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Key J, Gispert S, Koepf G, Steinhoff-Wagner J, Reichlmeir M, Auburger G. Translation Fidelity and Respiration Deficits in CLPP-Deficient Tissues: Mechanistic Insights from Mitochondrial Complexome Profiling. Int J Mol Sci 2023; 24:17503. [PMID: 38139332 PMCID: PMC10743472 DOI: 10.3390/ijms242417503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
The mitochondrial matrix peptidase CLPP is crucial during cell stress. Its loss causes Perrault syndrome type 3 (PRLTS3) with infertility, neurodegeneration, and a growth deficit. Its target proteins are disaggregated by CLPX, which also regulates heme biosynthesis via unfolding ALAS enzymes, providing access for pyridoxal-5'-phosphate (PLP). Despite efforts in diverse organisms with multiple techniques, CLPXP substrates remain controversial. Here, avoiding recombinant overexpression, we employed complexomics in mitochondria from three mouse tissues to identify endogenous targets. A CLPP absence caused the accumulation and dispersion of CLPX-VWA8 as AAA+ unfoldases, and of PLPBP. Similar changes and CLPX-VWA8 co-migration were evident for mitoribosomal central protuberance clusters, translation factors like GFM1-HARS2, the RNA granule components LRPPRC-SLIRP, and enzymes OAT-ALDH18A1. Mitochondrially translated proteins in testes showed reductions to <30% for MTCO1-3, the mis-assembly of the complex IV supercomplex, and accumulated metal-binding assembly factors COX15-SFXN4. Indeed, heavy metal levels were increased for iron, molybdenum, cobalt, and manganese. RT-qPCR showed compensatory downregulation only for Clpx mRNA; most accumulated proteins appeared transcriptionally upregulated. Immunoblots validated VWA8, MRPL38, MRPL18, GFM1, and OAT accumulation. Co-immunoprecipitation confirmed CLPX binding to MRPL38, GFM1, and OAT, so excess CLPX and PLP may affect their activity. Our data mechanistically elucidate the mitochondrial translation fidelity deficits which underlie progressive hearing impairment in PRLTS3.
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Affiliation(s)
- Jana Key
- Goethe University Frankfurt, University Hospital, Clinic of Neurology, Exp. Neurology, Heinrich Hoffmann Str. 7, 60590 Frankfurt am Main, Germany; (S.G.); (M.R.); (G.A.)
| | - Suzana Gispert
- Goethe University Frankfurt, University Hospital, Clinic of Neurology, Exp. Neurology, Heinrich Hoffmann Str. 7, 60590 Frankfurt am Main, Germany; (S.G.); (M.R.); (G.A.)
| | - Gabriele Koepf
- Goethe University Frankfurt, University Hospital, Clinic of Neurology, Exp. Neurology, Heinrich Hoffmann Str. 7, 60590 Frankfurt am Main, Germany; (S.G.); (M.R.); (G.A.)
| | - Julia Steinhoff-Wagner
- TUM School of Life Sciences, Animal Nutrition and Metabolism, Technical University of Munich, Liesel-Beckmann-Str. 2, 85354 Freising-Weihenstephan, Germany;
| | - Marina Reichlmeir
- Goethe University Frankfurt, University Hospital, Clinic of Neurology, Exp. Neurology, Heinrich Hoffmann Str. 7, 60590 Frankfurt am Main, Germany; (S.G.); (M.R.); (G.A.)
| | - Georg Auburger
- Goethe University Frankfurt, University Hospital, Clinic of Neurology, Exp. Neurology, Heinrich Hoffmann Str. 7, 60590 Frankfurt am Main, Germany; (S.G.); (M.R.); (G.A.)
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Du Z, Zhang Z, Han X, Xie H, Yan W, Tian D, Liu M, Rao C. Comprehensive Analysis of Sideroflexin 4 in Hepatocellular Carcinoma by Bioinformatics and Experiments. Int J Med Sci 2023; 20:1300-1315. [PMID: 37786439 PMCID: PMC10542026 DOI: 10.7150/ijms.86990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 08/01/2023] [Indexed: 10/04/2023] Open
Abstract
Background: Sideroflexins (SFXNs) are a family of highly conserved mitochondrial transporters which regulate iron homeostasis and mitochondrial respiratory chain. However, the roles and mechanisms of SFXNs in HCC remain unknown. Methods: SFXNs expression and prognostic value in HCC was comprehensively analyzed. Proteins interacting with SFXN4 were analyzed in STRING database. The co-expression genes of SFXN4 were analyzed in cBioPortal database, and function of SFXN4 co-expression genes were annotated. The putative transcription factors and miRNA targeting SFXN4 were analyzed in NetworkAnalyst. The correlation between SFXN4 expression and immune infiltration was analyzed by ssGSEA. Cancer pathway activity and drug sensitivity related to SFXN4 were explored in GSCALite. The roles of SFXN4 in proliferation, migration and invasion of HCC were assessed in vitro and in vivo. Results: SFXN4 was consistently elevated in HCC, positively correlated with clinicopathological characteristics and predicted poor outcome. Functional enrichment showed SFXN4 was mainly related to oxidative phosphorylation, reactive oxygen species and metabolic pathways. SFXN4 expression was regulated by multiple transcription factors and miRNAs, and SFXN4 expression in HCC was associated with several cancer pathways and drug sensitivity. SFXN4 expression correlated with immune infiltration in HCC. In vitro, knockdown of SFXN4 inhibited HCC proliferation, migration and invasion, and decreased the expression of cyclin D1 and MMP2. In vivo, knockdown of SFXN4 inhibited the growth of tumor xenografts in mice. Conclusion: SFXN4 was upregulated in HCC, predicted poor prognosis, and may facilitate HCC development and progression via various mechanisms. For HCC, SFXN4 may provide both prognostic information and therapeutic potential.
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Affiliation(s)
- Zhipeng Du
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhongchao Zhang
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xu Han
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Huaping Xie
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wei Yan
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Dean Tian
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Mei Liu
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Caijun Rao
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Yuan D, Liu J, Sang W, Li Q. Comprehensive analysis of the role of SFXN family in breast cancer. Open Med (Wars) 2023; 18:20230685. [PMID: 37020524 PMCID: PMC10068752 DOI: 10.1515/med-2023-0685] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 03/02/2023] [Accepted: 03/08/2023] [Indexed: 04/04/2023] Open
Abstract
Abstract
The sideroflexin (SFXN) family is a group of mitochondrial membrane proteins. Although the function of the SFXN family in mitochondria has been widely recognized, the expression levels, role, and prognostic value of this family in breast cancer (BC) have not been clearly articulated and systematically analysed. In our research, SFXN1 and SFXN2 were significantly upregulated in BC versus normal samples based on Gene Expression Profiling Interactive Analysis 2 and the Human Protein Atlas databases. We found that high SFXN1 expression was significantly related to poor prognosis in BC patients and that high SFXN2 expression was significantly associated with good prognosis in BC patients. Gene Ontology analysis of the SFXN family was performed based on the STRING database to explore the potential functions of this family, including biological processes, cellular components, and molecular functions. Based on the MethSurv database, we found that two SFXN1 CpG sites (5′-UTR-S_Shelf-cg06573254 and TSS200-Island-cg17647431), two SFXN2 CpG sites (3′-UTR-Open_Sea-cg04774043 and Body-Open_Sea-cg18994254), one SFXN3 CpG site (Body-S_Shelf-cg17858697), and nine SFXN5 CpG sites (1stExon;5′-UTR-Island-cg03856450, Body-Open_Sea-cg04016113, Body-Open_Sea-cg04197631, Body-Open_Sea-cg07558704, Body-Open_Sea-cg08383863, Body-Open_Sea-cg10040131, Body-Open_Sea-cg10588340, Body-Open_Sea-cg17046766, and Body-Open_Sea-cg22830638) were significantly related to the prognosis of BC patients. According to the ENCORI database, four negative regulatory miRNAs for SFXN1 (hsa-miR-22-3p, hsa-miR-140-5p, hsa-miR-532-5p, and hsa-miR-582-3p) and four negative regulatory miRNAs for SFXN2 (hsa-miR-9-5p, hsa-miR-34a-5p, hsa-miR-532-5p, and hsa-miR-885-5p) were related to poor prognosis for BC patients. This study suggests that SFXN1 and SFXN2 are valuable biomarkers and treatment targets for patients with BC.
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Affiliation(s)
- Ding Yuan
- Department of General Surgery, Shouguang City People’s Hospital , Shouguang , 262700 , China
| | - Jialiang Liu
- Department of General Surgery, Shouguang City People’s Hospital , Shouguang , 262700 , China
| | - Wenbo Sang
- Department of General Surgery, Shouguang City People’s Hospital , Shouguang , 262700 , China
| | - Qing Li
- Department of General Surgery, Shouguang City People’s Hospital , Shouguang , 262700 , China
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Sezer A, Kayhan G, Gursoy TR, Eyuboglu TS, Percin FE. A homozygous missense variant in the WRN gene segregating in a family with progressive pulmonary failure with recurrent spontaneous pneumothorax and interstitial lung disease. Am J Med Genet A 2023; 191:220-227. [PMID: 36214313 DOI: 10.1002/ajmg.a.62986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/24/2022] [Accepted: 09/24/2022] [Indexed: 12/14/2022]
Abstract
Interstitial lung disease (ILD) is a condition affecting the lung parenchyma by inflammation and fibrosis and can be caused by various exposures, connective tissue diseases (CTD), and genetic disorders. In this report, a family with five patients having progressive respiratory failure that begins with coughing in adolescence, followed by dyspnea and recurrent spontaneous pneumothorax, and death in early adulthood is presented. The patients were diagnosed to have ILD through clinical and radiological evaluations. Molecular genetic analyses of the family provided two homozygous rare variants in the WRN and SFXN5 genes, co-segregating with the phenotype. The network analyses pointed out that the variant in the WRN, rather than that in the SFXN5 gene, could be the main factor in the existence of the ILD phenotype, putatively through the altered DNA repair and telomere maintenance pathways. In silico analyses suggested that the variant could affect the exonuclease activity or the stability of the WRN protein. Moreover, the adolescent-onset pulmonary phenotype described in the case has not been reported in Werner Syndrome, the only disease known to be associated with biallelic WRN pathogenic variants. Thus, the present phenotype could be either a very atypical presentation of Werner syndrome or a new clinical entity associated with the WRN gene.
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Affiliation(s)
- Abdullah Sezer
- Department of Medical Genetics, Dr. Sami Ulus Maternity and Children's Training and Research Hospital, Ankara, Turkey.,Department of Medical Genetics, Faculty of Medicine, Gazi University, Ankara, Turkey
| | - Gulsum Kayhan
- Department of Medical Genetics, Faculty of Medicine, Gazi University, Ankara, Turkey
| | - Tugba Ramasli Gursoy
- Department of Pediatric Pulmonology, Faculty of Medicine, Gazi University, Ankara, Turkey
| | | | - Ferda E Percin
- Department of Medical Genetics, Faculty of Medicine, Gazi University, Ankara, Turkey
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Tesfay L, Paul BT, Hegde P, Brewer M, Habbani S, Jellison E, Moore T, Wu H, Torti SV, Torti FM. Complementary anti-cancer pathways triggered by inhibition of sideroflexin 4 in ovarian cancer. Sci Rep 2022; 12:19936. [PMID: 36402786 PMCID: PMC9675821 DOI: 10.1038/s41598-022-24391-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 11/15/2022] [Indexed: 11/21/2022] Open
Abstract
DNA damaging agents are a mainstay of standard chemotherapy for ovarian cancer. Unfortunately, resistance to such DNA damaging agents frequently develops, often due to increased activity of DNA repair pathways. Sideroflexin 4 (SFXN4) is a little-studied inner mitochondrial membrane protein. Here we demonstrate that SFXN4 plays a role in synthesis of iron sulfur clusters (Fe-S) in ovarian cancer cells and ovarian cancer tumor-initiating cells, and that knockdown of SFXN4 inhibits Fe-S biogenesis in ovarian cancer cells. We demonstrate that this has two important consequences that may be useful in anti-cancer therapy. First, inhibition of Fe-S biogenesis triggers the accumulation of excess iron, leading to oxidative stress. Second, because enzymes critical to multiple DNA repair pathways require Fe-S clusters for their function, DNA repair enzymes and DNA repair itself are inhibited by reduction of SFXN4. Through this dual mechanism, SFXN4 inhibition heightens ovarian cancer cell sensitivity to DNA-damaging drugs and DNA repair inhibitors used in ovarian cancer therapy, such as cisplatin and PARP inhibitors. Sensitization is achieved even in drug resistant ovarian cancer cells. Further, knockout of SFXN4 decreases DNA repair and profoundly inhibits tumor growth in a mouse model of ovarian cancer metastasis. Collectively, these results suggest that SFXN4 may represent a new target in ovarian cancer therapy.
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Affiliation(s)
- Lia Tesfay
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT, 06030, USA
| | - Bibbin T Paul
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT, 06030, USA
| | - Poornima Hegde
- Department of Pathology, University of Connecticut Health Center, Farmington, CT, 06030, USA
| | - Molly Brewer
- Department of Obstetrics and Gynecology, University of Connecticut Health Center, Farmington, CT, 06030, USA
| | - Samrin Habbani
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT, 06030, USA
- Department of Comparative Pathobiology, Purdue University College of Veterinary Medicine, West Lafayette, IN, 47907, USA
| | - Evan Jellison
- Department of Immunology, University of Connecticut Health Center, Farmington, CT, 06030, USA
| | - Timothy Moore
- Statistical Consulting Services, Center for Open Research Resources, University of Connecticut, Storrs, CT, 06269, USA
| | - Hao Wu
- Department of Statistics, University of Connecticut, Storrs, CT, 06269, USA
| | - Suzy V Torti
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT, 06030, USA.
| | - Frank M Torti
- Department of Medicine, University of Connecticut Health Center, Farmington, CT, 06030, USA
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A High-Throughput Search for SFXN1 Physical Partners Led to the Identification of ATAD3, HSD10 and TIM50. BIOLOGY 2022; 11:biology11091298. [PMID: 36138777 PMCID: PMC9495560 DOI: 10.3390/biology11091298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/23/2022] [Accepted: 08/28/2022] [Indexed: 11/25/2022]
Abstract
Simple Summary Mitochondria are central players in cell fate and cell death. Indeed, mitochondrial dysfunction has been observed in many diseases, including neurodegenerative diseases. The activity of these organelles relies on numerous mitochondrial transporters, among which the sideroflexins have received little attention to date despite their emerging importance in human health. To better understand the cellular functions of these transporters and their associations with diseases, we herein investigated the molecular partners of one human sideroflexin, SFXN1. Several proteins capable of interacting with SFXN1 were identified, including ATAD3 and HSD10, two mitochondrial proteins linked to neuronal disorders. Abstract Sideroflexins (SFXN, SLC56) are a family of evolutionarily conserved mitochondrial carriers potentially involved in iron homeostasis. One member of the SFXN family is SFXN1, recently identified as a human mitochondrial serine transporter. However, little is known about the SFXN1 interactome, necessitating a high-throughput search to better characterize SFXN1 mitochondrial functions. Via co-immunoprecipitation followed by shotgun mass spectrometry (coIP-MS), we identified 96 putative SFXN1 interactors in the MCF7 human cell line. Our in silico analysis of the SFXN1 interactome highlights biological processes linked to mitochondrial organization, electron transport chains and transmembrane transport. Among the potential physical partners, ATAD3A and 17β-HSD10, two proteins associated with neurological disorders, were confirmed using different human cell lines. Nevertheless, further work will be needed to investigate the significance of these interactions.
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Østergård Jensen S, Christen M, Rondahl V, Holland CT, Jagannathan V, Leeb T, Giger U. EHBP1L1 Frameshift Deletion in English Springer Spaniel Dogs with Dyserythropoietic Anemia and Myopathy Syndrome (DAMS) or Neonatal Losses. Genes (Basel) 2022; 13:genes13091533. [PMID: 36140701 PMCID: PMC9498568 DOI: 10.3390/genes13091533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 08/20/2022] [Accepted: 08/22/2022] [Indexed: 11/16/2022] Open
Abstract
Hereditary myopathies are well documented in dogs, whereas hereditary dyserythropoietic anemias are rarely seen. The aim of this study was to further characterize the clinical and clinicopathological features of and to identify the causative genetic variant for a dyserythropoietic anemia and myopathy syndrome (DAMS) in English springer spaniel dogs (ESSPs). Twenty-six ESSPs, including five dogs with DAMS and two puppies that died perinatally, were studied. Progressive weakness, muscle atrophy—particularly of the temporal and pelvic muscles—trismus, dysphagia, and regurgitation due to megaesophagus were observed at all ages. Affected dogs had a non-regenerative, microcytic hypochromic anemia with metarubricytosis, target cells, and acanthocytes. Marked erythroid hyperplasia and dyserythropoiesis with non-orderly maturation of erythrocytes and inappropriate microcytic metarubricytosis were present. Muscle biopsies showed centralized nuclei, central pallor, lipocyte infiltrates, and fibrosis, which was consistent with centronuclear myopathy. The genome sequencing of two affected dogs was compared to 782 genomes of different canine breeds. A homozygous frameshift single-base deletion in EHBP1L1 was identified; this gene was not previously associated with DAMS. Pedigree analysis confirmed that the affected ESSPs were related. Variant genotyping showed appropriate complete segregation in the family, which was consistent with an autosomal recessive mode of inheritance. This study expands the known genotype–phenotype correlation of EHBP1L1 and the list of potential causative genes in dyserythropoietic anemias and myopathies in humans. EHBP1L1 deficiency was previously reported as perinatally lethal in humans and knockout mice. Our findings enable the genetic testing of ESSP dogs for early diagnosis and disease prevention through targeted breeding strategies.
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Affiliation(s)
- Sarah Østergård Jensen
- Clinical Pathology Laboratory, The Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
- AniCura Small Animal Referral Hospital Bagarmossen, Ljusnevägen 17, Bagarmossen, 128 48 Stockholm, Sweden
| | - Matthias Christen
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001 Bern, Switzerland
| | | | - Christopher T. Holland
- Merewether Veterinary Hospital, Suite 2, 25 Llewellyn St, Merewether, NSW 2291, Australia
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001 Bern, Switzerland
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001 Bern, Switzerland
| | - Urs Giger
- Vetsuisse Faculty, University of Zürich, Winterthurerstrasse 260, 8057 Zürich, Switzerland
- Correspondence: ; Tel.: +1-610-565-1427
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Prospective role and immunotherapeutic targets of sideroflexin protein family in lung adenocarcinoma: evidence from bioinformatics validation. Funct Integr Genomics 2022; 22:1057-1072. [DOI: 10.1007/s10142-022-00883-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 07/08/2022] [Accepted: 07/08/2022] [Indexed: 11/27/2022]
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Yien YY, Perfetto M. Regulation of Heme Synthesis by Mitochondrial Homeostasis Proteins. Front Cell Dev Biol 2022; 10:895521. [PMID: 35832791 PMCID: PMC9272004 DOI: 10.3389/fcell.2022.895521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 05/12/2022] [Indexed: 11/19/2022] Open
Abstract
Heme plays a central role in diverse, life-essential processes that range from ubiquitous, housekeeping pathways such as respiration, to highly cell-specific ones such as oxygen transport by hemoglobin. The regulation of heme synthesis and its utilization is highly regulated and cell-specific. In this review, we have attempted to describe how the heme synthesis machinery is regulated by mitochondrial homeostasis as a means of coupling heme synthesis to its utilization and to the metabolic requirements of the cell. We have focused on discussing the regulation of mitochondrial heme synthesis enzymes by housekeeping proteins, transport of heme intermediates, and regulation of heme synthesis by macromolecular complex formation and mitochondrial metabolism. Recently discovered mechanisms are discussed in the context of the model organisms in which they were identified, while more established work is discussed in light of technological advancements.
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Yépez VA, Gusic M, Kopajtich R, Mertes C, Smith NH, Alston CL, Ban R, Beblo S, Berutti R, Blessing H, Ciara E, Distelmaier F, Freisinger P, Häberle J, Hayflick SJ, Hempel M, Itkis YS, Kishita Y, Klopstock T, Krylova TD, Lamperti C, Lenz D, Makowski C, Mosegaard S, Müller MF, Muñoz-Pujol G, Nadel A, Ohtake A, Okazaki Y, Procopio E, Schwarzmayr T, Smet J, Staufner C, Stenton SL, Strom TM, Terrile C, Tort F, Van Coster R, Vanlander A, Wagner M, Xu M, Fang F, Ghezzi D, Mayr JA, Piekutowska-Abramczuk D, Ribes A, Rötig A, Taylor RW, Wortmann SB, Murayama K, Meitinger T, Gagneur J, Prokisch H. Clinical implementation of RNA sequencing for Mendelian disease diagnostics. Genome Med 2022; 14:38. [PMID: 35379322 PMCID: PMC8981716 DOI: 10.1186/s13073-022-01019-9] [Citation(s) in RCA: 80] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 02/03/2022] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Lack of functional evidence hampers variant interpretation, leaving a large proportion of individuals with a suspected Mendelian disorder without genetic diagnosis after whole genome or whole exome sequencing (WES). Research studies advocate to further sequence transcriptomes to directly and systematically probe gene expression defects. However, collection of additional biopsies and establishment of lab workflows, analytical pipelines, and defined concepts in clinical interpretation of aberrant gene expression are still needed for adopting RNA sequencing (RNA-seq) in routine diagnostics. METHODS We implemented an automated RNA-seq protocol and a computational workflow with which we analyzed skin fibroblasts of 303 individuals with a suspected mitochondrial disease that previously underwent WES. We also assessed through simulations how aberrant expression and mono-allelic expression tests depend on RNA-seq coverage. RESULTS We detected on average 12,500 genes per sample including around 60% of all disease genes-a coverage substantially higher than with whole blood, supporting the use of skin biopsies. We prioritized genes demonstrating aberrant expression, aberrant splicing, or mono-allelic expression. The pipeline required less than 1 week from sample preparation to result reporting and provided a median of eight disease-associated genes per patient for inspection. A genetic diagnosis was established for 16% of the 205 WES-inconclusive cases. Detection of aberrant expression was a major contributor to diagnosis including instances of 50% reduction, which, together with mono-allelic expression, allowed for the diagnosis of dominant disorders caused by haploinsufficiency. Moreover, calling aberrant splicing and variants from RNA-seq data enabled detecting and validating splice-disrupting variants, of which the majority fell outside WES-covered regions. CONCLUSION Together, these results show that streamlined experimental and computational processes can accelerate the implementation of RNA-seq in routine diagnostics.
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Affiliation(s)
- Vicente A. Yépez
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
- Department of Informatics, Technical University of Munich, Garching, Germany
- Quantitative Biosciences Munich, Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
| | - Mirjana Gusic
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany
| | - Robert Kopajtich
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Christian Mertes
- Department of Informatics, Technical University of Munich, Garching, Germany
| | - Nicholas H. Smith
- Department of Informatics, Technical University of Munich, Garching, Germany
| | - Charlotte L. Alston
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH UK
- NHS Highly Specialised Services for Rare Mitochondrial Disorders, Royal Victoria Infirmary, Newcastle upon Tyne Hospitals NHS Foundation Trust, Queen Victoria Road, Newcastle upon Tyne, NE1 4LP UK
| | - Rui Ban
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
- Department of Pediatric Neurology, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Skadi Beblo
- Department of Women and Child Health, Hospital for Children and Adolescents, Center for Pediatric Research Leipzig (CPL), Center for Rare Diseases, University Hospitals, University of Leipzig, Leipzig, Germany
| | - Riccardo Berutti
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Holger Blessing
- Department for Inborn Metabolic Diseases, Children’s and Adolescents’ Hospital, University of Erlangen-Nürnberg, Erlangen, Germany
| | - Elżbieta Ciara
- Department of Medical Genetics, Children’s Memorial Health Institute, Warsaw, Poland
| | - Felix Distelmaier
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Heinrich-Heine-University, Düsseldorf, Germany
| | - Peter Freisinger
- Department of Pediatrics, Klinikum Reutlingen, Reutlingen, Germany
| | - Johannes Häberle
- University Children’s Hospital Zurich and Children’s Research Centre, Zürich, Switzerland
| | - Susan J. Hayflick
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, USA
| | - Maja Hempel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Yoshihito Kishita
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Juntendo University, Graduate School of Medicine, Tokyo, Japan
- Department of Life Science, Faculty of Science and Engineering, Kindai University, Osaka, Japan
| | - Thomas Klopstock
- Department of Neurology, Friedrich-Baur-Institute, University Hospital, Ludwig-Maximilians-Universität, Munich, Germany
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | | | - Costanza Lamperti
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Istituto Neurologico Carlo Besta, Milan, Italy
| | - Dominic Lenz
- Division of Neuropediatrics and Pediatric Metabolic Medicine, Center for Pediatric and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Christine Makowski
- Department of Pediatrics, Technical University of Munich, Munich, Germany
| | - Signe Mosegaard
- Research Unit for Molecular Medicine, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Michaela F. Müller
- Department of Informatics, Technical University of Munich, Garching, Germany
| | - Gerard Muñoz-Pujol
- Section of Inborn Errors of Metabolism-IBC, Department of Biochemistry and Molecular Genetics, Hospital Clínic, IDIBAPS, CIBERER, Barcelona, Spain
| | - Agnieszka Nadel
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Akira Ohtake
- Department of Pediatrics & Clinical Genomics, Faculty of Medicine, Saitama Medical University, Saitama, Japan
- Center for Intractable Diseases, Saitama Medical University Hospital, Saitama, Japan
| | - Yasushi Okazaki
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Juntendo University, Graduate School of Medicine, Tokyo, Japan
| | - Elena Procopio
- Inborn Metabolic and Muscular Disorders Unit, Anna Meyer Children Hospital, Florence, Italy
| | - Thomas Schwarzmayr
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Joél Smet
- Department of Pediatric Neurology and Metabolism, Ghent University Hospital, Ghent, Belgium
| | - Christian Staufner
- Division of Neuropediatrics and Pediatric Metabolic Medicine, Center for Pediatric and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Sarah L. Stenton
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Tim M. Strom
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Caterina Terrile
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Frederic Tort
- Section of Inborn Errors of Metabolism-IBC, Department of Biochemistry and Molecular Genetics, Hospital Clínic, IDIBAPS, CIBERER, Barcelona, Spain
| | - Rudy Van Coster
- Department of Pediatric Neurology and Metabolism, Ghent University Hospital, Ghent, Belgium
| | - Arnaud Vanlander
- Department of Pediatric Neurology and Metabolism, Ghent University Hospital, Ghent, Belgium
| | - Matias Wagner
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Manting Xu
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
- Department of Pediatric Neurology, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Fang Fang
- Department of Pediatric Neurology, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Daniele Ghezzi
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Istituto Neurologico Carlo Besta, Milan, Italy
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Johannes A. Mayr
- University Children’s Hospital, Paracelsus Medical University Salzburg, Salzburg, Austria
| | | | - Antonia Ribes
- Section of Inborn Errors of Metabolism-IBC, Department of Biochemistry and Molecular Genetics, Hospital Clínic, IDIBAPS, CIBERER, Barcelona, Spain
| | - Agnès Rötig
- Université de Paris, Institut Imagine, INSERM UMR 1163, Paris, France
| | - Robert W. Taylor
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH UK
- NHS Highly Specialised Services for Rare Mitochondrial Disorders, Royal Victoria Infirmary, Newcastle upon Tyne Hospitals NHS Foundation Trust, Queen Victoria Road, Newcastle upon Tyne, NE1 4LP UK
| | - Saskia B. Wortmann
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
- University Children’s Hospital, Paracelsus Medical University Salzburg, Salzburg, Austria
- Amalia Children’s Hospital, Radboudumc Nijmegen, Nijmegen, The Netherlands
| | - Kei Murayama
- Department of Metabolism, Chiba Children’s Hospital, Chiba, Japan
| | - Thomas Meitinger
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
| | - Julien Gagneur
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
- Department of Informatics, Technical University of Munich, Garching, Germany
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Holger Prokisch
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
- Department of Pediatric Neurology, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
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11
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Jackson TD, Crameri JJ, Muellner-Wong L, Frazier AE, Palmer CS, Formosa LE, Hock DH, Fujihara KM, Stait T, Sharpe AJ, Thorburn DR, Ryan MT, Stroud DA, Stojanovski D. Sideroflexin 4 is a complex I assembly factor that interacts with the MCIA complex and is required for the assembly of the ND2 module. Proc Natl Acad Sci U S A 2022; 119:e2115566119. [PMID: 35333655 PMCID: PMC9060475 DOI: 10.1073/pnas.2115566119] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 02/11/2022] [Indexed: 12/23/2022] Open
Abstract
SignificanceMitochondria are double-membraned eukaryotic organelles that house the proteins required for generation of ATP, the energy currency of cells. ATP generation within mitochondria is performed by five multisubunit complexes (complexes I to V), the assembly of which is an intricate process. Mutations in subunits of these complexes, or the suite of proteins that help them assemble, lead to a severe multisystem condition called mitochondrial disease. We show that SFXN4, a protein that causes mitochondrial disease when mutated, assists with the assembly of complex I. This finding explains why mutations in SFXN4 cause mitochondrial disease and is surprising because SFXN4 belongs to a family of amino acid transporter proteins, suggesting that it has undergone a dramatic shift in function through evolution.
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Affiliation(s)
- Thomas D. Jackson
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, VIC 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Jordan J. Crameri
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, VIC 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Linden Muellner-Wong
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, VIC 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, VIC 3052, Australia
| | - Ann E. Frazier
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Catherine S. Palmer
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, VIC 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Luke E. Formosa
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3168, Australia
| | - Daniella H. Hock
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, VIC 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Kenji M. Fujihara
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Tegan Stait
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, VIC 3052, Australia
- Victorian Clinical Genetic Services, Royal Children’s Hospital, Melbourne, VIC 3052, Australia
| | - Alice J. Sharpe
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3168, Australia
| | - David R. Thorburn
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
- Victorian Clinical Genetic Services, Royal Children’s Hospital, Melbourne, VIC 3052, Australia
| | - Michael T. Ryan
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3168, Australia
| | - David A. Stroud
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, VIC 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, VIC 3052, Australia
| | - Diana Stojanovski
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, VIC 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia
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12
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Beecher G, Fleming MD, Liewluck T. Hereditary myopathies associated with hematological abnormalities. Muscle Nerve 2022; 65:374-390. [PMID: 34985130 DOI: 10.1002/mus.27474] [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: 08/09/2021] [Revised: 12/10/2021] [Accepted: 12/11/2021] [Indexed: 01/19/2023]
Abstract
The diagnostic evaluation of a patient with suspected hereditary muscle disease can be challenging. Clinicians rely largely on clinical history and examination features, with additional serological, electrodiagnostic, radiologic, histopathologic, and genetic investigations assisting in definitive diagnosis. Hematological testing is inexpensive and widely available, but frequently overlooked in the hereditary myopathy evaluation. Hematological abnormalities are infrequently encountered in this setting; however, their presence provides a valuable clue, helps refine the differential diagnosis, tailors further investigation, and assists interpretation of variants of uncertain significance. A diverse spectrum of hematological abnormalities is associated with hereditary myopathies, including anemias, leukocyte abnormalities, and thrombocytopenia. Recurrent rhabdomyolysis in certain glycolytic enzymopathies co-occurs with hemolytic anemia, often chronic and mild in phosphofructokinase and phosphoglycerate kinase deficiencies, or acute and fever-associated in aldolase-A and triosephosphate isomerase deficiency. Sideroblastic anemia, commonly severe, accompanies congenital-to-childhood onset mitochondrial myopathies including Pearson marrow-pancreas syndrome and mitochondrial myopathy, lactic acidosis, and sideroblastic anemia phenotypes. Congenital megaloblastic macrocytic anemia and mitochondrial dysfunction characterize SFXN4-related myopathy. Neutropenia, chronic or cyclical, with recurrent infections, infantile-to-childhood onset skeletal myopathy and cardiomyopathy are typical of Barth syndrome, while chronic neutropenia without infection occurs rarely in DNM2-centronuclear myopathy. Peripheral eosinophilia may accompany eosinophilic inflammation in recessive calpainopathy. Lipid accumulation in leukocytes on peripheral blood smear (Jordans' anomaly) is pathognomonic for neutral lipid storage diseases. Mild thrombocytopenia occurs in autosomal dominant, childhood-onset STIM1 tubular aggregate myopathy, STIM1 and ORAI1 deficiency syndromes, and GNE myopathy. Herein, we review these hereditary myopathies in which hematological features play a prominent role.
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Affiliation(s)
- Grayson Beecher
- Division of Neuromuscular Medicine, Department of Neurology, Mayo Clinic, Rochester, Minnesota, USA
| | - Mark D Fleming
- Department of Pathology, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Teerin Liewluck
- Division of Neuromuscular Medicine, Department of Neurology, Mayo Clinic, Rochester, Minnesota, USA
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13
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Ziemann M, Lim SC, Kang Y, Samuel S, Sanchez IL, Gantier M, Stojanovski D, McKenzie M. MicroRNA-101-3p Modulates Mitochondrial Metabolism via the Regulation of Complex II Assembly. J Mol Biol 2021; 434:167361. [PMID: 34808225 DOI: 10.1016/j.jmb.2021.167361] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/17/2021] [Accepted: 11/11/2021] [Indexed: 12/27/2022]
Abstract
MicroRNA-101-3p (miR-101-3p) is a tumour suppressor that regulates cancer proliferation and apoptotic signalling. Loss of miR-101-3p increases the expression of the Polycomb Repressive Complex 2 (PRC2) subunit enhancer of zeste homolog 2 (EZH2), resulting in alterations to the epigenome and enhanced tumorigenesis. MiR-101-3p has also been shown to modulate various aspects of cellular metabolism, however little is known about the mechanisms involved. To investigate the metabolic pathways that are regulated by miR-101-3p, we performed transcriptome and functional analyses of osteosarcoma cells transfected with miR-101-3p. We found that miR-101-3p downregulates multiple mitochondrial processes, including oxidative phosphorylation, pyruvate metabolism, the citric acid cycle and phospholipid metabolism. We also found that miR-101-3p transfection disrupts the transcription of mitochondrial DNA (mtDNA) via the downregulation of the mitochondrial transcription initiation complex proteins TFB2M and Mic60. These alterations in transcript expression disrupt mitochondrial function, with significant decreases in both basal (54%) and maximal (67%) mitochondrial respiration rates. Native gel electrophoresis revealed that this diminished respiratory capacity was associated with reduced steady-state levels of mature succinate dehydrogenase (complex II), with a corresponding reduction of complex II enzymatic activity. Furthermore, miR-101-3p transfection reduced the expression of the SDHB subunit, with a concomitant disruption of the assembly of the SDHC subunit into mature complex II. Overall, we describe a new role for miR-101-3p as a modulator of mitochondrial metabolism via its regulation of multiple mitochondrial processes, including mtDNA transcription and complex II biogenesis.
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Affiliation(s)
- Mark Ziemann
- School of Life and Environmental Sciences, Faculty of Science, Engineering and Built Environment, Deakin University, 3216 Geelong, Australia. https://twitter.com/@mdziemann
| | - Sze Chern Lim
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, 3168 Melbourne, Australia
| | - Yilin Kang
- Department of Biochemistry and Pharmacology and The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, 3052 Melbourne, Australia
| | - Sona Samuel
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria 3002, Australia
| | - Isabel Lopez Sanchez
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria 3002, Australia; Ophthalmology, University of Melbourne, Department of Surgery Melbourne, Victoria 3000, Australia. https://twitter.com/@DrIsabelLopez
| | - Michael Gantier
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, 3168 Melbourne, Australia; Department of Molecular and Translational Science, Monash University, 3168 Melbourne, Australia. https://twitter.com/@GantierLab
| | - Diana Stojanovski
- Department of Biochemistry and Pharmacology and The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, 3052 Melbourne, Australia
| | - Matthew McKenzie
- School of Life and Environmental Sciences, Faculty of Science, Engineering and Built Environment, Deakin University, 3216 Geelong, Australia; Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, 3168 Melbourne, Australia; Department of Molecular and Translational Science, Monash University, 3168 Melbourne, Australia.
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14
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Dietz JV, Fox JL, Khalimonchuk O. Down the Iron Path: Mitochondrial Iron Homeostasis and Beyond. Cells 2021; 10:cells10092198. [PMID: 34571846 PMCID: PMC8468894 DOI: 10.3390/cells10092198] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 08/22/2021] [Accepted: 08/23/2021] [Indexed: 12/20/2022] Open
Abstract
Cellular iron homeostasis and mitochondrial iron homeostasis are interdependent. Mitochondria must import iron to form iron–sulfur clusters and heme, and to incorporate these cofactors along with iron ions into mitochondrial proteins that support essential functions, including cellular respiration. In turn, mitochondria supply the cell with heme and enable the biogenesis of cytosolic and nuclear proteins containing iron–sulfur clusters. Impairment in cellular or mitochondrial iron homeostasis is deleterious and can result in numerous human diseases. Due to its reactivity, iron is stored and trafficked through the body, intracellularly, and within mitochondria via carefully orchestrated processes. Here, we focus on describing the processes of and components involved in mitochondrial iron trafficking and storage, as well as mitochondrial iron–sulfur cluster biogenesis and heme biosynthesis. Recent findings and the most pressing topics for future research are highlighted.
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Affiliation(s)
- Jonathan V. Dietz
- Department of Biochemistry, University of Nebraska, Lincoln, NE 68588, USA;
| | - Jennifer L. Fox
- Department of Chemistry and Biochemistry, College of Charleston, Charleston, SC 29424, USA;
| | - Oleh Khalimonchuk
- Department of Biochemistry, University of Nebraska, Lincoln, NE 68588, USA;
- Nebraska Redox Biology Center, University of Nebraska, Lincoln, NE 68588, USA
- Fred and Pamela Buffett Cancer Center, Omaha, NE 68198, USA
- Correspondence:
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15
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Attwood MM, Schiöth HB. Characterization of Five Transmembrane Proteins: With Focus on the Tweety, Sideroflexin, and YIP1 Domain Families. Front Cell Dev Biol 2021; 9:708754. [PMID: 34350187 PMCID: PMC8327215 DOI: 10.3389/fcell.2021.708754] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 06/28/2021] [Indexed: 11/25/2022] Open
Abstract
Transmembrane proteins are involved in many essential cell processes such as signal transduction, transport, and protein trafficking, and hence many are implicated in different disease pathways. Further, as the structure and function of proteins are correlated, investigating a group of proteins with the same tertiary structure, i.e., the same number of transmembrane regions, may give understanding about their functional roles and potential as therapeutic targets. This analysis investigates the previously unstudied group of proteins with five transmembrane-spanning regions (5TM). More than half of the 58 proteins identified with the 5TM architecture belong to 12 families with two or more members. Interestingly, more than half the proteins in the dataset function in localization activities through movement or tethering of cell components and more than one-third are involved in transport activities, particularly in the mitochondria. Surprisingly, no receptor activity was identified within this dataset in large contrast with other TM groups. The three major 5TM families, which comprise nearly 30% of the dataset, include the tweety family, the sideroflexin family and the Yip1 domain (YIPF) family. We also analyzed the evolutionary origin of these three families. The YIPF family appears to be the most ancient with presence in bacteria and archaea, while the tweety and sideroflexin families are first found in eukaryotes. We found no evidence of common decent for these three families. About 30% of the 5TM proteins have prominent expression in the brain, liver, or testis. Importantly, 60% of these proteins are identified as cancer prognostic markers, where they are associated with clinical outcomes of various tumor types. Nearly 10% of the 5TMs are still not fully characterized and further investigation of their functional activities and expression is warranted. This study provides the first comprehensive analysis of proteins with the 5TM architecture, providing details of their unique characteristics.
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Affiliation(s)
- Misty M Attwood
- Functional Pharmacology, Department of Neuroscience, Uppsala University, Uppsala, Sweden
| | - Helgi B Schiöth
- Functional Pharmacology, Department of Neuroscience, Uppsala University, Uppsala, Sweden.,Institute for Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, Moscow, Russia
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16
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Rondelli CM, Perfetto M, Danoff A, Bergonia H, Gillis S, O'Neill L, Jackson L, Nicolas G, Puy H, West R, Phillips JD, Yien YY. The ubiquitous mitochondrial protein unfoldase CLPX regulates erythroid heme synthesis by control of iron utilization and heme synthesis enzyme activation and turnover. J Biol Chem 2021; 297:100972. [PMID: 34280433 PMCID: PMC8361296 DOI: 10.1016/j.jbc.2021.100972] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 07/13/2021] [Accepted: 07/15/2021] [Indexed: 11/19/2022] Open
Abstract
Heme plays a critical role in catalyzing life-essential redox reactions in all cells, and its synthesis must be tightly balanced with cellular requirements. Heme synthesis in eukaryotes is tightly regulated by the mitochondrial AAA+ unfoldase CLPX (caseinolytic mitochondrial matrix peptidase chaperone subunit X), which promotes heme synthesis by activation of δ-aminolevulinate synthase (ALAS/Hem1) in yeast and regulates turnover of ALAS1 in human cells. However, the specific mechanisms by which CLPX regulates heme synthesis are unclear. In this study, we interrogated the mechanisms by which CLPX regulates heme synthesis in erythroid cells. Quantitation of enzyme activity and protein degradation showed that ALAS2 stability and activity were both increased in the absence of CLPX, suggesting that CLPX primarily regulates ALAS2 by control of its turnover, rather than its activation. However, we also showed that CLPX is required for PPOX (protoporphyrinogen IX oxidase) activity and maintenance of FECH (ferrochelatase) levels, which are the terminal enzymes in heme synthesis, likely accounting for the heme deficiency and porphyrin accumulation observed in Clpx−/− cells. Lastly, CLPX is required for iron utilization for hemoglobin synthesis during erythroid differentiation. Collectively, our data show that the role of CLPX in yeast ALAS/Hem1 activation is not conserved in vertebrates as vertebrates rely on CLPX to regulate ALAS turnover as well as PPOX and FECH activity. Our studies reveal that CLPX mutations may cause anemia and porphyria via dysregulation of ALAS, FECH, and PPOX activities, as well as of iron metabolism.
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Affiliation(s)
- Catherine M Rondelli
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA
| | - Mark Perfetto
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA; Pittsburgh Heart, Lung and Blood Vascular Medicine Institute and Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Aidan Danoff
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA
| | - Hector Bergonia
- Division of Hematology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Samantha Gillis
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA
| | - Leah O'Neill
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA
| | - Laurie Jackson
- Division of Hematology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Gael Nicolas
- Centre de Recherche sur l'inflammation, Université Paris Diderot, Site Bichat, Sorbonne Paris Cité, Paris, France
| | - Herve Puy
- Centre de Recherche sur l'inflammation, Université Paris Diderot, Site Bichat, Sorbonne Paris Cité, Paris, France; Centre Français des Porphyries, Hôpital Louis Mourier, APHP, Colombes, France
| | - Richard West
- Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, USA
| | - John D Phillips
- Division of Hematology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Yvette Y Yien
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA; Pittsburgh Heart, Lung and Blood Vascular Medicine Institute and Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.
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17
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Jayaraman A, Zhou T, Jayaraman S. Histone Modifier Differentially Regulates Gene Expression and Unravels Survival Role of MicroRNA-494 in Jurkat Leukemia. Microrna 2021; 10:39-50. [PMID: 33845753 DOI: 10.2174/2211536610666210412153322] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 11/12/2020] [Accepted: 02/22/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Although the protein-coding genes are subject to histone hyperacetylation-mediated regulation, it is unclear whether microRNAs are similarly regulated in the T cell leukemia Jurkat. OBJECTIVE To determine whether treatment with the histone modifier Trichostatin A could concurrently alter the expression profiles of microRNAs and protein-coding genes. METHODS Changes in histone hyperacetylation and viability in response to drug treatment were analyzed, respectively, using western blotting and flow cytometry. Paired global expression profiling of microRNAs and coding genes was performed and highly regulated genes validated by qRT-PCR. The interrelationships between the drug-induced miR-494 upregulation, the expression of putative target genes, and T cell receptor-mediated apoptosis were evaluated using qRT-PCR, flow cytometry, and western blotting following lipid-mediated transfection with specific anti-microRNA inhibitors. RESULTS Treatment of Jurkat cells with Trichostatin A resulted in histone hyperacetylation and apoptosis. Global expression profiling indicated prominent upregulation of miR-494 in contrast to differential regulation of many protein-coding and non-coding genes validated by qRT-PCR. Although transfection with synthetic anti-miR-494 inhibitors failed to block drug-induced apoptosis or miR-494 upregulation, it induced the transcriptional repression of the PVRIG gene. Surprisingly, miR-494 inhibition in conjunction with low doses of Trichostatin A enhanced the weak T cell receptor-mediated apoptosis, indicating a subtle pro-survival role of miR-494. Interestingly, this pro-survival effect was overwhelmed by mitogen-mediated T cell activation and higher drug doses, which mediated caspase-dependent apoptosis. CONCLUSION Our results unravel a pro-survival function of miR-494 and its putative interaction with the PVRIG gene and the apoptotic machinery in Jurkat cells.
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Affiliation(s)
- Arathi Jayaraman
- Dept. of Medicine, the University of Illinois at Chicago, Chicago, IL 60612. United States
| | - Tong Zhou
- Dept. of Medicine, the University of Illinois at Chicago, Chicago, IL 60612. United States
| | - Sundararajan Jayaraman
- Dept. of Medicine, the University of Illinois at Chicago, Chicago, IL 60612. United States
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18
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Acoba MG, Alpergin ESS, Renuse S, Fernández-Del-Río L, Lu YW, Khalimonchuk O, Clarke CF, Pandey A, Wolfgang MJ, Claypool SM. The mitochondrial carrier SFXN1 is critical for complex III integrity and cellular metabolism. Cell Rep 2021; 34:108869. [PMID: 33730581 PMCID: PMC8048093 DOI: 10.1016/j.celrep.2021.108869] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 01/18/2021] [Accepted: 02/24/2021] [Indexed: 12/13/2022] Open
Abstract
Mitochondrial carriers (MCs) mediate the passage of small molecules across the inner mitochondrial membrane (IMM), enabling regulated crosstalk between compartmentalized reactions. Despite MCs representing the largest family of solute carriers in mammals, most have not been subjected to a comprehensive investigation, limiting our understanding of their metabolic contributions. Here, we functionally characterize SFXN1, a member of the non-canonical, sideroflexin family. We find that SFXN1, an integral IMM protein with an uneven number of transmembrane domains, is a TIM22 complex substrate. SFXN1 deficiency leads to mitochondrial respiratory chain impairments, most detrimental to complex III (CIII) biogenesis, activity, and assembly, compromising coenzyme Q levels. The CIII dysfunction is independent of one-carbon metabolism, the known primary role for SFXN1 as a mitochondrial serine transporter. Instead, SFXN1 supports CIII function by participating in heme and α-ketoglutarate metabolism. Our findings highlight the multiple ways that SFXN1-based amino acid transport impacts mitochondrial and cellular metabolic efficiency.
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Affiliation(s)
- Michelle Grace Acoba
- Department of Physiology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ebru S Selen Alpergin
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Santosh Renuse
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; McKusick-Nathans Institute of Genetic Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Lucía Fernández-Del-Río
- Department of Chemistry and Biochemistry and Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Ya-Wen Lu
- Department of Physiology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Oleh Khalimonchuk
- Department of Biochemistry and Nebraska Redox Biology Center, University of Nebraska, Lincoln, NE 68588, USA; Fred & Pamela Buffett Cancer Center, Omaha, NE 68198, USA
| | - Catherine F Clarke
- Department of Chemistry and Biochemistry and Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Akhilesh Pandey
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; McKusick-Nathans Institute of Genetic Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Departments of Pathology and Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Michael J Wolfgang
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Steven M Claypool
- Department of Physiology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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19
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Bao B, An W, Lu Q, Wang Y, Lu Z, Tu J, Zhang H, Duan Y, Yuan W, Zhu X, Jia H. Sfxn1 is essential for erythrocyte maturation via facilitating hemoglobin production in zebrafish. Biochim Biophys Acta Mol Basis Dis 2021; 1867:166096. [PMID: 33524530 DOI: 10.1016/j.bbadis.2021.166096] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 12/19/2020] [Accepted: 01/26/2021] [Indexed: 12/31/2022]
Abstract
Previous reports revealed that mutation of mitochondrial inner-membrane located protein SFXN1 led to pleiotropic hematological and skeletal defects in mice, associated with the presence of hypochromic erythroid cell, iron overload in mitochondrion of erythroblast and the development of sideroblastic anemia (SA). However, the potential role of sfxn1 during erythrocyte differentiation and the development of anemia, especially the pathological molecular mechanism still remains elusive. In this study, the correlation between sfxn1 and erythroid cell development is explored through zebrafish in vivo coupled with human hematopoietic cells assay ex vivo. Both knockdown and knockout of sfxn1 result in hypochromic anemia phenotype in zebrafish. Further analyses demonstrate that the development of anemia attributes to the biosynthetic deficiency of hemoglobin, which is caused by the biosynthetic disorder of heme that associates with one‑carbon (1C) metabolism process of mitochondrial branch in erythrocyte. Sfxn1 is also involved in the differentiation and maturation of erythrocyte in inducible human umbilical cord blood stem cells. In addition, we found that functional disruption of sfxn1 causes hypochromic anemia that is distinct from SA. These findings reveal that sfxn1 is genetically conserved and essential for the maturation of erythrocyte via facilitating the production of hemoglobin, which may provide a possible guidance for the future clinical treatment of sfxn1 mutation associated hematological disorders.
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Affiliation(s)
- Binghao Bao
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, China
| | - Wenbin An
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Disease Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, ,China
| | - Qunwei Lu
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, China
| | - Yaqin Wang
- Department of Pediatrics, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Zhichao Lu
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, China
| | - Jiayi Tu
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, China
| | - Heng Zhang
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, China
| | - Yongjuan Duan
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Disease Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, ,China
| | - Weiping Yuan
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Disease Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, ,China.
| | - Xiaofan Zhu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Disease Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, ,China.
| | - Haibo Jia
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, China.
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20
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Tifoun N, De las Heras JM, Guillaume A, Bouleau S, Mignotte B, Le Floch N. Insights into the Roles of the Sideroflexins/SLC56 Family in Iron Homeostasis and Iron-Sulfur Biogenesis. Biomedicines 2021; 9:103. [PMID: 33494450 PMCID: PMC7911444 DOI: 10.3390/biomedicines9020103] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 01/25/2023] Open
Abstract
Sideroflexins (SLC56 family) are highly conserved multi-spanning transmembrane proteins inserted in the inner mitochondrial membrane in eukaryotes. Few data are available on their molecular function, but since their first description, they were thought to be metabolite transporters probably required for iron utilization inside the mitochondrion. Such as numerous mitochondrial transporters, sideroflexins remain poorly characterized. The prototypic member SFXN1 has been recently identified as the previously unknown mitochondrial transporter of serine. Nevertheless, pending questions on the molecular function of sideroflexins remain unsolved, especially their link with iron metabolism. Here, we review the current knowledge on sideroflexins, their presumed mitochondrial functions and the sparse-but growing-evidence linking sideroflexins to iron homeostasis and iron-sulfur cluster biogenesis. Since an imbalance in iron homeostasis can be detrimental at the cellular and organismal levels, we also investigate the relationship between sideroflexins, iron and physiological disorders. Investigating Sideroflexins' functions constitutes an emerging research field of great interest and will certainly lead to the main discoveries of mitochondrial physio-pathology.
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Affiliation(s)
- Nesrine Tifoun
- LGBC, UVSQ, Université Paris-Saclay, 78000 Versailles, France; (N.T.); (J.M.D.l.H.); (A.G.); (S.B.); (B.M.)
| | - José M. De las Heras
- LGBC, UVSQ, Université Paris-Saclay, 78000 Versailles, France; (N.T.); (J.M.D.l.H.); (A.G.); (S.B.); (B.M.)
| | - Arnaud Guillaume
- LGBC, UVSQ, Université Paris-Saclay, 78000 Versailles, France; (N.T.); (J.M.D.l.H.); (A.G.); (S.B.); (B.M.)
| | - Sylvina Bouleau
- LGBC, UVSQ, Université Paris-Saclay, 78000 Versailles, France; (N.T.); (J.M.D.l.H.); (A.G.); (S.B.); (B.M.)
| | - Bernard Mignotte
- LGBC, UVSQ, Université Paris-Saclay, 78000 Versailles, France; (N.T.); (J.M.D.l.H.); (A.G.); (S.B.); (B.M.)
- École Pratique des Hautes Études, PSL University, 75014 Paris, France
| | - Nathalie Le Floch
- LGBC, UVSQ, Université Paris-Saclay, 78000 Versailles, France; (N.T.); (J.M.D.l.H.); (A.G.); (S.B.); (B.M.)
- GCGP Department, IUT de Vélizy/Rambouillet, UVSQ, Université Paris-Saclay, 78120 Rambouillet, France
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21
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Sedley L. Advances in Nutritional Epigenetics-A Fresh Perspective for an Old Idea. Lessons Learned, Limitations, and Future Directions. Epigenet Insights 2020; 13:2516865720981924. [PMID: 33415317 PMCID: PMC7750768 DOI: 10.1177/2516865720981924] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 11/25/2020] [Indexed: 12/11/2022] Open
Abstract
Nutritional epigenetics is a rapidly expanding field of research, and the natural modulation of the genome is a non-invasive, sustainable, and personalized alternative to gene-editing for chronic disease management. Genetic differences and epigenetic inflexibility resulting in abnormal gene expression, differential or aberrant methylation patterns account for the vast majority of diseases. The expanding understanding of biological evolution and the environmental influence on epigenetics and natural selection requires relearning of once thought to be well-understood concepts. This research explores the potential for natural modulation by the less understood epigenetic modifications such as ubiquitination, nitrosylation, glycosylation, phosphorylation, and serotonylation concluding that the under-appreciated acetylation and mitochondrial dependant downstream epigenetic post-translational modifications may be the pinnacle of the epigenomic hierarchy, essential for optimal health, including sustainable cellular energy production. With an emphasis on lessons learned, this conceptional exploration provides a fresh perspective on methylation, demonstrating how increases in environmental methane drive an evolutionary down regulation of endogenous methyl groups synthesis and demonstrates how epigenetic mechanisms are cell-specific, making supplementation with methyl cofactors throughout differentiation unpredictable. Interference with the epigenomic hierarchy may result in epigenetic inflexibility, symptom relief and disease concomitantly and may be responsible for the increased incidence of neurological disease such as autism spectrum disorder.
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Affiliation(s)
- Lynda Sedley
- Bachelor of Health Science (Nutritional Medicine),
GC Biomedical Science (Genomics), The Research and Educational Institute of
Environmental and Nutritional Epigenetics, Queensland, Australia
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22
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Gyimesi G, Hediger MA. Sequence Features of Mitochondrial Transporter Protein Families. Biomolecules 2020; 10:E1611. [PMID: 33260588 PMCID: PMC7761412 DOI: 10.3390/biom10121611] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/20/2020] [Accepted: 11/22/2020] [Indexed: 02/08/2023] Open
Abstract
Mitochondrial carriers facilitate the transfer of small molecules across the inner mitochondrial membrane (IMM) to support mitochondrial function and core cellular processes. In addition to the classical SLC25 (solute carrier family 25) mitochondrial carriers, the past decade has led to the discovery of additional protein families with numerous members that exhibit IMM localization and transporter-like properties. These include mitochondrial pyruvate carriers, sideroflexins, and mitochondrial cation/H+ exchangers. These transport proteins were linked to vital physiological functions and disease. Their structures and transport mechanisms are, however, still largely unknown and understudied. Protein sequence analysis per se can often pinpoint hotspots that are of functional or structural importance. In this review, we summarize current knowledge about the sequence features of mitochondrial transporters with a special focus on the newly included SLC54, SLC55 and SLC56 families of the SLC solute carrier superfamily. Taking a step further, we combine sequence conservation analysis with transmembrane segment and secondary structure prediction methods to extract residue positions and sequence motifs that likely play a role in substrate binding, binding site gating or structural stability. We hope that our review will help guide future experimental efforts by the scientific community to unravel the transport mechanisms and structures of these novel mitochondrial carriers.
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Affiliation(s)
- Gergely Gyimesi
- Membrane Transport Discovery Lab, Department of Nephrology and Hypertension, and Department of Biomedical Research, Inselspital, University of Bern, Kinderklinik, Freiburgstrasse 15, CH-3010 Bern, Switzerland;
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23
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Saneto RP. Mitochondrial diseases: expanding the diagnosis in the era of genetic testing. JOURNAL OF TRANSLATIONAL GENETICS AND GENOMICS 2020; 4:384-428. [PMID: 33426505 PMCID: PMC7791531 DOI: 10.20517/jtgg.2020.40] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mitochondrial diseases are clinically and genetically heterogeneous. These diseases were initially described a little over three decades ago. Limited diagnostic tools created disease descriptions based on clinical, biochemical analytes, neuroimaging, and muscle biopsy findings. This diagnostic mechanism continued to evolve detection of inherited oxidative phosphorylation disorders and expanded discovery of mitochondrial physiology over the next two decades. Limited genetic testing hampered the definitive diagnostic identification and breadth of diseases. Over the last decade, the development and incorporation of massive parallel sequencing has identified approximately 300 genes involved in mitochondrial disease. Gene testing has enlarged our understanding of how genetic defects lead to cellular dysfunction and disease. These findings have expanded the understanding of how mechanisms of mitochondrial physiology can induce dysfunction and disease, but the complete collection of disease-causing gene variants remains incomplete. This article reviews the developments in disease gene discovery and the incorporation of gene findings with mitochondrial physiology. This understanding is critical to the development of targeted therapies.
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Affiliation(s)
- Russell P. Saneto
- Center for Integrative Brain Research, Neuroscience Institute, Seattle, WA 98101, USA
- Department of Neurology/Division of Pediatric Neurology, Seattle Children’s Hospital/University of Washington, Seattle, WA 98105, USA
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24
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Keene KL, Hyacinth HI, Bis JC, Kittner SJ, Mitchell BD, Cheng YC, Pare G, Chong M, O’Donnell M, Meschia JF, Chen WM, Sale MM, Rich SS, Nalls MA, Zonderman AB, Evans MK, Wilson JG, Correa A, Markus HS, Traylor M, Lewis CM, Carty CL, Reiner A, Haessler J, Langefeld CD, Gottesman R, Mosley TH, Woo D, Yaffe K, Liu Y, Longstreth WT, Psaty BM, Kooperberg C, Lange LA, Sacco R, Rundek T, Lee JM, Cruchaga C, Furie KL, Arnett DK, Benavente OR, Grewal RP, Peddareddygari LR, Dichgans M, Malik R, Worrall BB, Fornage M. Genome-Wide Association Study Meta-Analysis of Stroke in 22 000 Individuals of African Descent Identifies Novel Associations With Stroke. Stroke 2020; 51:2454-2463. [PMID: 32693751 PMCID: PMC7387190 DOI: 10.1161/strokeaha.120.029123] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 06/18/2020] [Indexed: 01/07/2023]
Abstract
BACKGROUND AND PURPOSE Stroke is a complex disease with multiple genetic and environmental risk factors. Blacks endure a nearly 2-fold greater risk of stroke and are 2× to 3× more likely to die from stroke than European Americans. METHODS The COMPASS (Consortium of Minority Population Genome-Wide Association Studies of Stroke) has conducted a genome-wide association meta-analysis of stroke in >22 000 individuals of African ancestry (3734 cases, 18 317 controls) from 13 cohorts. RESULTS In meta-analyses, we identified one single nucleotide polymorphism (rs55931441) near the HNF1A gene that reached genome-wide significance (P=4.62×10-8) and an additional 29 variants with suggestive evidence of association (P<1×10-6), representing 24 unique loci. For validation, a look-up analysis for a 100 kb region flanking the COMPASS single nucleotide polymorphism was performed in SiGN (Stroke Genetics Network) Europeans, SiGN Hispanics, and METASTROKE (Europeans). Using a stringent Bonferroni correction P value of 2.08×10-3 (0.05/24 unique loci), we were able to validate associations at the HNF1A locus in both SiGN (P=8.18×10-4) and METASTROKE (P=1.72×10-3) European populations. Overall, 16 of 24 loci showed evidence for validation across multiple populations. Previous studies have reported associations between variants in the HNF1A gene and lipids, C-reactive protein, and risk of coronary artery disease and stroke. Suggestive associations with variants in the SFXN4 and TMEM108 genes represent potential novel ischemic stroke loci. CONCLUSIONS These findings represent the most thorough investigation of genetic determinants of stroke in individuals of African descent, to date.
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Affiliation(s)
- Keith L. Keene
- Department of Biology; Brody School of Medicine Center for Health Disparities, East Carolina University, Greenville, NC
| | - Hyacinth I. Hyacinth
- Aflac Cancer and Blood Disorder Center of Emory University and Children’s Healthcare of Atlanta University, Atlanta, GA
| | | | - Steven J. Kittner
- Baltimore Veterans Administration Medical Center and University of Maryland School of Medicine, Baltimore, MD
| | - Braxton D. Mitchell
- Baltimore Veterans Administration Medical Center and University of Maryland School of Medicine, Baltimore, MD
| | - Yu-Ching Cheng
- Baltimore Veterans Administration Medical Center and University of Maryland School of Medicine, Baltimore, MD
| | - Guillaume Pare
- McMaster University and Population Health Research Institute, Hamilton Ontario
| | - Michael Chong
- McMaster University and Population Health Research Institute, Hamilton Ontario
| | | | | | - Wei-Min Chen
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA
| | - Michele M. Sale
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA
| | - Mike A. Nalls
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD
- Data Tecnica International, Glen Echo, MD
| | - Alan B. Zonderman
- Laboratory of Epidemiology and Population Science, National Institute on Aging, Baltimore, MD
| | - Michele K. Evans
- Laboratory of Epidemiology and Population Science, National Institute on Aging, Baltimore, MD
| | | | - Adolfo Correa
- University of Mississippi Medical Center, Jackson, MS
| | | | - Matthew Traylor
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, United Kingdom
| | - Cathryn M. Lewis
- Social, Genetic and Developmental Psychiatry Centre, King’s College London, London, United Kingdom
| | - Cara L. Carty
- Initiative for Research and Education to Advance Community Health, Washington State University, Seattle, WA
| | - Alexander Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Jeff Haessler
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Carl D. Langefeld
- Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC
| | | | | | - Daniel Woo
- Department of Neurology, University of Cincinnati, Cincinnati, OH
| | | | - YongMei Liu
- Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC
| | | | - Bruce M. Psaty
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology and Health Services, University of Washington, Seattle, WA; Kaiser Permanente Washington Health Research Institute, Seattle, WA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | | | - Ralph Sacco
- University of Miami, Miller School of Medicine, Miami, FL
| | - Tatjana Rundek
- University of Miami, Miller School of Medicine, Miami, FL
| | - Jin-Moo Lee
- Washington University School of Medicine, St. Louis, MO
| | | | - Karen L. Furie
- Brown University Warren Alpert Medical School, Providence, RI
| | - Donna K. Arnett
- University of Kentucky, College of Public Health, Lexington, KY
| | | | - Raji P. Grewal
- Neuroscience Institute, Saint Francis Medical Center, Trenton, NJ
| | | | - Martin Dichgans
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Rainer Malik
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Germany
| | | | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX
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25
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Impact of cardiovascular involvement on the clinical course of paediatric mitochondrial disorders. Orphanet J Rare Dis 2020; 15:196. [PMID: 32736646 PMCID: PMC7393884 DOI: 10.1186/s13023-020-01466-w] [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: 05/21/2020] [Accepted: 07/21/2020] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Primary mitochondrial disorders (PMD) are rare conditions resulting in progressive multi-organ failure. Cardiovascular involvement (CVI) has been reported in paediatric patients. However, its age-related prevalence, clinical presentation and prognostic impact are unresolved. We detailed CVI in a cohort of children diagnosed with PMD over two decades at a tertiary referral centre. RESULTS We enrolled 86 PMD patients (M/F = 30/56; mean age 6.4 ± 8.58 years). CVI was detected in 31 patients (36%), with mean age at onset of 5.7 ± 7.8 years including the pre- and neonatal phase in 14, often representing the first sign of PMD (42% of those with CVI). Heart disease resulted more common in males and in children with specific aetiologies (Barth, TMEM70 and MELAS syndromes). Hypertrophic, non-compaction and dilated cardiomyopathies were the prevalent disorders, although pulmonary arterial hypertension was also found. Adverse cardiac events (heart failure, resuscitated cardiac arrest, ICD/PM implantation, sudden death) occurred in 19% of children with CVI over a follow-up period of 5.4 ± 4.3 years. All-cause mortality was higher in patients with CVI compared to those without CVI (45.1% vs 21.8%; p < 0.01); female sex, age at onset < 5 years, acute heart failure at presentation and diabetes also proved independent predictors of outcome. CONCLUSION Cardiovascular involvement occurred in over one-third of children diagnosed with PMD, often at a very early age, and was associated with adverse prognosis. Final outcome of PMD-related CVI was influenced by the specific underlying aetiology, suggesting the need for tailored management of heart failure and sudden death prevention.
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26
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La Morgia C, Maresca A, Caporali L, Valentino ML, Carelli V. Mitochondrial diseases in adults. J Intern Med 2020; 287:592-608. [PMID: 32463135 DOI: 10.1111/joim.13064] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/07/2020] [Accepted: 02/21/2020] [Indexed: 02/07/2023]
Abstract
Mitochondrial medicine is a field that expanded exponentially in the last 30 years. Individually rare, mitochondrial diseases as a whole are probably the most frequent genetic disorder in adults. The complexity of their genotype-phenotype correlation, in terms of penetrance and clinical expressivity, natural history and diagnostic algorithm derives from the dual genetic determination. In fact, in addition to the about 1.500 genes encoding mitochondrial proteins that reside in the nuclear genome (nDNA), we have the 13 proteins encoded by the mitochondrial genome (mtDNA), for which 22 specific tRNAs and 2 rRNAs are also needed. Thus, besides Mendelian genetics, we need to consider all peculiarities of how mtDNA is inherited, maintained and expressed to fully understand the pathogenic mechanisms of these disorders. Yet, from the initial restriction to the narrow field of oxidative phosphorylation dysfunction, the landscape of mitochondrial functions impinging on cellular homeostasis, driving life and death, is impressively enlarged. Finally, from the clinical standpoint, starting from the neuromuscular field, where brain and skeletal muscle were the primary targets of mitochondrial dysfunction as energy-dependent tissues, after three decades virtually any subspecialty of medicine is now involved. We will summarize the key clinical pictures and pathogenic mechanisms of mitochondrial diseases in adults.
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Affiliation(s)
- C La Morgia
- From the, Dipartimento di Scienze Biomediche e Neuromotorie, Università di Bologna, Bologna, Italy.,IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna, Italy
| | - A Maresca
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna, Italy
| | - L Caporali
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna, Italy
| | - M L Valentino
- From the, Dipartimento di Scienze Biomediche e Neuromotorie, Università di Bologna, Bologna, Italy.,IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna, Italy
| | - V Carelli
- From the, Dipartimento di Scienze Biomediche e Neuromotorie, Università di Bologna, Bologna, Italy.,IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna, Italy
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27
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Forward genetic analysis using OCT screening identifies Sfxn3 mutations leading to progressive outer retinal degeneration in mice. Proc Natl Acad Sci U S A 2020; 117:12931-12942. [PMID: 32457148 DOI: 10.1073/pnas.1921224117] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Retinal disease and loss of vision can result from any disruption of the complex pathways controlling retinal development and homeostasis. Forward genetics provides an excellent tool to find, in an unbiased manner, genes that are essential to these processes. Using N-ethyl-N-nitrosourea mutagenesis in mice in combination with a screening protocol using optical coherence tomography (OCT) and automated meiotic mapping, we identified 11 mutations presumably causative of retinal phenotypes in genes previously known to be essential for retinal integrity. In addition, we found multiple statistically significant gene-phenotype associations that have not been reported previously and decided to target one of these genes, Sfxn3 (encoding sideroflexin-3), using CRISPR/Cas9 technology. We demonstrate, using OCT, light microscopy, and electroretinography, that two Sfxn3 -/- mouse lines developed progressive and severe outer retinal degeneration. Electron microscopy showed thinning of the retinal pigment epithelium and disruption of the external limiting membrane. Using single-cell RNA sequencing of retinal cells isolated from C57BL/6J mice, we demonstrate that Sfxn3 is expressed in several bipolar cell subtypes, retinal ganglion cells, and some amacrine cell subtypes but not significantly in Müller cells or photoreceptors. In situ hybridization confirmed these findings. Furthermore, pathway analysis suggests that Sfxn3 may be associated with synaptic homeostasis. Importantly, electron microscopy analysis showed disruption of synapses and synaptic ribbons in the outer plexiform layer of Sfxn3 -/- mice. Our work describes a previously unknown requirement for Sfxn3 in retinal function.
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28
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Cunningham CN, Rutter J. 20,000 picometers under the OMM: diving into the vastness of mitochondrial metabolite transport. EMBO Rep 2020; 21:e50071. [PMID: 32329174 DOI: 10.15252/embr.202050071] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 02/17/2020] [Accepted: 03/27/2020] [Indexed: 12/14/2022] Open
Abstract
The metabolic compartmentalization enabled by mitochondria is key feature of many cellular processes such as energy conversion to ATP production, redox balance, and the biosynthesis of heme, urea, nucleotides, lipids, and others. For a majority of these functions, metabolites need to be transported across the impermeable inner mitochondrial membrane by dedicated carrier proteins. Here, we examine the substrates, structural features, and human health implications of four mitochondrial metabolite carrier families: the SLC25A family, the mitochondrial ABCB transporters, the mitochondrial pyruvate carrier (MPC), and the sideroflexin proteins.
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Affiliation(s)
- Corey N Cunningham
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Jared Rutter
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA.,Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
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29
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Paul BT, Tesfay L, Winkler CR, Torti FM, Torti SV. Sideroflexin 4 affects Fe-S cluster biogenesis, iron metabolism, mitochondrial respiration and heme biosynthetic enzymes. Sci Rep 2019; 9:19634. [PMID: 31873120 PMCID: PMC6928202 DOI: 10.1038/s41598-019-55907-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 12/03/2019] [Indexed: 12/12/2022] Open
Abstract
Sideroflexin4 (SFXN4) is a member of a family of nuclear-encoded mitochondrial proteins. Rare germline mutations in SFXN4 lead to phenotypic characteristics of mitochondrial disease including impaired mitochondrial respiration and hematopoetic abnormalities. We sought to explore the function of this protein. We show that knockout of SFXN4 has profound effects on Fe-S cluster formation. This in turn diminishes mitochondrial respiratory chain complexes and mitochondrial respiration and causes a shift to glycolytic metabolism. SFXN4 knockdown reduces the stability and activity of cellular Fe-S proteins, affects iron metabolism by influencing the cytosolic aconitase-IRP1 switch, redistributes iron from the cytosol to mitochondria, and impacts heme synthesis by reducing levels of ferrochelatase and inhibiting translation of ALAS2. We conclude that SFXN4 is essential for normal functioning of mitochondria, is necessary for Fe-S cluster biogenesis and iron homeostasis, and plays a critical role in mitochondrial respiration and synthesis of heme.
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Affiliation(s)
- Bibbin T Paul
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT, 06030, USA
| | - Lia Tesfay
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT, 06030, USA
| | - C R Winkler
- Institute for Critical Technology and Applied Science, Nanoscale Characterization and Fabrication Laboratory, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Frank M Torti
- Department of Medicine, University of Connecticut Health Center, Farmington, CT, 06030, USA
| | - Suzy V Torti
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT, 06030, USA.
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30
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Sofou K, Hedberg-Oldfors C, Kollberg G, Thomsen C, Wiksell Å, Oldfors A, Tulinius M. Prenatal onset of mitochondrial disease is associated with sideroflexin 4 deficiency. Mitochondrion 2019; 47:76-81. [DOI: 10.1016/j.mito.2019.04.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 04/13/2019] [Accepted: 04/29/2019] [Indexed: 11/28/2022]
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Mon EE, Wei FY, Ahmad RNR, Yamamoto T, Moroishi T, Tomizawa K. Regulation of mitochondrial iron homeostasis by sideroflexin 2. J Physiol Sci 2018; 69:359-373. [PMID: 30570704 PMCID: PMC6373408 DOI: 10.1007/s12576-018-0652-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 12/10/2018] [Indexed: 02/08/2023]
Abstract
Mitochondrial iron is indispensable for heme biosynthesis and iron–sulfur cluster assembly. Several mitochondrial transmembrane proteins have been implicated to function in the biosynthesis of heme and iron–sulfur clusters by transporting reaction intermediates. However, several mitochondrial proteins related to iron metabolism remain uncharacterized. Here, we show that human sideroflexin 2 (SFXN2), a member of the SFXN protein family, is involved in mitochondrial iron metabolism. SFXN2 is an evolutionarily conserved protein that localized to mitochondria via its transmembrane domain. SFXN2-knockout (KO) cells had an increased mitochondrial iron content, which was associated with decreases in the heme content and heme-dependent enzyme activities. By contrast, the activities of iron–sulfur cluster-dependent enzymes were unchanged in SFXN2-KO cells. Moreover, abnormal iron metabolism impaired mitochondrial respiration in SFXN2-KO cells and accelerated iron-mediated death of these cells. Our findings demonstrate that SFXN2 functions in mitochondrial iron metabolism by regulating heme biosynthesis.
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Affiliation(s)
- Ei Ei Mon
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Honjo 1-1-1, Chuo-Ku, Kumamoto, 860-8556, Japan
| | - Fan-Yan Wei
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Honjo 1-1-1, Chuo-Ku, Kumamoto, 860-8556, Japan. .,Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), Kawaguchi, 332-0012, Japan.
| | - Raja Norazireen Raja Ahmad
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Honjo 1-1-1, Chuo-Ku, Kumamoto, 860-8556, Japan
| | - Takahiro Yamamoto
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Honjo 1-1-1, Chuo-Ku, Kumamoto, 860-8556, Japan
| | - Toshiro Moroishi
- Department of Molecular Enzymology, Faculty of Life Sciences, Kumamoto University, Kumamoto, 860-8556, Japan.,Center for Metabolic Regulation of Healthy Aging, Faculty of Life Sciences, Kumamoto University, Kumamoto, 860-8556, Japan.,Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), Kawaguchi, 332-0012, Japan
| | - Kazuhito Tomizawa
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Honjo 1-1-1, Chuo-Ku, Kumamoto, 860-8556, Japan. .,Center for Metabolic Regulation of Healthy Aging, Faculty of Life Sciences, Kumamoto University, Kumamoto, 860-8556, Japan. .,Neutron Therapy Research Center, Okayama University, Okayama, 700-8558, Japan.
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32
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Yépez VA, Kremer LS, Iuso A, Gusic M, Kopajtich R, Koňaříková E, Nadel A, Wachutka L, Prokisch H, Gagneur J. OCR-Stats: Robust estimation and statistical testing of mitochondrial respiration activities using Seahorse XF Analyzer. PLoS One 2018; 13:e0199938. [PMID: 29995917 PMCID: PMC6040740 DOI: 10.1371/journal.pone.0199938] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 06/16/2018] [Indexed: 12/02/2022] Open
Abstract
The accurate quantification of cellular and mitochondrial bioenergetic activity is of great interest in medicine and biology. Mitochondrial stress tests performed with Seahorse Bioscience XF Analyzers allow the estimation of different bioenergetic measures by monitoring the oxygen consumption rates (OCR) of living cells in multi-well plates. However, studies of the statistical best practices for determining aggregated OCR measurements and comparisons have been lacking. Therefore, to understand how OCR behaves across different biological samples, wells, and plates, we performed mitochondrial stress tests in 126 96-well plates involving 203 fibroblast cell lines. We show that the noise of OCR is multiplicative, that outlier data points can concern individual measurements or all measurements of a well, and that the inter-plate variation is greater than the intra-plate variation. Based on these insights, we developed a novel statistical method, OCR-Stats, that: i) robustly estimates OCR levels modeling multiplicative noise and automatically identifying outlier data points and outlier wells; and ii) performs statistical testing between samples, taking into account the different magnitudes of the between- and within-plate variations. This led to a significant reduction of the coefficient of variation across plates of basal respiration by 45% and of maximal respiration by 29%. Moreover, using positive and negative controls, we show that our statistical test outperforms the existing methods, which suffer from an excess of either false positives (within-plate methods), or false negatives (between-plate methods). Altogether, this study provides statistical good practices to support experimentalists in designing, analyzing, testing, and reporting the results of mitochondrial stress tests using this high throughput platform.
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Affiliation(s)
- Vicente A. Yépez
- Department of Informatics, Technical University of Munich, Garching, Germany
- Quantitative Biosciences Munich, Gene Center, Department of Biochemistry, Ludwig-Maximilians Universität München, Munich, Germany
| | - Laura S. Kremer
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
- Institute of Human Genetics, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
| | - Arcangela Iuso
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
- Institute of Human Genetics, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
| | - Mirjana Gusic
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
- Institute of Human Genetics, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
| | - Robert Kopajtich
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
- Institute of Human Genetics, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
| | - Eliška Koňaříková
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
- Institute of Human Genetics, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
| | - Agnieszka Nadel
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
- Institute of Human Genetics, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
| | - Leonhard Wachutka
- Department of Informatics, Technical University of Munich, Garching, Germany
| | - Holger Prokisch
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
- Institute of Human Genetics, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
| | - Julien Gagneur
- Department of Informatics, Technical University of Munich, Garching, Germany
- Quantitative Biosciences Munich, Gene Center, Department of Biochemistry, Ludwig-Maximilians Universität München, Munich, Germany
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Single-Cell RNA-Seq of Mouse Dopaminergic Neurons Informs Candidate Gene Selection for Sporadic Parkinson Disease. Am J Hum Genet 2018; 102:427-446. [PMID: 29499164 DOI: 10.1016/j.ajhg.2018.02.001] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 02/01/2018] [Indexed: 12/22/2022] Open
Abstract
Genetic variation modulating risk of sporadic Parkinson disease (PD) has been primarily explored through genome-wide association studies (GWASs). However, like many other common genetic diseases, the impacted genes remain largely unknown. Here, we used single-cell RNA-seq to characterize dopaminergic (DA) neuron populations in the mouse brain at embryonic and early postnatal time points. These data facilitated unbiased identification of DA neuron subpopulations through their unique transcriptional profiles, including a postnatal neuroblast population and substantia nigra (SN) DA neurons. We use these population-specific data to develop a scoring system to prioritize candidate genes in all 49 GWAS intervals implicated in PD risk, including genes with known PD associations and many with extensive supporting literature. As proof of principle, we confirm that the nigrostriatal pathway is compromised in Cplx1-null mice. Ultimately, this systematic approach establishes biologically pertinent candidates and testable hypotheses for sporadic PD, informing a new era of PD genetic research.
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Kafina MD, Paw BH. Using the Zebrafish as an Approach to Examine the Mechanisms of Vertebrate Erythropoiesis. Methods Mol Biol 2018; 1698:11-36. [PMID: 29076082 DOI: 10.1007/978-1-4939-7428-3_2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The zebrafish, Danio rerio, is a powerful model for the study of erythropoiesis and defining the genetic basis of hematological diseases. The mechanisms of erythroid differentiation are highly conserved in the zebrafish, permitting translational research studies and the modeling of erythropoiesis in higher vertebrates. An advantage of the system is the ability to manipulate gene expression and observe the effect on erythroid development in vivo, with relative ease and rapidity. The production of optically transparent embryos also makes it an attractive tool for visual analysis of circulating erythrocytes that can be used to study erythropoiesis. Through large-scale chemical mutagenesis screens, a variety of zebrafish blood mutants have been identified that are used for gene discoveries and the recapitulation of human diseases. Experimental techniques including in situ hybridization, o-dianisidine staining, flow cytometry, and microinjection are now commonly employed to study red blood cell biochemistry and erythropoiesis in the zebrafish. These techniques have been applied for identifying novel genes required for the hemoglobin synthesis, isolating blood cell lineages, visualizing genetic expression within erythroid tissues, and characterizing the phenotype of blood disorders. The applications of zebrafish methodology to the study of erythropoiesis and optimized step-by-step protocols are discussed in this chapter.
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Affiliation(s)
- Martin D Kafina
- Hematology Division, Department of Medicine, Brigham & Women's Hospital, Boston, MA, 02115, USA
| | - Barry H Paw
- Hematology Division, Department of Medicine, Brigham & Women's Hospital, Boston, MA, 02115, USA. .,Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA. .,Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA. .,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA. .,Hematology-Oncology Division, Department of Medicine, Boston Children's Hospital, Boston, MA, 02115, USA. .,BWH Hematology, Harvard Institutes of Medicine, Room 616, 77 Avenue Louis Pasteur, Boston, MA, 02115-5727, USA.
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35
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Hikmat O, Tzoulis C, Klingenberg C, Rasmussen M, Tallaksen CME, Brodtkorb E, Fiskerstrand T, McFarland R, Rahman S, Bindoff LA. The presence of anaemia negatively influences survival in patients with POLG disease. J Inherit Metab Dis 2017; 40:861-866. [PMID: 28865037 DOI: 10.1007/s10545-017-0084-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 08/15/2017] [Accepted: 08/18/2017] [Indexed: 10/18/2022]
Abstract
BACKGROUND Mitochondria play an important role in iron metabolism and haematopoietic cell homeostasis. Recent studies in mice showed that a mutation in the catalytic subunit of polymerase gamma (POLG) was associated with haematopoietic dysfunction including anaemia. The aim of this study was to analyse the frequency of anaemia in a large cohort of patients with POLG related disease. METHODS We conducted a multi-national, retrospective study of 61 patients with confirmed, pathogenic biallelic POLG mutations from six centres, four in Norway and two in the United Kingdom. Clinical, laboratory and genetic data were collected using a structured questionnaire. Anaemia was defined as an abnormally low haemoglobin value adjusted for age and sex. Univariate survival analysis was performed using log-rank test to compare differences in survival time between categories. RESULTS Anaemia occurred in 67% (41/61) of patients and in 23% (14/61) it was already present at clinical presentation. The frequency of anaemia in patients with early onset disease including Alpers syndrome and myocerebrohepatopathy spectrum (MCHS) was high (72%) and 35% (8/23) of these had anaemia at presentation. Survival analysis showed that the presence of anaemia was associated with a significantly worse survival (P = 0.004). CONCLUSION Our study reveals that anaemia can be a feature of POLG-related disease. Further, we show that its presence is associated with significantly worse prognosis either because anaemia itself is impacting survival or because it reflects the presence of more serious disease. In either case, our data suggests anaemia is a marker for negative prognosis.
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Affiliation(s)
- Omar Hikmat
- Department of Pediatrics, Haukeland University Hospital, 5021, Bergen, Norway
- Department of Clinical Medicine (K1), University of Bergen, Bergen, Norway
| | - Charalampos Tzoulis
- Department of Clinical Medicine (K1), University of Bergen, Bergen, Norway
- Department of Neurology, Haukeland University Hospital, 5021, Bergen, Norway
| | - Claus Klingenberg
- Department of Paediatric and Adolescent Medicine, University Hospital of North Norway, Tromsø, Norway
- Paediatric Research Group, Department of Clinical Medicine, UiT- The Arctic University of Norway, Tromsø, Norway
| | - Magnhild Rasmussen
- Women and Children's Division, Department of Clinical Neurosciences for Children, Oslo University Hospital, Oslo, Norway
- Unit for Congenital and Hereditary Neuromuscular Disorders, Department of Neurology, Oslo University Hospital, Oslo, Norway
| | - Chantal M E Tallaksen
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Eylert Brodtkorb
- Department of Neuroscience, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Neurology and Clinical Neurophysiology, St. Olav's University Hospital, Trondheim, Norway
| | - Torunn Fiskerstrand
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Science (K2), University of Bergen, Bergen, Norway
| | - Robert McFarland
- Wellcome Trust Centre for Mitochondrial Research, Institute of Neuroscience, The Medical School Framlington Place, Newcastle University, Newcastle upon Tyne, UK
| | - Shamima Rahman
- Mitochondrial Research Group, UCL Great Ormond Street Institute of Child Health, London, UK
- Metabolic Unit, Great Ormond Street Hospital NHS Foundation trust, London, UK
| | - Laurence A Bindoff
- Department of Clinical Medicine (K1), University of Bergen, Bergen, Norway.
- Department of Neurology, Haukeland University Hospital, 5021, Bergen, Norway.
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36
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Chung J, Wittig JG, Ghamari A, Maeda M, Dailey TA, Bergonia H, Kafina MD, Coughlin EE, Minogue CE, Hebert AS, Li L, Kaplan J, Lodish HF, Bauer DE, Orkin SH, Cantor AB, Maeda T, Phillips JD, Coon JJ, Pagliarini DJ, Dailey HA, Paw BH. Erythropoietin signaling regulates heme biosynthesis. eLife 2017; 6. [PMID: 28553927 PMCID: PMC5478267 DOI: 10.7554/elife.24767] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 05/28/2017] [Indexed: 11/13/2022] Open
Abstract
Heme is required for survival of all cells, and in most eukaryotes, is produced through a series of eight enzymatic reactions. Although heme production is critical for many cellular processes, how it is coupled to cellular differentiation is unknown. Here, using zebrafish, murine, and human models, we show that erythropoietin (EPO) signaling, together with the GATA1 transcriptional target, AKAP10, regulates heme biosynthesis during erythropoiesis at the outer mitochondrial membrane. This integrated pathway culminates with the direct phosphorylation of the crucial heme biosynthetic enzyme, ferrochelatase (FECH) by protein kinase A (PKA). Biochemical, pharmacological, and genetic inhibition of this signaling pathway result in a block in hemoglobin production and concomitant intracellular accumulation of protoporphyrin intermediates. Broadly, our results implicate aberrant PKA signaling in the pathogenesis of hematologic diseases. We propose a unifying model in which the erythroid transcriptional program works in concert with post-translational mechanisms to regulate heme metabolism during normal development. DOI:http://dx.doi.org/10.7554/eLife.24767.001 Heme is an iron-containing compound that is important for all living things, from bacteria to humans. Our red blood cells use heme to carry oxygen and deliver it throughout the body. The amount of heme that is produced must be tightly regulated. Too little or too much heme in a person’s red blood cells can lead to blood-related diseases such as anemia and porphyria. Yet, while scientists knew the enzymes needed to make heme, they did not know how these enzymes were controlled. Now, Chung et al. show that an important signaling molecule called erythropoietin controls how much heme is produced when red blood cells are made. The experiments used a combination of red blood cells from humans and mice as well as zebrafish, which are useful model organisms because their blood develops in a similar way to humans. When Chung et al. inhibited components of erythropoietin signaling, heme production was blocked too and the red blood cells could not work properly. These new findings pave the way to look at human patients with blood-related disorders to determine if they have defects in the erythropoietin signaling cascade. In the future, this avenue of research might lead to better treatments for a variety of blood diseases in humans. DOI:http://dx.doi.org/10.7554/eLife.24767.002
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Affiliation(s)
- Jacky Chung
- Division of Hematology, Brigham and Women's Hospital, Harvard Medical School, Boston, United States
| | - Johannes G Wittig
- Division of Hematology, Brigham and Women's Hospital, Harvard Medical School, Boston, United States
| | - Alireza Ghamari
- Division of Hematology-Oncology, Boston Children's Hospital, Harvard Medical School, Boston, United States
| | - Manami Maeda
- Division of Hematology, Brigham and Women's Hospital, Harvard Medical School, Boston, United States
| | - Tamara A Dailey
- Department of Microbiology, University of Georgia, Athens, United States.,Department of Biochemistry and Molecular Biology, University of Georgia, Athens, United States
| | - Hector Bergonia
- Division of Hematology and Hematologic Malignancies, University of Utah School of Medicine, Salt Lake City, United States
| | - Martin D Kafina
- Division of Hematology, Brigham and Women's Hospital, Harvard Medical School, Boston, United States
| | | | - Catherine E Minogue
- Department of Chemistry, University of Wisconsin-Madison, Madison, United States
| | | | - Liangtao Li
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, United States
| | - Jerry Kaplan
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, United States
| | - Harvey F Lodish
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, United States
| | - Daniel E Bauer
- Division of Hematology-Oncology, Boston Children's Hospital, Harvard Medical School, Boston, United States.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, United States
| | - Stuart H Orkin
- Division of Hematology-Oncology, Boston Children's Hospital, Harvard Medical School, Boston, United States.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, United States
| | - Alan B Cantor
- Division of Hematology-Oncology, Boston Children's Hospital, Harvard Medical School, Boston, United States.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, United States
| | - Takahiro Maeda
- Division of Hematology, Brigham and Women's Hospital, Harvard Medical School, Boston, United States
| | - John D Phillips
- Division of Hematology and Hematologic Malignancies, University of Utah School of Medicine, Salt Lake City, United States
| | - Joshua J Coon
- Genome Center of Wisconsin, Madison, United States.,Department of Chemistry, University of Wisconsin-Madison, Madison, United States.,Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, United States
| | - David J Pagliarini
- Department of Biochemistry, University of Wisconsin-Madison, Madison, United States
| | - Harry A Dailey
- Department of Microbiology, University of Georgia, Athens, United States.,Department of Biochemistry and Molecular Biology, University of Georgia, Athens, United States
| | - Barry H Paw
- Division of Hematology, Brigham and Women's Hospital, Harvard Medical School, Boston, United States.,Division of Hematology-Oncology, Boston Children's Hospital, Harvard Medical School, Boston, United States.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, United States
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Grillo AS, SantaMaria AM, Kafina MD, Cioffi AG, Huston NC, Han M, Seo YA, Yien YY, Nardone C, Menon AV, Fan J, Svoboda DC, Anderson JB, Hong JD, Nicolau BG, Subedi K, Gewirth AA, Wessling-Resnick M, Kim J, Paw BH, Burke MD. Restored iron transport by a small molecule promotes absorption and hemoglobinization in animals. Science 2017; 356:608-616. [PMID: 28495746 PMCID: PMC5470741 DOI: 10.1126/science.aah3862] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 11/30/2016] [Accepted: 03/21/2017] [Indexed: 12/15/2022]
Abstract
Multiple human diseases ensue from a hereditary or acquired deficiency of iron-transporting protein function that diminishes transmembrane iron flux in distinct sites and directions. Because other iron-transport proteins remain active, labile iron gradients build up across the corresponding protein-deficient membranes. Here we report that a small-molecule natural product, hinokitiol, can harness such gradients to restore iron transport into, within, and/or out of cells. The same compound promotes gut iron absorption in DMT1-deficient rats and ferroportin-deficient mice, as well as hemoglobinization in DMT1- and mitoferrin-deficient zebrafish. These findings illuminate a general mechanistic framework for small molecule-mediated site- and direction-selective restoration of iron transport. They also suggest that small molecules that partially mimic the function of missing protein transporters of iron, and possibly other ions, may have potential in treating human diseases.
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Affiliation(s)
- Anthony S Grillo
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Anna M SantaMaria
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Martin D Kafina
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Alexander G Cioffi
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Nicholas C Huston
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Murui Han
- Department of Pharmaceutical Sciences, Northeastern University, Boston, MA 02115, USA
| | - Young Ah Seo
- Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Yvette Y Yien
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Christopher Nardone
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Archita V Menon
- Department of Pharmaceutical Sciences, Northeastern University, Boston, MA 02115, USA
| | - James Fan
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Dillon C Svoboda
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Jacob B Anderson
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - John D Hong
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Bruno G Nicolau
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Kiran Subedi
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Andrew A Gewirth
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Marianne Wessling-Resnick
- Department of Genetic and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA.
| | - Jonghan Kim
- Department of Pharmaceutical Sciences, Northeastern University, Boston, MA 02115, USA.
| | - Barry H Paw
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
- Division of Hematology-Oncology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Martin D Burke
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carle-Illinois College of Medicine, University of Illinois at Urbana-Champaign, Champaign, IL 61820, USA
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Kropp J, Carrillo JA, Namous H, Daniels A, Salih SM, Song J, Khatib H. Male fertility status is associated with DNA methylation signatures in sperm and transcriptomic profiles of bovine preimplantation embryos. BMC Genomics 2017; 18:280. [PMID: 28381255 PMCID: PMC5382486 DOI: 10.1186/s12864-017-3673-y] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 03/31/2017] [Indexed: 11/12/2022] Open
Abstract
Background Infertility in dairy cattle is a concern where reduced fertilization rates and high embryonic loss are contributing factors. Studies of the paternal contribution to reproductive performance are limited. However, recent discoveries have shown that, in addition to DNA, sperm delivers transcription factors and epigenetic components that are required for fertilization and proper embryonic development. Hence, characterization of the paternal contribution at the time of fertilization is warranted. We hypothesized that sire fertility is associated with differences in DNA methylation patterns in sperm and that the embryonic transcriptomic profiles are influenced by the fertility status of the bull. Embryos were generated in vitro by fertilization with either a high or low fertility Holstein bull. Blastocysts derived from each high and low fertility bulls were evaluated for morphology, development, and transcriptomic analysis using RNA-Sequencing. Additionally, DNA methylation signatures of sperm from high and low fertility sires were characterized by performing whole-genome DNA methylation binding domain sequencing. Results Embryo morphology and developmental capacity did not differ between embryos generated from either a high or low fertility bull. However, RNA-Sequencing revealed 98 genes to be differentially expressed at a false discovery rate < 1%. A total of 65 genes were upregulated in high fertility bull derived embryos, and 33 genes were upregulated in low fertility derived embryos. Expression of the genes CYCS, EEA1, SLC16A7, MEPCE, and TFB2M was validated in three new pairs of biological replicates of embryos. The role of the differentially expressed gene TFB2M in embryonic development was further assessed through expression knockdown at the zygotic stage, which resulted in decreased development to the blastocyst stage. Assessment of the epigenetic signature of spermatozoa between high and low fertility bulls revealed 76 differentially methylated regions. Conclusions Despite similar morphology and development to the blastocyst stage, preimplantation embryos derived from high and low fertility bulls displayed significant transcriptomic differences. The relationship between the paternal contribution and the embryonic transcriptome is unclear, although differences in methylated regions were identified which could influence the reprogramming of the early embryo. Further characterization of paternal factors delivered to the oocyte could lead to the identification of biomarkers for better selection of sires to improve reproductive efficiency. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3673-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jenna Kropp
- Department of Animal Sciences, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - José A Carrillo
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, 20742, USA
| | - Hadjer Namous
- Department of Animal Sciences, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Alyssa Daniels
- Department of Animal Sciences, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Sana M Salih
- Department of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, WI, 53792, USA.,Present address: Department of Obstetrics and Gynecology, West Virginia University, Morgantown, WV, 26508, USA
| | - Jiuzhou Song
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, 20742, USA
| | - Hasan Khatib
- Department of Animal Sciences, University of Wisconsin-Madison, Madison, WI, 53706, USA.
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McDermott-Roe C, Leleu M, Rowe GC, Palygin O, Bukowy JD, Kuo J, Rech M, Hermans-Beijnsberger S, Schaefer S, Adami E, Creemers EE, Heinig M, Schroen B, Arany Z, Petretto E, Geurts AM. Transcriptome-wide co-expression analysis identifies LRRC2 as a novel mediator of mitochondrial and cardiac function. PLoS One 2017; 12:e0170458. [PMID: 28158196 PMCID: PMC5291451 DOI: 10.1371/journal.pone.0170458] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 01/05/2017] [Indexed: 11/19/2022] Open
Abstract
Mitochondrial dysfunction contributes to myriad monogenic and complex pathologies. To understand the underlying mechanisms, it is essential to define the full complement of proteins that modulate mitochondrial function. To identify such proteins, we performed a meta-analysis of publicly available gene expression data. Gene co-expression analysis of a large and heterogeneous compendium of microarray data nominated a sub-population of transcripts that whilst highly correlated with known mitochondrial protein-encoding transcripts (MPETs), are not themselves recognized as generating proteins either localized to the mitochondrion or pertinent to functions therein. To focus the analysis on a medically-important condition with a strong yet incompletely understood mitochondrial component, candidates were cross-referenced with an MPET-enriched module independently generated via genome-wide co-expression network analysis of a human heart failure gene expression dataset. The strongest uncharacterized candidate in the analysis was Leucine Rich Repeat Containing 2 (LRRC2). LRRC2 was found to be localized to the mitochondria in human cells and transcriptionally-regulated by the mitochondrial master regulator Pgc-1α. We report that Lrrc2 transcript abundance correlates with that of β-MHC, a canonical marker of cardiac hypertrophy in humans and experimentally demonstrated an elevation in Lrrc2 transcript in in vitro and in vivo rodent models of cardiac hypertrophy as well as in patients with dilated cardiomyopathy. RNAi-mediated Lrrc2 knockdown in a rat-derived cardiomyocyte cell line resulted in enhanced expression of canonical hypertrophic biomarkers as well as increased mitochondrial mass in the context of increased Pgc-1α expression. In conclusion, our meta-analysis represents a simple yet powerful springboard for the nomination of putative mitochondrially-pertinent proteins relevant to cardiac function and enabled the identification of LRRC2 as a novel mitochondrially-relevant protein and regulator of the hypertrophic response.
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Affiliation(s)
- Chris McDermott-Roe
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI, United States of America
| | - Marion Leleu
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Glenn C. Rowe
- Division of Cardiovascular Disease, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Oleg Palygin
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI, United States of America
| | - John D. Bukowy
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI, United States of America
| | - Judy Kuo
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI, United States of America
| | - Monika Rech
- Center for Heart Failure Research, Department of Cardiology, CARIM School for Cardiovascular Diseases, Maastricht University, Maastricht, The Netherlands
| | - Steffie Hermans-Beijnsberger
- Center for Heart Failure Research, Department of Cardiology, CARIM School for Cardiovascular Diseases, Maastricht University, Maastricht, The Netherlands
| | - Sebastian Schaefer
- National Heart Research Institute Singapore, National Heart Centre Singapore, Singapore, Singapore
| | - Eleonora Adami
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Esther E. Creemers
- Experimental Cardiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Matthias Heinig
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Blanche Schroen
- Center for Heart Failure Research, Department of Cardiology, CARIM School for Cardiovascular Diseases, Maastricht University, Maastricht, The Netherlands
| | - Zoltan Arany
- Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Enrico Petretto
- MRC Clinical Sciences Centre, Imperial College London, London, UK, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Aron M. Geurts
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI, United States of America
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40
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Abstract
INTRODUCTION Mitochondria are cellular organelles that perform numerous bioenergetic, biosynthetic, and regulatory functions and play a central role in iron metabolism. Extracellular iron is taken up by cells and transported to the mitochondria, where it is utilized for synthesis of cofactors essential to the function of enzymes involved in oxidation-reduction reactions, DNA synthesis and repair, and a variety of other cellular processes. Areas covered: This article reviews the trafficking of iron to the mitochondria and normal mitochondrial iron metabolism, including heme synthesis and iron-sulfur cluster biogenesis. Much of our understanding of mitochondrial iron metabolism has been revealed by pathologies that disrupt normal iron metabolism. These conditions affect not only iron metabolism but mitochondrial function and systemic health. Therefore, this article also discusses these pathologies, including conditions of systemic and mitochondrial iron dysregulation as well as cancer. Literature covering these areas was identified via PubMed searches using keywords: Iron, mitochondria, Heme Synthesis, Iron-sulfur Cluster, and Cancer. References cited by publications retrieved using this search strategy were also consulted. Expert commentary: While much has been learned about mitochondrial and its iron, key questions remain. Developing a better understanding of mitochondrial iron and its regulation will be paramount in developing therapies for syndromes that affect mitochondrial iron.
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Affiliation(s)
- Bibbin T. Paul
- Department of Molecular Biology and Biophysics, University of Connecticut Health, Farmington, Connecticut
| | - David H. Manz
- Department of Molecular Biology and Biophysics, University of Connecticut Health, Farmington, Connecticut
- School of Dental Medicine, University of Connecticut Health, Farmington, Connecticut
| | - Frank M. Torti
- Department of Medicine, University of Connecticut Health, Farmington, Connecticut
| | - Suzy V. Torti
- Department of Molecular Biology and Biophysics, University of Connecticut Health, Farmington, Connecticut
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41
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Kremer LS, Prokisch H. Identification of Disease-Causing Mutations by Functional Complementation of Patient-Derived Fibroblast Cell Lines. Methods Mol Biol 2017; 1567:391-406. [PMID: 28276032 DOI: 10.1007/978-1-4939-6824-4_24] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Diagnosis of mitochondrial disorders is still hampered by their phenotypic and genotypic heterogeneity. In many cases, exome sequencing, the state-of-the-art method for genetically diagnosing mitochondrial disease patients, does not allow direct identification of the disease-associated gene but rather results in a list of variants in candidate genes. Here, we present a method to validate the disease-causing variant based on functional complementation assays. First, cell lines expressing a wild-type cDNA of the candidate genes are generated by lentiviral infection of patient-derived fibroblasts. Next, oxidative phosphorylation is measured by the Seahorse XF analyzer to assess rescue efficiency.
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Affiliation(s)
- Laura S Kremer
- Institute of Human Genetics, Helmholtz Zentrum München, Ingolstaedter Landstr. 1, 85764, Neuherberg, Germany
- Institute of Human Genetics, Technische Universität München, 81675, Munich, Germany
| | - Holger Prokisch
- Institute of Human Genetics, Helmholtz Zentrum München, Ingolstaedter Landstr. 1, 85764, Neuherberg, Germany.
- Institute of Human Genetics, Technische Universität München, 81675, Munich, Germany.
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42
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Liu HY, Huang J, Li T, Wu D, Wang HD, Wang Y, Wang T, Guo LJ, Guo QN, Huang FF, Wang RL, Wang YT. Clinical and molecular cytogenetic analyses of four patients with imbalanced translocations. Mol Cytogenet 2016; 9:31. [PMID: 27099631 PMCID: PMC4837590 DOI: 10.1186/s13039-016-0244-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 04/12/2016] [Indexed: 01/24/2023] Open
Abstract
Background Chromosomal abnormalities that result in genomic imbalances are main causes of congenital and developmental anomalies including intellectual disability and multiple congenital malformations. In this report we describe four patients from three families with imbalanced translocations. Only a small percentage of imbalanced translocation individuals can be born to live, most of them were aborted in embryonic period. It is of great significances to precisely analysis the chromosome variation to study the relationship between genotype and phenotype. Results Four patients showed common clinical manifestations including delayed growth, intellectual disability, language barrier and facial dysmorphisms. In addition to the above features, lower limbs dysplasia and both foot eversion were found in patient 1, brachydactylic hand, cerebellar ataxia and congenital heart defects were also found in patient 4. Conventional karyotype analysis revealed abnormal karyotypes 46, XX, der (6) t (6: 10) (p23; q24), 46, XX, der (20) t (3; 20) (p23; p13) and 46, XX, der (22) t (3; 22) (q27; q13.3) in the four patients, respectively. Array-CGH analyses confirmed 23.6 Mb duplication on 10q25.1-q26.3 and 0.9 Mb deletions on 6p25.3, 19.9 Mb duplication on 3p24.3-p26.3 and 0.25 Mb deletion on 20p13 and 12.5 Mb duplication on 3q27.2-q29 and 1.9 Mb deletions on 22q13.2-q13.33 in the four patients, respectively. Conclusion Parents with balanced translocation are passed the imbalanced chromosome to patient, and the partial monosomy and partial trisomy lead to multiple congenital malformations of four patients. Electronic supplementary material The online version of this article (doi:10.1186/s13039-016-0244-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hong Yan Liu
- Department of Medical Genetics Institute, People's Hospital of Zhengzhou University (Henan Provincial People's Hospital), Zhengzhou, 450003 Henan China
| | - Jia Huang
- Department of Medical Genetics Institute, People's Hospital of Zhengzhou University (Henan Provincial People's Hospital), Zhengzhou, 450003 Henan China
| | - Tao Li
- Department of Medical Genetics Institute, People's Hospital of Zhengzhou University (Henan Provincial People's Hospital), Zhengzhou, 450003 Henan China
| | - Dong Wu
- Department of Medical Genetics Institute, People's Hospital of Zhengzhou University (Henan Provincial People's Hospital), Zhengzhou, 450003 Henan China
| | - Hong Dan Wang
- Department of Medical Genetics Institute, People's Hospital of Zhengzhou University (Henan Provincial People's Hospital), Zhengzhou, 450003 Henan China
| | - Yue Wang
- Department of Gynaecology and Obstetrics, People's Hospital of Zhengzhou University (Henan Provincial People's Hospital), Zhengzhou, 450003 Henan China
| | - Tao Wang
- Department of Medical Genetics Institute, People's Hospital of Zhengzhou University (Henan Provincial People's Hospital), Zhengzhou, 450003 Henan China
| | - Liang Jie Guo
- Department of Medical Genetics Institute, People's Hospital of Zhengzhou University (Henan Provincial People's Hospital), Zhengzhou, 450003 Henan China
| | - Qian Nan Guo
- Department of Medical Genetics Institute, People's Hospital of Zhengzhou University (Henan Provincial People's Hospital), Zhengzhou, 450003 Henan China
| | - Fei Fei Huang
- Department of Medical Genetics Institute, People's Hospital of Zhengzhou University (Henan Provincial People's Hospital), Zhengzhou, 450003 Henan China
| | - Rui Li Wang
- Department of Ultrasonography, People's Hospital of Zhengzhou University (Henan Provincial People's Hospital), Zhengzhou, 450003 Henan China
| | - Ying Tai Wang
- Department of Medical Genetics Institute, People's Hospital of Zhengzhou University (Henan Provincial People's Hospital), Zhengzhou, 450003 Henan China
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43
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Shmukler BE, Huston NC, Thon JN, Ni CW, Kourkoulis G, Lawson ND, Paw BH, Alper SL. Homozygous knockout of the piezo1 gene in the zebrafish is not associated with anemia. Haematologica 2015; 100:e483-5. [PMID: 26294733 DOI: 10.3324/haematol.2015.132449] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Boris E Shmukler
- Renal Division, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Nicholas C Huston
- Hematology Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jonathan N Thon
- Hematology Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Chih-Wen Ni
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA, USA
| | - George Kourkoulis
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA, USA
| | - Nathan D Lawson
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA, USA
| | - Barry H Paw
- Hematology Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA Hematology-Oncology Division, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Seth L Alper
- Renal Division, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
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44
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Mayr JA, Haack TB, Freisinger P, Karall D, Makowski C, Koch J, Feichtinger RG, Zimmermann FA, Rolinski B, Ahting U, Meitinger T, Prokisch H, Sperl W. Spectrum of combined respiratory chain defects. J Inherit Metab Dis 2015; 38:629-40. [PMID: 25778941 PMCID: PMC4493854 DOI: 10.1007/s10545-015-9831-y] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 02/20/2015] [Accepted: 02/23/2015] [Indexed: 01/22/2023]
Abstract
Inherited disorders of mitochondrial energy metabolism form a large and heterogeneous group of metabolic diseases. More than 250 gene defects have been reported to date and this number continues to grow. Mitochondrial diseases can be grouped into (1) disorders of oxidative phosphorylation (OXPHOS) subunits and their assembly factors, (2) defects of mitochondrial DNA, RNA and protein synthesis, (3) defects in the substrate-generating upstream reactions of OXPHOS, (4) defects in relevant cofactors and (5) defects in mitochondrial homeostasis. Deficiency of more than one respiratory chain enzyme is a common finding. Combined defects are found in 49 % of the known disease-causing genes of mitochondrial energy metabolism and in 57 % of patients with OXPHOS defects identified in our diagnostic centre. Combined defects of complexes I, III, IV and V are typically due to deficiency of mitochondrial DNA replication, RNA metabolism or translation. Defects in cofactors can result in combined defects of various combinations, and defects of mitochondrial homeostasis can result in a generalised decrease of all OXPHOS enzymes. Noteworthy, identification of combined defects can be complicated by different degrees of severity of each affected enzyme. Furthermore, even defects of single respiratory chain enzymes can result in combined defects due to aberrant formation of respiratory chain supercomplexes. Combined OXPHOS defects have a great variety of clinical manifestations in terms of onset, course severity and tissue involvement. They can present as classical encephalomyopathy but also with hepatopathy, nephropathy, haematologic findings and Perrault syndrome in a subset of disorders.
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Affiliation(s)
- Johannes A Mayr
- Department of Paediatrics, Paracelsus Medical University, SALK Salzburg, Salzburg, 5020, Austria,
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45
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Chung J, Bauer DE, Ghamari A, Nizzi CP, Deck KM, Kingsley PD, Yien YY, Huston NC, Chen C, Schultz IJ, Dalton AJ, Wittig JG, Palis J, Orkin SH, Lodish HF, Eisenstein RS, Cantor AB, Paw BH. The mTORC1/4E-BP pathway coordinates hemoglobin production with L-leucine availability. Sci Signal 2015; 8:ra34. [PMID: 25872869 PMCID: PMC4402725 DOI: 10.1126/scisignal.aaa5903] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
In multicellular organisms, the mechanisms by which diverse cell types acquire distinct amino acids and how cellular function adapts to their availability are fundamental questions in biology. We found that increased neutral essential amino acid (NEAA) uptake was a critical component of erythropoiesis. As red blood cells matured, expression of the amino acid transporter gene Lat3 increased, which increased NEAA import. Inadequate NEAA uptake by pharmacologic inhibition or RNAi-mediated knockdown of LAT3 triggered a specific reduction in hemoglobin production in zebrafish embryos and murine erythroid cells through the mTORC1 (mammalian target of rapamycin complex 1)/4E-BP (eukaryotic translation initiation factor 4E-binding protein) pathway. CRISPR-mediated deletion of members of the 4E-BP family in murine erythroid cells rendered them resistant to mTORC1 and LAT3 inhibition and restored hemoglobin production. These results identify a developmental role for LAT3 in red blood cells and demonstrate that mTORC1 serves as a homeostatic sensor that couples hemoglobin production at the translational level to sufficient uptake of NEAAs, particularly L-leucine.
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MESH Headings
- Adaptor Proteins, Signal Transducing
- Amino Acid Transport Systems, Basic/genetics
- Amino Acid Transport Systems, Basic/metabolism
- Animals
- Animals, Genetically Modified
- CRISPR-Cas Systems
- Carrier Proteins/genetics
- Carrier Proteins/metabolism
- Cell Cycle Proteins
- Cell Line, Tumor
- Cells, Cultured
- Embryo, Mammalian/blood supply
- Embryo, Mammalian/embryology
- Embryo, Mammalian/metabolism
- Embryo, Nonmammalian/embryology
- Embryo, Nonmammalian/metabolism
- Erythroid Cells/metabolism
- Erythropoiesis/genetics
- Eukaryotic Initiation Factors/genetics
- Eukaryotic Initiation Factors/metabolism
- Gene Expression Regulation, Developmental
- HEK293 Cells
- Hemoglobins/genetics
- Hemoglobins/metabolism
- Humans
- Immunoblotting
- Leucine/metabolism
- Mechanistic Target of Rapamycin Complex 1
- Mice
- Microscopy, Confocal
- Multiprotein Complexes/genetics
- Multiprotein Complexes/metabolism
- Phosphoproteins/genetics
- Phosphoproteins/metabolism
- RNA Interference
- Reverse Transcriptase Polymerase Chain Reaction
- Signal Transduction/genetics
- TOR Serine-Threonine Kinases/genetics
- TOR Serine-Threonine Kinases/metabolism
- Zebrafish
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Affiliation(s)
- Jacky Chung
- Division of Hematology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Daniel E Bauer
- Division of Hematology-Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA. Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Alireza Ghamari
- Division of Hematology-Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA. Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Christopher P Nizzi
- Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Kathryn M Deck
- Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Paul D Kingsley
- Department of Pediatrics, Center for Pediatric Biomedical Research, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Yvette Y Yien
- Division of Hematology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Nicholas C Huston
- Division of Hematology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Caiyong Chen
- Division of Hematology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Iman J Schultz
- Division of Hematology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Arthur J Dalton
- Division of Hematology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Johannes G Wittig
- Division of Hematology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - James Palis
- Department of Pediatrics, Center for Pediatric Biomedical Research, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Stuart H Orkin
- Division of Hematology-Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA. Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Harvey F Lodish
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Richard S Eisenstein
- Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Alan B Cantor
- Division of Hematology-Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA. Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Barry H Paw
- Division of Hematology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA. Division of Hematology-Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA. Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA.
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