Italy.
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Fisher JJ, McKeating DR, Cuffe JS, Bianco-Miotto T, Holland OJ, Perkins AV. Proteomic Analysis of Placental Mitochondria Following Trophoblast Differentiation. Front Physiol 2019; 10:1536. [PMID: 31920727 PMCID: PMC6933824 DOI: 10.3389/fphys.2019.01536] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 12/05/2019] [Indexed: 12/15/2022] Open
Abstract
As gestation proceeds the human placenta is in a constant state of renewal and placental debris is released into the maternal circulation where it can trigger adverse physiological and immunological responses. Trophoblast cells of the placenta differentiate from mononuclear cytotrophoblast cells to fuse and form the syncytiotrophoblast, a multinuclear layer that covers the entire surface of the placenta. As part of this process there are significant changes to cellular cytoskeletal organization and organelle morphology. In this study we have examined the molecular changes that occur in mitochondria from these two cellular compartments and identified differential expression of key proteins that underpin changes in mitochondrial morphology, metabolism and function. Mitochondria were isolated for term placental tissue and separated according to size and density by sequential differential centrifugation. Isolated mitochondrial populations were then subjected to proteomics using HPLC separation of peptides and MS identification. Differential expression of proteins of interest was confirmed by western blots. Using a bioinformatics approach we also examined published protein databases to confirm our observations. In total 651 proteins were differentially regulated in mitochondria from cytotrophoblast versus syncytiotrophoblast. Of these 29 were statistically significant and chosen for subsequent analysis. These included subunits of ATP synthase that would affect ATP production and cristae structure, carbohydrate metabolizing enzymes phospoenolpyruvate carboxykinase-2, pyruvate carboxylase (PC) and pyruvate dehydrogenase (PDH), fatty acid metabolizing enzyme acyl-CoA dehydrogenase, stress responses such a glucose regulated protein-78 and protein disulfide isomerase, and mitochondrial dynamics proteins mitofusin 1 and 2. Placental cell biology and mitochondrial function is central to the pathogenesis of many gestational disorders such as preeclampsia, pre-term birth, fetal growth restriction and gestational diabetes. These studies show important shifts in mitochondrial metabolism and dynamics post trophoblast differentiation and provide key molecular targets for study in pathological pregnancies.
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Affiliation(s)
- Joshua J Fisher
- School of Medical Science, Griffith Health, Griffith University, Southport, QLD, Australia
| | - Daniel R McKeating
- School of Medical Science, Griffith Health, Griffith University, Southport, QLD, Australia
| | - James S Cuffe
- School of Biomedical Sciences, Faculty of Medicine, The University of Queensland, St Lucia, QLD, Australia
| | - Tina Bianco-Miotto
- School of Agriculture, Food and Wine, Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia
| | - Olivia J Holland
- School of Medical Science, Griffith Health, Griffith University, Southport, QLD, Australia
| | - Anthony V Perkins
- School of Medical Science, Griffith Health, Griffith University, Southport, QLD, Australia
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Wang T, Zhu W, Zhang H, Wen X, Yin S, Jia Y. Integrated analysis of proteomics and metabolomics reveals the potential sex determination mechanism in Odontobutis potamophila. J Proteomics 2019; 208:103482. [PMID: 31401171 DOI: 10.1016/j.jprot.2019.103482] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 07/28/2019] [Accepted: 08/05/2019] [Indexed: 02/06/2023]
Abstract
Odontobutis potamophila is a valuable species for aquaculture in China, which shows asexually dimorphic growth pattern. In this study, the integrated proteomics and metabolomics were used to analyze the sex determination mechanism. A total of 2781 significantly different regulated proteins were identified by proteomics and 2693 significantly different expressed metabolites were identified by metabolomics. Among them, 2560 proteins and 1701 metabolites were significantly up-regulated in testes, whereas 221 proteins and 992 metabolites were significantly up-regulated in ovaries. Venn diagram analysis showed 513 proteins were differentially regulated at both protein and metabolite levels. Correlation analysis of differentially-regulated proteins and metabolites were identified by Gene Ontology annotation and Kyoto Encyclopedia of Genes and Genomes pathway analysis. The results showed lipid metabolism plays an important role in sex determination. The metabolites decanoyl-CoA, leukotriene, 3-dehydrosphinganine, and arachidonate were the biomarkers in testes, whereas estrone and taurocholate were the biomarkers in ovaries. Interaction networks of the significant differentially co-regulated proteins and metabolites in the process of lipid metabolism showed arachidonic acid metabolism and steroid hormone biosynthesis were the most important pathways in sex determination. The findings of this study provide valuable information for selective breeding of O. potamophila. SIGNIFICANCE OF THE STUDY: The male O. potamophila grows substantially larger and at a quicker rate than the female. Thus, males have greater economic value than females. However, limited research was done to analyze the sex determination mechanism of O. potamophila, which seriously hindered the development of whole-male O. potamophila breeding. In this study, four key proteins (Ctnnb1, Piwil1, Hsd17b1, and Dnali1), six most important biomarkers (decanoyl-CoA, leukotriene, 3-dehydrosphinganine, arachidonate, estrone, and taurocholate) and two key pathways (arachidonic acid metabolism and steroid hormone biosynthesis) in sex determination of O. potamophila were found by integrated application of iTRAQ and LC-MS techniques. The results give valuable information for molecular breeding of O. potamophila in aquaculture.
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Affiliation(s)
- Tao Wang
- College of Marine Science and Engineering, Nanjing Normal University, Nanjing, Jiangsu 210023, China; Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, Jiangsu 222005, China
| | - Wenxu Zhu
- College of Marine Science and Engineering, Nanjing Normal University, Nanjing, Jiangsu 210023, China; Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, Jiangsu 222005, China
| | - Hongyan Zhang
- College of Marine Science and Engineering, Nanjing Normal University, Nanjing, Jiangsu 210023, China; Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, Jiangsu 222005, China
| | - Xin Wen
- College of Marine Science and Engineering, Nanjing Normal University, Nanjing, Jiangsu 210023, China; Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, Jiangsu 222005, China
| | - Shaowu Yin
- College of Marine Science and Engineering, Nanjing Normal University, Nanjing, Jiangsu 210023, China; Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, Jiangsu 222005, China.
| | - Yongyi Jia
- Zhejiang Institute of Freshwater Fisheries, Huzhou 313001, China.
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Barshad G, Zlotnikov-Poznianski N, Gal L, Schuldiner M, Mishmar D. Disease-causing mutations in subunits of OXPHOS complex I affect certain physical interactions. Sci Rep 2019; 9:9987. [PMID: 31292494 PMCID: PMC6620328 DOI: 10.1038/s41598-019-46446-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 06/28/2019] [Indexed: 11/09/2022] Open
Abstract
Mitochondrial complex I (CI) is the largest multi-subunit oxidative phosphorylation (OXPHOS) protein complex. Recent availability of a high-resolution human CI structure, and from two non-human mammals, enabled predicting the impact of mutations on interactions involving each of the 44 CI subunits. However, experimentally assessing the impact of the predicted interactions requires an easy and high-throughput method. Here, we created such a platform by cloning all 37 nuclear DNA (nDNA) and 7 mitochondrial DNA (mtDNA)-encoded human CI subunits into yeast expression vectors to serve as both 'prey' and 'bait' in the split murine dihydrofolate reductase (mDHFR) protein complementation assay (PCA). We first demonstrated the capacity of this approach and then used it to examine reported pathological OXPHOS CI mutations that occur at subunit interaction interfaces. Our results indicate that a pathological frame-shift mutation in the MT-ND2 gene, causing the replacement of 126 C-terminal residues by a stretch of only 30 amino acids, resulted in loss of specificity in ND2-based interactions involving these residues. Hence, the split mDHFR PCA is a powerful assay for assessing the impact of disease-causing mutations on pairwise protein-protein interactions in the context of a large protein complex, thus offering a possible mechanistic explanation for the underlying pathogenicity.
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Affiliation(s)
- Gilad Barshad
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | | | - Lihi Gal
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Dan Mishmar
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
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Dysregulation in the Brain Protein Profile of Zebrafish Lacking the Parkinson’s Disease-Related Protein DJ-1. Mol Neurobiol 2019; 56:8306-8322. [DOI: 10.1007/s12035-019-01667-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 05/31/2019] [Indexed: 02/07/2023]
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36
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Nie H, Yu X, He H, Zhou L, Li Q, Song C, Wang D, Ren T, Chen Z, Huang H, Dai X, Zhou Y. Hepatocyte miR-33a mediates mitochondrial dysfunction and hepatosteatosis by suppressing NDUFA5. J Cell Mol Med 2018; 22:6285-6293. [PMID: 30324697 PMCID: PMC6237601 DOI: 10.1111/jcmm.13918] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 07/16/2018] [Accepted: 08/26/2018] [Indexed: 12/11/2022] Open
Abstract
Emerging evidence suggests that microRNAs (miRNAs) are essential for metabolic haemostasis of liver tissues. Among them, miR‐33a is supposed to modulate the cholesterol export and fatty acid oxidation, but whether miR‐33a involves in the process of fatty liver disease is unclear. To disclose the hypothesis, we utilized miR‐33a mimic and antisense to explore their effects in primary hepatocytes or high‐fat diet (HFD)‐fed mice. Treatment with palmitic acid (PA) or HFD significantly increased the expression of miR‐33a in hepatocytes or liver tissues. In primary hepatocytes, miR‐33a mimic decreased mitochondrial function, including reduction of ATP production and oxygen consumption, whereas miR‐33a inhibition protected PA‐induced mitochondrial dysfunction. Interestingly, miR‐33a selectively suppressed mitochondrial complex I activity and protein expression, but not other complexes. Through bioinformatics prediction, we found miR‐33a directly targeted on the 3′‐UTR of NDUFA5. Dual‐luciferase reporter analysis further confirmed the direct suppression of miR‐33a on NDUFA5 expression. More importantly, administration of miR‐33a antisense could effectively restore HFD‐induced mitochondrial dysfunction through up‐regulation of NDUFA5 levels. Mice treated with miR‐33a antisense also exhibited improved liver function and structural disorders under obese status. Taken together, miR‐33a was an important mediator of hepatocyte mitochondrial function, and the therapeutic benefits implied miR‐33a antisense had the potential clinical application in combating the fatty liver disease.
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Affiliation(s)
- Hezhongrong Nie
- Center of Clinical Laboratory, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Xiaohong Yu
- Center of Clinical Laboratory, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Haihong He
- Center of Clinical Laboratory, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Lintao Zhou
- Center of Clinical Laboratory, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Qing Li
- Center of Clinical Laboratory, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Chunli Song
- Center of Clinical Laboratory, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Damin Wang
- Center of Clinical Laboratory, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Tingyu Ren
- Center of Clinical Laboratory, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Zeyan Chen
- Center of Clinical Laboratory, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Hanlian Huang
- Center of Clinical Laboratory, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Xiaoyan Dai
- Center of Clinical Laboratory, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Yiwen Zhou
- Center of Clinical Laboratory, Shenzhen Hospital, Southern Medical University, Shenzhen, China
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Skibiel AL, Zachut M, do Amaral BC, Levin Y, Dahl GE. Liver proteomic analysis of postpartum Holstein cows exposed to heat stress or cooling conditions during the dry period. J Dairy Sci 2018; 101:705-716. [DOI: 10.3168/jds.2017-13258] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 09/19/2017] [Indexed: 12/25/2022]
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38
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Massoz S, Hanikenne M, Bailleul B, Coosemans N, Radoux M, Miranda-Astudillo H, Cardol P, Larosa V, Remacle C. In vivo chlorophyll fluorescence screening allows the isolation of a Chlamydomonas mutant defective for NDUFAF3, an assembly factor involved in mitochondrial complex I assembly. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 92:584-595. [PMID: 28857403 DOI: 10.1111/tpj.13677] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 08/11/2017] [Accepted: 08/21/2017] [Indexed: 05/16/2023]
Abstract
The qualitative screening method used to select complex I mutants in the microalga Chlamydomonas, based on reduced growth under heterotrophic conditions, is not suitable for high-throughput screening. In order to develop a fast screening method based on measurements of chlorophyll fluorescence, we first demonstrated that complex I mutants displayed decreased photosystem II efficiency in the genetic background of a photosynthetic mutation leading to reduced formation of the electrochemical proton gradient in the chloroplast (pgrl1 mutation). In contrast, single mutants (complex I and pgrl1 mutants) could not be distinguished from the wild type by their photosystem II efficiency under the conditions tested. We next performed insertional mutagenesis on the pgrl1 mutant. Out of about 3000 hygromycin-resistant insertional transformants, 46 had decreased photosystem II efficiency and three were complex I mutants. One of the mutants was tagged and whole genome sequencing identified the resistance cassette in NDUFAF3, a homolog of the human NDUFAF3 gene, encoding for an assembly factor involved in complex I assembly. Complemented strains showed restored complex I activity and assembly. Overall, we describe here a screening method which is fast and particularly suited for the identification of Chlamydomonas complex I mutants.
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Affiliation(s)
- Simon Massoz
- InBioS - Genetics and Physiology of Microalgae, Chemin de la vallée, 4, 4000 Liège, University of Liège, Belgium
- PhytoSYSTEMS, Chemin de la vallée, 4, 4000 Liège, University of Liège, Belgium
| | - Marc Hanikenne
- PhytoSYSTEMS, Chemin de la vallée, 4, 4000 Liège, University of Liège, Belgium
- InBioS - Functional Genomics and Plant Molecular Imaging, Chemin de la vallée, 4, 4000 Liège, University of Liège, Belgium
| | - Benjamin Bailleul
- InBioS - Genetics and Physiology of Microalgae, Chemin de la vallée, 4, 4000 Liège, University of Liège, Belgium
| | - Nadine Coosemans
- InBioS - Genetics and Physiology of Microalgae, Chemin de la vallée, 4, 4000 Liège, University of Liège, Belgium
- PhytoSYSTEMS, Chemin de la vallée, 4, 4000 Liège, University of Liège, Belgium
| | - Michèle Radoux
- InBioS - Genetics and Physiology of Microalgae, Chemin de la vallée, 4, 4000 Liège, University of Liège, Belgium
- PhytoSYSTEMS, Chemin de la vallée, 4, 4000 Liège, University of Liège, Belgium
| | - Hector Miranda-Astudillo
- InBioS - Genetics and Physiology of Microalgae, Chemin de la vallée, 4, 4000 Liège, University of Liège, Belgium
- PhytoSYSTEMS, Chemin de la vallée, 4, 4000 Liège, University of Liège, Belgium
| | - Pierre Cardol
- InBioS - Genetics and Physiology of Microalgae, Chemin de la vallée, 4, 4000 Liège, University of Liège, Belgium
- PhytoSYSTEMS, Chemin de la vallée, 4, 4000 Liège, University of Liège, Belgium
| | - Véronique Larosa
- InBioS - Genetics and Physiology of Microalgae, Chemin de la vallée, 4, 4000 Liège, University of Liège, Belgium
| | - Claire Remacle
- InBioS - Genetics and Physiology of Microalgae, Chemin de la vallée, 4, 4000 Liège, University of Liège, Belgium
- PhytoSYSTEMS, Chemin de la vallée, 4, 4000 Liège, University of Liège, Belgium
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39
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Theunissen TEJ, Gerards M, Hellebrekers DMEI, van Tienen FH, Kamps R, Sallevelt SCEH, Hartog ENMMD, Scholte HR, Verdijk RM, Schoonderwoerd K, de Coo IFM, Szklarczyk R, Smeets HJM. Selection and Characterization of Palmitic Acid Responsive Patients with an OXPHOS Complex I Defect. Front Mol Neurosci 2017; 10:336. [PMID: 29093663 PMCID: PMC5651253 DOI: 10.3389/fnmol.2017.00336] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 10/03/2017] [Indexed: 12/19/2022] Open
Abstract
Mitochondrial disorders are genetically and clinically heterogeneous, mainly affecting high energy-demanding organs due to impaired oxidative phosphorylation (OXPHOS). Currently, effective treatments for OXPHOS defects, with complex I deficiency being the most prevalent, are not available. Yet, clinical practice has shown that some complex I deficient patients benefit from a high-fat or ketogenic diet, but it is unclear how these therapeutic diets influence mitochondrial function and more importantly, which complex I patients could benefit from such treatment. Dietary studies in a complex I deficient patient with exercise intolerance showed increased muscle endurance on a high-fat diet compared to a high-carbohydrate diet. We performed whole-exome sequencing to characterize the genetic defect. A pathogenic homozygous p.G212V missense mutation was identified in the TMEM126B gene, encoding an early assembly factor of complex I. A complementation study in fibroblasts confirmed that the p.G212V mutation caused the complex I deficiency. The mechanism turned out to be an incomplete assembly of the peripheral arm of complex I, leading to a decrease in the amount of mature complex I. The patient clinically improved on a high-fat diet, which was supported by the 25% increase in maximal OXPHOS capacity in TMEM126B defective fibroblast by the saturated fatty acid palmitic acid, whereas oleic acid did not have any effect in those fibroblasts. Fibroblasts of other patients with a characterized complex I gene defect were tested in the same way. Patient fibroblasts with complex I defects in NDUFS7 and NDUFAF5 responded to palmitic acid, whereas ACAD9, NDUFA12, and NDUFV2 defects were non-responding. Although the data are too limited to draw a definite conclusion on the mechanism, there is a tendency that protein defects involved in early assembly complexes, improve with palmitic acid, whereas proteins defects involved in late assembly, do not. Our data show at a clinical and biochemical level that a high fat diet can be beneficial for complex I patients and that our cell line assay will be an easy tool for the selection of patients, who might potentially benefit from this therapeutic diet.
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Affiliation(s)
- Tom E J Theunissen
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, Netherlands.,Department of Genetics and Cell Biology, School for Oncology and Developmental Biology, Maastricht University Medical Centre, Maastricht, Netherlands
| | - Mike Gerards
- Maastricht Centre for Systems Biology, Maastricht University, Maastricht, Netherlands
| | | | - Florence H van Tienen
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, Netherlands
| | - Rick Kamps
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, Netherlands
| | - Suzanne C E H Sallevelt
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, Netherlands
| | | | - Hans R Scholte
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, Netherlands
| | - Robert M Verdijk
- Department of Pathology, Erasmus Medical Center, Rotterdam, Netherlands
| | - Kees Schoonderwoerd
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, Netherlands
| | | | - Radek Szklarczyk
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, Netherlands
| | - Hubert J M Smeets
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, Netherlands.,Department of Genetics and Cell Biology, School for Oncology and Developmental Biology, Maastricht University Medical Centre, Maastricht, Netherlands.,Maastricht Centre for Systems Biology, Maastricht University, Maastricht, Netherlands
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40
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Doucet-Beaupré H, Gilbert C, Profes MS, Chabrat A, Pacelli C, Giguère N, Rioux V, Charest J, Deng Q, Laguna A, Ericson J, Perlmann T, Ang SL, Cicchetti F, Parent M, Trudeau LE, Lévesque M. Lmx1a and Lmx1b regulate mitochondrial functions and survival of adult midbrain dopaminergic neurons. Proc Natl Acad Sci U S A 2016; 113:E4387-96. [PMID: 27407143 PMCID: PMC4968767 DOI: 10.1073/pnas.1520387113] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The LIM-homeodomain transcription factors Lmx1a and Lmx1b play critical roles during the development of midbrain dopaminergic progenitors, but their functions in the adult brain remain poorly understood. We show here that sustained expression of Lmx1a and Lmx1b is required for the survival of adult midbrain dopaminergic neurons. Strikingly, inactivation of Lmx1a and Lmx1b recreates cellular features observed in Parkinson's disease. We found that Lmx1a/b control the expression of key genes involved in mitochondrial functions, and their ablation results in impaired respiratory chain activity, increased oxidative stress, and mitochondrial DNA damage. Lmx1a/b deficiency caused axonal pathology characterized by α-synuclein(+) inclusions, followed by a progressive loss of dopaminergic neurons. These results reveal the key role of these transcription factors beyond the early developmental stages and provide mechanistic links between mitochondrial dysfunctions, α-synuclein aggregation, and the survival of dopaminergic neurons.
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Affiliation(s)
- Hélène Doucet-Beaupré
- Department of Psychiatry and Neurosciences, Faculty of Medicine, Université Laval, Quebec QC G1V 0A6, Canada; Centre de Recherche de l'Institut Universitaire en Santé Mentale de Québec, Quebec, QC G1J 2G3, Canada
| | - Catherine Gilbert
- Department of Psychiatry and Neurosciences, Faculty of Medicine, Université Laval, Quebec QC G1V 0A6, Canada; Centre de Recherche de l'Institut Universitaire en Santé Mentale de Québec, Quebec, QC G1J 2G3, Canada
| | - Marcos Schaan Profes
- Department of Psychiatry and Neurosciences, Faculty of Medicine, Université Laval, Quebec QC G1V 0A6, Canada; Centre de Recherche de l'Institut Universitaire en Santé Mentale de Québec, Quebec, QC G1J 2G3, Canada
| | - Audrey Chabrat
- Department of Psychiatry and Neurosciences, Faculty of Medicine, Université Laval, Quebec QC G1V 0A6, Canada; Centre de Recherche de l'Institut Universitaire en Santé Mentale de Québec, Quebec, QC G1J 2G3, Canada
| | - Consiglia Pacelli
- Department of Pharmacology, Central Nervous System Research Group, Faculty of Medicine, Université de Montréal, Montreal, QC H3T 1J4, Canada; Department of Neurosciences, Central Nervous System Research Group, Faculty of Medicine, Université de Montréal, Montreal, QC H3T 1J4, Canada
| | - Nicolas Giguère
- Department of Pharmacology, Central Nervous System Research Group, Faculty of Medicine, Université de Montréal, Montreal, QC H3T 1J4, Canada; Department of Neurosciences, Central Nervous System Research Group, Faculty of Medicine, Université de Montréal, Montreal, QC H3T 1J4, Canada
| | - Véronique Rioux
- Department of Psychiatry and Neurosciences, Faculty of Medicine, Université Laval, Quebec QC G1V 0A6, Canada; Centre de Recherche de l'Institut Universitaire en Santé Mentale de Québec, Quebec, QC G1J 2G3, Canada
| | - Julien Charest
- Department of Psychiatry and Neurosciences, Faculty of Medicine, Université Laval, Quebec QC G1V 0A6, Canada; Centre de Recherche de l'Institut Universitaire en Santé Mentale de Québec, Quebec, QC G1J 2G3, Canada
| | - Qiaolin Deng
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Ariadna Laguna
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden; The Ludwig Institute for Cancer Research, 171 77 Stockholm, Sweden
| | - Johan Ericson
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Thomas Perlmann
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden; The Ludwig Institute for Cancer Research, 171 77 Stockholm, Sweden
| | - Siew-Lan Ang
- The Francis Crick Institute, London, NW1 2BE, United Kingdom
| | - Francesca Cicchetti
- Department of Psychiatry and Neurosciences, Faculty of Medicine, Université Laval, Quebec QC G1V 0A6, Canada; Centre de recherche du Centre Hospitalier Universitaire de Québec, Quebec, QC G1V 4G2, Canada
| | - Martin Parent
- Department of Psychiatry and Neurosciences, Faculty of Medicine, Université Laval, Quebec QC G1V 0A6, Canada; Centre de Recherche de l'Institut Universitaire en Santé Mentale de Québec, Quebec, QC G1J 2G3, Canada
| | - Louis-Eric Trudeau
- Department of Pharmacology, Central Nervous System Research Group, Faculty of Medicine, Université de Montréal, Montreal, QC H3T 1J4, Canada; Department of Neurosciences, Central Nervous System Research Group, Faculty of Medicine, Université de Montréal, Montreal, QC H3T 1J4, Canada
| | - Martin Lévesque
- Department of Psychiatry and Neurosciences, Faculty of Medicine, Université Laval, Quebec QC G1V 0A6, Canada; Centre de Recherche de l'Institut Universitaire en Santé Mentale de Québec, Quebec, QC G1J 2G3, Canada;
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41
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Chintalapudi SR, Morales-Tirado VM, Williams RW, Jablonski MM. Multipronged approach to identify and validate a novel upstream regulator of Sncg in mouse retinal ganglion cells. FEBS J 2016; 283:678-93. [PMID: 26663874 DOI: 10.1111/febs.13620] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 10/22/2015] [Accepted: 12/03/2015] [Indexed: 11/26/2022]
Abstract
Loss of retinal ganglion cells (RGCs) is one of the hallmarks of retinal neurodegenerative diseases, glaucoma being one of the most common. Mechanistic studies on RGCs are hindered by the lack of sufficient primary cells and consensus regarding their signature markers. Recently, γ-synuclein (SNCG) has been shown to be highly expressed in the somas and axons of RGCs. In various mouse models of glaucoma, downregulation of Sncg gene expression correlates with RGC loss. To investigate the role of Sncg in RGCs, we used a novel systems genetics approach to identify a gene that modulates Sncg expression, followed by confirmatory studies in both healthy and diseased retinae. We found that chromosome 1 harbors an expression quantitative trait locus that modulates Sncg expression in the mouse retina, and identified the prefoldin-2 (PFDN2) gene as the candidate upstream modulator of Sncg expression. Our immunohistochemical analyses revealed similar expression patterns in both mouse and human healthy retinae, with PFDN2 colocalizing with SNCG in RGCs and their axons. In contrast, in retinae from glaucoma subjects, SNCG levels were significantly reduced, although PFDN2 levels were maintained. Using a novel flow cytometry-based RGC isolation method, we obtained viable populations of murine RGCs. Knocking down Pfdn2 expression in primary murine RGCs significantly reduced Sncg expression, confirming that Pfdn2 regulates Sncg expression in murine RGCs. Gene Ontology analysis indicated shared mitochondrial function associated with Sncg and Pfdn2. These data solidify the relationship between Sncg and Pfdn2 in RGCs, and provide a novel mechanism for maintaining RGC health.
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Affiliation(s)
- Sumana R Chintalapudi
- Department of Ophthalmology, The Hamilton Eye Institute, The University of Tennessee Health Science Center, Memphis, TN, USA.,Department of Anatomy and Neurobiology, The University of Tennessee Health Science Center, Memphis, TN, USA
| | - Vanessa M Morales-Tirado
- Department of Ophthalmology, The Hamilton Eye Institute, The University of Tennessee Health Science Center, Memphis, TN, USA.,Department of Anatomy and Neurobiology, The University of Tennessee Health Science Center, Memphis, TN, USA.,Department of Microbiology, Immunology and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN, USA
| | - Robert W Williams
- Department of Anatomy and Neurobiology, The University of Tennessee Health Science Center, Memphis, TN, USA.,Department of Genetics, Genomics and Informatics, The University of Tennessee Health Science Center, Memphis, TN, USA
| | - Monica M Jablonski
- Department of Ophthalmology, The Hamilton Eye Institute, The University of Tennessee Health Science Center, Memphis, TN, USA.,Department of Anatomy and Neurobiology, The University of Tennessee Health Science Center, Memphis, TN, USA
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42
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Hasegawa Y, Taylor D, Ovchinnikov DA, Wolvetang EJ, de Torrenté L, Mar JC. Variability of Gene Expression Identifies Transcriptional Regulators of Early Human Embryonic Development. PLoS Genet 2015; 11:e1005428. [PMID: 26288249 PMCID: PMC4546122 DOI: 10.1371/journal.pgen.1005428] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 07/06/2015] [Indexed: 11/18/2022] Open
Abstract
An analysis of gene expression variability can provide an insightful window into how regulatory control is distributed across the transcriptome. In a single cell analysis, the inter-cellular variability of gene expression measures the consistency of transcript copy numbers observed between cells in the same population. Application of these ideas to the study of early human embryonic development may reveal important insights into the transcriptional programs controlling this process, based on which components are most tightly regulated. Using a published single cell RNA-seq data set of human embryos collected at four-cell, eight-cell, morula and blastocyst stages, we identified genes with the most stable, invariant expression across all four developmental stages. Stably-expressed genes were found to be enriched for those sharing indispensable features, including essentiality, haploinsufficiency, and ubiquitous expression. The stable genes were less likely to be associated with loss-of-function variant genes or human recessive disease genes affected by a DNA copy number variant deletion, suggesting that stable genes have a functional impact on the regulation of some of the basic cellular processes. Genes with low expression variability at early stages of development are involved in regulation of DNA methylation, responses to hypoxia and telomerase activity, whereas by the blastocyst stage, low-variability genes are enriched for metabolic processes as well as telomerase signaling. Based on changes in expression variability, we identified a putative set of gene expression markers of morulae and blastocyst stages. Experimental validation of a blastocyst-expressed variability marker demonstrated that HDDC2 plays a role in the maintenance of pluripotency in human ES and iPS cells. Collectively our analyses identified new regulators involved in human embryonic development that would have otherwise been missed using methods that focus on assessment of the average expression levels; in doing so, we highlight the value of studying expression variability for single cell RNA-seq data.
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Affiliation(s)
- Yu Hasegawa
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, New York, United States of America; Division of Life Science, Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Deanne Taylor
- RMANJ Reproductive Medicine Associates of New Jersey, Morristown, New Jersey, United States of America; Division of Reproductive Endocrinology, Department of Obstetrics, Gynecology, and Reproductive Science, Robert Wood Johnson Medical School, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Dmitry A Ovchinnikov
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, Queensland, Australia
| | - Ernst J Wolvetang
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, Queensland, Australia
| | - Laurence de Torrenté
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Jessica C Mar
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, New York, United States of America; Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York, United States of America
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43
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Cardiac metabolic pathways affected in the mouse model of barth syndrome. PLoS One 2015; 10:e0128561. [PMID: 26030409 PMCID: PMC4451073 DOI: 10.1371/journal.pone.0128561] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 04/28/2015] [Indexed: 12/31/2022] Open
Abstract
Cardiolipin (CL) is a mitochondrial phospholipid essential for electron transport chain (ETC) integrity. CL-deficiency in humans is caused by mutations in the tafazzin (Taz) gene and results in a multisystem pediatric disorder, Barth syndrome (BTHS). It has been reported that tafazzin deficiency destabilizes mitochondrial respiratory chain complexes and affects supercomplex assembly. The aim of this study was to investigate the impact of Taz-knockdown on the mitochondrial proteomic landscape and metabolic processes, such as stability of respiratory chain supercomplexes and their interactions with fatty acid oxidation enzymes in cardiac muscle. Proteomic analysis demonstrated reduction of several polypeptides of the mitochondrial respiratory chain, including Rieske and cytochrome c1 subunits of complex III, NADH dehydrogenase alpha subunit 5 of complex I and the catalytic core-forming subunit of F0F1-ATP synthase. Taz gene knockdown resulted in upregulation of enzymes of folate and amino acid metabolic pathways in heart mitochondria, demonstrating that Taz-deficiency causes substantive metabolic remodeling in cardiac muscle. Mitochondrial respiratory chain supercomplexes are destabilized in CL-depleted mitochondria from Taz knockdown hearts resulting in disruption of the interactions between ETC and the fatty acid oxidation enzymes, very long-chain acyl-CoA dehydrogenase and long-chain 3-hydroxyacyl-CoA dehydrogenase, potentially affecting the metabolic channeling of reducing equivalents between these two metabolic pathways. Mitochondria-bound myoglobin was significantly reduced in Taz-knockdown hearts, potentially disrupting intracellular oxygen delivery to the oxidative phosphorylation system. Our results identify the critical pathways affected by the Taz-deficiency in mitochondria and establish a future framework for development of therapeutic options for BTHS.
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44
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Enquobahrie DA, Moore A, Muhie S, Tadesse MG, Lin S, Williams MA. Early Pregnancy Maternal Blood DNA Methylation in Repeat Pregnancies and Change in Gestational Diabetes Mellitus Status—A Pilot Study. Reprod Sci 2015; 22:904-10. [PMID: 25676578 DOI: 10.1177/1933719115570903] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Repeat pregnancies with different perinatal outcomes minimize underlying maternal genetic diversity and provide unique opportunities to investigate nongenetic risk factors and epigenetic mechanisms of pregnancy complications. We investigated gestational diabetes mellitus (GDM)-related differential DNA methylation in early pregnancy peripheral blood samples collected from women who had a change in GDM status in repeat pregnancies. Six study participants were randomly selected from among women who had 2 consecutive pregnancies, only 1 of which was complicated by GDM (case pregnancy) and the other was not (control pregnancy). Epigenome-wide DNA methylation was profiled using Illumina HumanMethylation 27 BeadChips. Differential Identification using Mixture Ensemble and false discovery rate (<10%) cutoffs were used to identify differentially methylated targets between the 2 pregnancies of each participant. Overall, 27 target sites, 17 hypomethylated (fold change [FC] range: 0.77-0.99) and 10 hypermethylated (FC range: 1.01-1.09), were differentially methylated between GDM and control pregnancies among 5 or more study participants. Novel genes were related to identified hypomethylated (such as NDUFC1, HAPLN3, HHLA3, and RHOG) or hypermethylated sites (such as SEP11, ZAR1, and DDR). Genes related to identified sites participated in cell morphology, cellular assembly, cellular organization, cellular compromise, and cell cycle. Our findings support early pregnancy peripheral blood DNA methylation differences in repeat pregnancies with change in GDM status. Similar, larger, and repeat pregnancy studies can enhance biomarker discovery and mechanistic studies of GDM.
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Affiliation(s)
- Daniel A Enquobahrie
- Center for Perinatal Studies, Swedish Medical Center, Seattle, WA, USA Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Amy Moore
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Seid Muhie
- Walter Reed Army Hospital, Washington DC, USA
| | - Mahlet G Tadesse
- Department of Mathematics and Statistics, Georgetown University, Washington DC, USA
| | - Shili Lin
- Department of Statistics, The Ohio State University, Columbus, OH, USA
| | - Michelle A Williams
- Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
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45
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Torraco A, Peralta S, Iommarini L, Diaz F. Mitochondrial Diseases Part I: mouse models of OXPHOS deficiencies caused by defects in respiratory complex subunits or assembly factors. Mitochondrion 2015; 21:76-91. [PMID: 25660179 DOI: 10.1016/j.mito.2015.01.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 11/22/2014] [Accepted: 01/05/2015] [Indexed: 10/24/2022]
Abstract
Mitochondrial disorders are the most common inborn errors of metabolism affecting the oxidative phosphorylation system (OXPHOS). Because of the poor knowledge of the pathogenic mechanisms, a cure for these disorders is still unavailable and all the treatments currently in use are supportive more than curative. Therefore, in the past decade a great variety of mouse models have been developed to assess the in vivo function of several mitochondrial proteins involved in human diseases. Due to the genetic and physiological similarity to humans, mice represent reliable models to study the pathogenic mechanisms of mitochondrial disorders and are precious to test new therapeutic approaches. Here we summarize the features of several mouse models of mitochondrial diseases directly related to defects in subunits of the OXPHOS complexes or in assembly factors. We discuss how these models recapitulate many human conditions and how they have contributed to the understanding of mitochondrial function in health and disease.
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Affiliation(s)
- Alessandra Torraco
- Unit for Neuromuscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Viale di San Paolo, 15-00146 Rome, Italy.
| | - Susana Peralta
- Department of Neurology, University of Miami, Miller School of Medicine, Miami, FL 33136, USA.
| | - Luisa Iommarini
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, Via Irnerio 42, 40126 Bologna, Italy.
| | - Francisca Diaz
- Department of Neurology, University of Miami, Miller School of Medicine, Miami, FL 33136, USA.
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