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Liang Z, Hu S, Dong Y, Miao L, Zhu W, Feng B, Fu J, Luo M, Wang L, Dong Z. Molecular characterization and function of hif1a and fih1 in response to acute thermal stress in American shad (Alosa sapidissima). FISH PHYSIOLOGY AND BIOCHEMISTRY 2024; 50:1563-1581. [PMID: 38789648 DOI: 10.1007/s10695-024-01356-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 05/03/2024] [Indexed: 05/26/2024]
Abstract
In order to evaluate the function of hypoxia-inducible factor-1 alpha (hif1α) and factor inhibiting hif1α (fih1) in response to thermal stress, we first conducted a functional analysis of A. sapidissima hif1α and fih1, and determined hif1α and fih1 expressions in different tissues in response to thermal stress based on identified housekeeping genes (HKGs). The results showed that hif1α and fih1 were mainly located in the nucleus and cytoplasm. The full length cDNA sequence of hif1α and fih1 was 4073 bp and 2759 bp, respectively. The cDNA sequence of hif1α includes 15 exons encoding 750 amino acid residues, and the full length cDNA sequence of fih1 contains 9 exons encoding 354 amino acid residues. During the acute thermal stress transferring from 16 ± 0.5 °C (control) to 20 ± 0.5 °C, 25 ± 0.5 °C, and 30 ± 0.5 °C for 15 min, it was found that the expression trends of hif1α and fih1 showed an inhibitory regulation in the heart, while they consistently expressed in brain, intestine, muscle, gill, kidney and liver. In conclusion, this is the first study to identify the tissue-specific HKGs in A. sapidissima and found that ef1α and β-actin are the most suitable HKGs. Hif1α and Fih1 are mainly the nuclear and cytoplasmic proteins, respectively, having high levels in the heart and brain. Alosa sapidissima countered a temperature increase from 16 to 25 ℃ by regulating the expressions of hif1α and fih1, but their physiological regulatory functions were unable to cope with acute thermal stress when the temperature difference was 14 ℃ (from 16 to 30 ℃).
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Affiliation(s)
- Zhengyuan Liang
- Wuxi Fisheries College, Nanjing Agricultural University, No.9 East Shanshui Road, Wuxi Jiangsu, 214081, China
- Wuxi Raysun Fishery Science and Technology Company, Xingyuan North Road No. 401, P.O. Box D20-501, Wuxi Jiangsu, 214000, China
| | - Songqin Hu
- Wuxi Fisheries College, Nanjing Agricultural University, No.9 East Shanshui Road, Wuxi Jiangsu, 214081, China
| | - Yalun Dong
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs; Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi Jiangsu, 214081, China
| | - Linghong Miao
- Wuxi Fisheries College, Nanjing Agricultural University, No.9 East Shanshui Road, Wuxi Jiangsu, 214081, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs; Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi Jiangsu, 214081, China
| | - Wenbin Zhu
- Wuxi Fisheries College, Nanjing Agricultural University, No.9 East Shanshui Road, Wuxi Jiangsu, 214081, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs; Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi Jiangsu, 214081, China
| | - Bingbing Feng
- Fisheries Technology Extension Center of Jiangsu Province, Hanzhongmen Street No. 300, Nanjing Jiangsu, 210036, China
| | - Jianjun Fu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs; Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi Jiangsu, 214081, China
| | - Mingkun Luo
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs; Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi Jiangsu, 214081, China
| | - Lanmei Wang
- Wuxi Fisheries College, Nanjing Agricultural University, No.9 East Shanshui Road, Wuxi Jiangsu, 214081, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs; Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi Jiangsu, 214081, China
| | - Zaije Dong
- Wuxi Fisheries College, Nanjing Agricultural University, No.9 East Shanshui Road, Wuxi Jiangsu, 214081, China.
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs; Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi Jiangsu, 214081, China.
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Uno M, Bono H. Transcriptional Signatures of Domestication Revealed through Meta-Analysis of Pig, Chicken, Wild Boar, and Red Junglefowl Gene Expression Data. Animals (Basel) 2024; 14:1998. [PMID: 38998110 PMCID: PMC11240496 DOI: 10.3390/ani14131998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 06/25/2024] [Accepted: 07/04/2024] [Indexed: 07/14/2024] Open
Abstract
Domesticated animals have undergone significant changes in their behavior, morphology, and physiological functions during domestication. To identify the changes in gene expression associated with domestication, we collected the RNA-seq data of pigs, chickens, wild boars, and red junglefowl from public databases and performed a meta-analysis. Gene expression was quantified, and the expression ratio between domesticated animals and their wild ancestors (DW-ratio) was calculated. Genes were classified as "upregulated", "downregulated", or "unchanged" based on their DW-ratio, and the DW-score was calculated for each gene. Gene set enrichment analysis revealed that genes upregulated in pigs were related to defense from viral infection, whereas those upregulated in chickens were associated with aminoglycan and carbohydrate derivative catabolic processes. Genes commonly upregulated in pigs and chickens are involved in the immune response, olfactory learning, epigenetic regulation, cell division, and extracellular matrix. In contrast, genes upregulated in wild boar and red junglefowl are related to stress response, cell proliferation, cardiovascular function, neural regulation, and energy metabolism. These findings provide valuable insights into the genetic basis of the domestication process and highlight potential candidate genes for breeding applications.
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Affiliation(s)
- Motoki Uno
- Graduate School of Integrated Sciences for Life, Hiroshima University, 3-10-23 Kagamiyama, Higashi-Hiroshima 739-0046, Japan
| | - Hidemasa Bono
- Graduate School of Integrated Sciences for Life, Hiroshima University, 3-10-23 Kagamiyama, Higashi-Hiroshima 739-0046, Japan
- Genome Editing Innovation Center, Hiroshima University, 3-10-23 Kagamiyama, Higashi-Hiroshima 739-0046, Japan
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Takenaka Y, Hirasaki M, Bono H, Nakamura S, Kakinuma Y. Transcriptome Analysis Reveals Enhancement of Cardiogenesis-Related Signaling Pathways by S-Nitroso- N -Pivaloyl- d -Penicillamine: Implications for Improved Diastolic Function and Cardiac Performance. J Cardiovasc Pharmacol 2024; 83:433-445. [PMID: 38422186 DOI: 10.1097/fjc.0000000000001552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Accepted: 02/10/2024] [Indexed: 03/02/2024]
Abstract
ABSTRACT We previously reported a novel compound called S-nitroso- N -pivaloyl- d -penicillamine (SNPiP), which was screened from a group of nitric oxide donor compounds with a basic chemical structure of S-nitroso- N -acetylpenicillamine, to activate the nonneuronal acetylcholine system. SNPiP-treated mice exhibited improved cardiac output and enhanced diastolic function, without an increase in heart rate. The nonneuronal acetylcholine-activating effects included increased resilience to ischemia, modulation of energy metabolism preference, and activation of angiogenesis. Here, we performed transcriptome analysis of SNPiP-treated mice ventricles to elucidate how SNPiP exerts beneficial effects on cardiac function. A time-course study (24 and 48 hours after SNPiP administration) revealed that SNPiP initially induced Wnt and cyclic guanosine monophosphate-protein kinase G signaling pathways, along with upregulation of genes involved in cardiac muscle tissue development and oxytocin signaling pathway. We also observed enrichment of glycolysis-related genes in response to SNPiP treatment, resulting in a metabolic shift from oxidative phosphorylation to glycolysis, which was suggested by reduced cardiac glucose contents while maintaining adenosine tri-phosphate levels. In addition, SNPiP significantly upregulated atrial natriuretic peptide and sarcolipin, which play crucial roles in calcium handling and cardiac performance. These findings suggest that SNPiP may have therapeutic potential based on the pleiotropic mechanisms elucidated in this study.
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Affiliation(s)
- Yasuhiro Takenaka
- Department of Bioregulatory Science, Graduate School of Medicine, Nippon Medical School, Tokyo, Japan
| | - Masataka Hirasaki
- Department of Clinical Cancer Genomics, International Medical Center, Saitama Medical University, Saitama, Japan
| | - Hidemasa Bono
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan; and
| | - Shigeo Nakamura
- Department of Chemistry, Nippon Medical School, Tokyo, Japan
| | - Yoshihiko Kakinuma
- Department of Bioregulatory Science, Graduate School of Medicine, Nippon Medical School, Tokyo, Japan
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Hamper M, Schmidt-Kastner R. Sleep Disorder Kleine-Levin Syndrome (KLS) Joins the List of Polygenic Brain Disorders Associated with Obstetric Complications. Cell Mol Neurobiol 2023; 43:3393-3403. [PMID: 37553546 DOI: 10.1007/s10571-023-01391-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 07/17/2023] [Indexed: 08/10/2023]
Abstract
Kleine-Levin Syndrome is a rare neurological disorder with onset typically during adolescence that is characterized by recurrent episodes of hypersomnia, behavioral changes, and cognitive abnormalities, in the absence of structural changes in neuroimaging. As for many functional brain disorders, the exact disease mechanism in Kleine-Levin Syndrome is presently unknown, preventing the development of specific treatment approaches or protective measures. Here we review the pathophysiology and genetics of this functional brain disorder and then present a specific working hypothesis. A neurodevelopmental mechanism has been suspected based on associations with obstetric complications. Recent studies have focused on genetic factors whereby the first genome-wide association study (GWAS) in Kleine-Levin Syndrome has defined a linkage at the TRANK1 locus. A Gene x Environment interaction model involving obstetric complications was proposed based on concepts developed for other functional brain disorders. To stimulate future research, we here performed annotations of the genes under consideration for Kleine-Levin Syndrome in relation to factors expected to be associated with obstetric complications. Annotations used data-mining of gene/protein lists related to for hypoxia, ischemia, and vascular factors and targeted literature searches. Tentative links for TRANK1, four additional genes in the TRANK1 locus, and LMOD3-LMO2 are described. Protein interaction data for TRANK1 indicate links to CBX2, CBX4, and KDM3A, that in turn can be tied to hypoxia. Taken together, the neurological sleep disorder, Kleine-Levin Syndrome, shows genetic and mechanistic overlap with well analyzed brain disorders such as schizophrenia, autism spectrum disorder and ADHD in which polygenic predisposition interacts with external events during brain development, including obstetric complications.
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Affiliation(s)
- Michael Hamper
- Florida Atlantic University (FAU), CE Schmidt College of Medicine, Boca Raton, FL, USA
| | - Rainald Schmidt-Kastner
- Florida Atlantic University (FAU), CE Schmidt College of Medicine, Boca Raton, FL, USA.
- Dept. Clinical Neurosciences, CE Schmidt College of Medicine, Florida Atlantic University (FAU), 777 Glades Road, Boca Raton, FL, 33431, USA.
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Piryaei Z, Salehi Z, Ebrahimie E, Ebrahimi M, Kavousi K. Meta-analysis of integrated ChIP-seq and transcriptome data revealed genomic regions affected by estrogen receptor alpha in breast cancer. BMC Med Genomics 2023; 16:219. [PMID: 37715225 PMCID: PMC10503144 DOI: 10.1186/s12920-023-01655-z] [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: 02/24/2023] [Accepted: 09/04/2023] [Indexed: 09/17/2023] Open
Abstract
BACKGROUND The largest group of patients with breast cancer are estrogen receptor-positive (ER+) type. The estrogen receptor acts as a transcription factor and triggers cell proliferation and differentiation. Hence, investigating ER-DNA interaction genomic regions can help identify genes directly regulated by ER and understand the mechanism of ER action in cancer progression. METHODS In the present study, we employed a workflow to do a meta-analysis of ChIP-seq data of ER+ cell lines stimulated with 10 nM and 100 nM of E2. All publicly available data sets were re-analyzed with the same platform. Then, the known and unknown batch effects were removed. Finally, the meta-analysis was performed to obtain meta-differentially bound sites in estrogen-treated MCF7 cell lines compared to vehicles (as control). Also, the meta-analysis results were compared with the results of T47D cell lines for more precision. Enrichment analyses were also employed to find the functional importance of common meta-differentially bound sites and associated genes among both cell lines. RESULTS Remarkably, POU5F1B, ZNF662, ZNF442, KIN, ZNF410, and SGSM2 transcription factors were recognized in the meta-analysis but not in individual studies. Enrichment of the meta-differentially bound sites resulted in the candidacy of pathways not previously reported in breast cancer. PCGF2, HNF1B, and ZBED6 transcription factors were also predicted through the enrichment analysis of associated genes. In addition, comparing the meta-analysis results of both ChIP-seq and RNA-seq data showed that many transcription factors affected by ER were up-regulated. CONCLUSION The meta-analysis of ChIP-seq data of estrogen-treated MCF7 cell line leads to the identification of new binding sites of ER that have not been previously reported. Also, enrichment of the meta-differentially bound sites and their associated genes revealed new terms and pathways involved in the development of breast cancer which should be examined in future in vitro and in vivo studies.
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Affiliation(s)
- Zeynab Piryaei
- Department of Bioinformatics, Kish International Campus University of Tehran, Kish, Iran
- Laboratory of Complex Biological Systems and Bioinformatics (CBB), Department of Bioinformatics, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Zahra Salehi
- Laboratory of Complex Biological Systems and Bioinformatics (CBB), Department of Bioinformatics, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
- Hematology-Oncology and Stem Cell Transplantation Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Esmaeil Ebrahimie
- Genomics Research Platform, School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, VIC, Australia
| | - Mansour Ebrahimi
- School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Kaveh Kavousi
- Laboratory of Complex Biological Systems and Bioinformatics (CBB), Department of Bioinformatics, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran.
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Yonezawa S, Bono H. Meta-Analysis of Heat-Stressed Transcriptomes Using the Public Gene Expression Database from Human and Mouse Samples. Int J Mol Sci 2023; 24:13444. [PMID: 37686255 PMCID: PMC10487629 DOI: 10.3390/ijms241713444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 08/21/2023] [Accepted: 08/29/2023] [Indexed: 09/10/2023] Open
Abstract
Climate change has significantly increased the frequency of our exposure to heat, adversely affecting human health and industries. Heat stress is an environmental stress defined as the exposure of organisms and cells to abnormally high temperatures. To comprehensively explain the mechanisms underlying an organism's response to heat stress, it is essential to investigate and analyze genes that have been under-represented or less well-known in previous studies. In this study, we analyzed heat stress-responsive genes using a meta-analysis of numerous gene expression datasets from the public database. We obtained 322 human and 242 mouse pairs as the heat exposure and control data. The meta-analysis of these data identified 76 upregulated and 37 downregulated genes common to both humans and mice. We performed enrichment, protein-protein interaction network, and transcription factor target gene analyses for these genes. Furthermore, we conducted an integrated analysis of these genes using publicly available chromatin immunoprecipitation sequencing (ChIP-seq) data for HSF1, HSF2, and PPARGC1A (PGC-1α) as well as gene2pubmed data from the existing literature. The results identified previously overlooked genes, such as ABHD3, ZFAND2A, and USPL1, as commonly upregulated genes. Further functional analysis of these genes can contribute to coping with climate change and potentially lead to technological advancements.
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Affiliation(s)
- Sora Yonezawa
- Laboratory of Genome Informatics, Graduate School of Integrated Sciences for Life, Hiroshima University, 3-10-23 Kagamiyama, Higashi-Hiroshima City 739-0046, Japan;
| | - Hidemasa Bono
- Laboratory of Genome Informatics, Graduate School of Integrated Sciences for Life, Hiroshima University, 3-10-23 Kagamiyama, Higashi-Hiroshima City 739-0046, Japan;
- Laboratory of BioDX, Genome Editing Innovation Center, Hiroshima University, 3-10-23 Kagamiyama, Higashi-Hiroshima City 739-0046, Japan
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Bläsius FM, Greven J, Guo W, Bolierakis E, He Z, Lübke C, Simon TP, Hildebrand F, Horst K. Local YB-1, Epo, and EpoR concentrations in fractured bones: results from a porcine model of multiple trauma. Eur J Med Res 2023; 28:25. [PMID: 36639666 PMCID: PMC9837984 DOI: 10.1186/s40001-023-00996-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 01/05/2023] [Indexed: 01/15/2023] Open
Abstract
Little is known about the impact of multiple trauma (MT)-related systemic hypoxia on osseous protein concentration of the hypoxia transcriptome. To shed light on this issue, we investigated erythropoietin (Epo), erythropoietin receptor (EpoR), and Y-box binding protein 1 (YB-1) concentrations in the fracture zone in a porcine MT + traumatic hemorrhage (TH) model. Sixteen male domestic pigs were randomized into two groups: an MT + TH group and a sham group. A tibia fracture, lung contusion, and TH were induced in the MT + TH group. The total observation period was 72 h. YB-1 concentrations in bone marrow (BM) were significantly lower in the fracture zone of the MT + TH animals than in the sham animals. Significant downregulation of BM-localized EpoR concentration in both unfractured and fractured bones was observed in the MT + TH animals relative to the sham animals. In BM, Epo concentrations were higher in the fracture zone of the MT + TH animals compared with that in the sham animals. Significantly higher Epo concentrations were detected in the BM of fractured bone compared to that in cortical bone. Our results provide the first evidence that MT + TH alters hypoxia-related protein concentrations. The impacts of both the fracture and concomitant injuries on protein concentrations need to be studied in more detail to shed light on the hypoxia transcriptome in fractured and healthy bones after MT + TH.
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Affiliation(s)
- Felix Marius Bläsius
- grid.1957.a0000 0001 0728 696XDeptartment of Orthopaedics, Trauma and Reconstructive Surgery, University Hospital, RWTH University, Pauwelsstraße 30, 52074 Aachen, Germany ,grid.1957.a0000 0001 0728 696XInsitute of Pharmacology and Toxicology, University Hospital, RWTH University, Aachen, Germany
| | - Johannes Greven
- grid.1957.a0000 0001 0728 696XDeptartment of Orthopaedics, Trauma and Reconstructive Surgery, University Hospital, RWTH University, Pauwelsstraße 30, 52074 Aachen, Germany
| | - Weijun Guo
- grid.1957.a0000 0001 0728 696XDeptartment of Orthopaedics, Trauma and Reconstructive Surgery, University Hospital, RWTH University, Pauwelsstraße 30, 52074 Aachen, Germany
| | - Eftychios Bolierakis
- grid.1957.a0000 0001 0728 696XDeptartment of Orthopaedics, Trauma and Reconstructive Surgery, University Hospital, RWTH University, Pauwelsstraße 30, 52074 Aachen, Germany
| | - Zhizhen He
- grid.1957.a0000 0001 0728 696XDeptartment of Orthopaedics, Trauma and Reconstructive Surgery, University Hospital, RWTH University, Pauwelsstraße 30, 52074 Aachen, Germany
| | - Cavan Lübke
- grid.1957.a0000 0001 0728 696XDepartment of Intensive Care and Intermediate Care, University Hospital, RWTH University, Aachen, Germany
| | - Tim-Philipp Simon
- grid.1957.a0000 0001 0728 696XDepartment of Intensive Care and Intermediate Care, University Hospital, RWTH University, Aachen, Germany
| | - Frank Hildebrand
- grid.1957.a0000 0001 0728 696XDeptartment of Orthopaedics, Trauma and Reconstructive Surgery, University Hospital, RWTH University, Pauwelsstraße 30, 52074 Aachen, Germany
| | - Klemens Horst
- grid.1957.a0000 0001 0728 696XDeptartment of Orthopaedics, Trauma and Reconstructive Surgery, University Hospital, RWTH University, Pauwelsstraße 30, 52074 Aachen, Germany
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Welch N, Singh SS, Musich R, Mansuri MS, Bellar A, Mishra S, Chelluboyina AK, Sekar J, Attaway AH, Li L, Willard B, Hornberger TA, Dasarathy S. Shared and unique phosphoproteomics responses in skeletal muscle from exercise models and in hyperammonemic myotubes. iScience 2022; 25:105325. [PMID: 36345342 PMCID: PMC9636548 DOI: 10.1016/j.isci.2022.105325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 08/22/2022] [Accepted: 10/07/2022] [Indexed: 11/06/2022] Open
Abstract
Skeletal muscle generation of ammonia, an endogenous cytotoxin, is increased during exercise. Perturbations in ammonia metabolism consistently occur in chronic diseases, and may blunt beneficial skeletal muscle molecular responses and protein homeostasis with exercise. Phosphorylation of skeletal muscle proteins mediates cellular signaling responses to hyperammonemia and exercise. Comparative bioinformatics and machine learning-based analyses of published and experimentally derived phosphoproteomics data identified differentially expressed phosphoproteins that were unique and shared between hyperammonemic murine myotubes and skeletal muscle from exercise models. Enriched processes identified in both hyperammonemic myotubes and muscle from exercise models with selected experimental validation included protein kinase A (PKA), calcium signaling, mitogen-activated protein kinase (MAPK) signaling, and protein homeostasis. Our approach of feature extraction from comparative untargeted "omics" data allows for selection of preclinical models that recapitulate specific human exercise responses and potentially optimize functional capacity and skeletal muscle protein homeostasis with exercise in chronic diseases.
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Affiliation(s)
- Nicole Welch
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, OH 44195, USA
- Department of Gastroenterology and Hepatology, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Shashi Shekhar Singh
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Ryan Musich
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, OH 44195, USA
| | - M. Shahid Mansuri
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Annette Bellar
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Saurabh Mishra
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, OH 44195, USA
| | | | - Jinendiran Sekar
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Amy H. Attaway
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Ling Li
- Proteomics Core, Cleveland Clinic, Cleveland, OH 44195, USA
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53706, USA
| | - Belinda Willard
- Proteomics Core, Cleveland Clinic, Cleveland, OH 44195, USA
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53706, USA
| | - Troy A. Hornberger
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53706, USA
| | - Srinivasan Dasarathy
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, OH 44195, USA
- Department of Gastroenterology and Hepatology, Cleveland Clinic, Cleveland, OH 44195, USA
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Vora M, Pyonteck SM, Popovitchenko T, Matlack TL, Prashar A, Kane NS, Favate J, Shah P, Rongo C. The hypoxia response pathway promotes PEP carboxykinase and gluconeogenesis in C. elegans. Nat Commun 2022; 13:6168. [PMID: 36257965 PMCID: PMC9579151 DOI: 10.1038/s41467-022-33849-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 10/05/2022] [Indexed: 12/31/2022] Open
Abstract
Actively dividing cells, including some cancers, rely on aerobic glycolysis rather than oxidative phosphorylation to generate energy, a phenomenon termed the Warburg effect. Constitutive activation of the Hypoxia Inducible Factor (HIF-1), a transcription factor known for mediating an adaptive response to oxygen deprivation (hypoxia), is a hallmark of the Warburg effect. HIF-1 is thought to promote glycolysis and suppress oxidative phosphorylation. Here, we instead show that HIF-1 can promote gluconeogenesis. Using a multiomics approach, we reveal the genomic, transcriptomic, and metabolomic landscapes regulated by constitutively active HIF-1 in C. elegans. We use RNA-seq and ChIP-seq under aerobic conditions to analyze mutants lacking EGL-9, a key negative regulator of HIF-1. We integrate these approaches to identify over two hundred genes directly and functionally upregulated by HIF-1, including the PEP carboxykinase PCK-1, a rate-limiting mediator of gluconeogenesis. This activation of PCK-1 by HIF-1 promotes survival in response to both oxidative and hypoxic stress. Our work identifies functional direct targets of HIF-1 in vivo, comprehensively describing the metabolome induced by HIF-1 activation in an organism.
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Affiliation(s)
- Mehul Vora
- The Waksman Institute, Rutgers The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Stephanie M Pyonteck
- The Waksman Institute, Rutgers The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Tatiana Popovitchenko
- The Waksman Institute, Rutgers The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Tarmie L Matlack
- The Waksman Institute, Rutgers The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Aparna Prashar
- The Department of Genetics, Rutgers The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Nanci S Kane
- The Waksman Institute, Rutgers The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - John Favate
- The Department of Genetics, Rutgers The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Premal Shah
- The Department of Genetics, Rutgers The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Christopher Rongo
- The Waksman Institute, Rutgers The State University of New Jersey, Piscataway, NJ, 08854, USA. .,The Department of Genetics, Rutgers The State University of New Jersey, Piscataway, NJ, 08854, USA.
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Ono Y, Bono H. Exploratory meta-analysis of hypoxic transcriptomes using a precise transcript reference sequence set. Life Sci Alliance 2022; 6:6/1/e202201518. [PMID: 36216516 PMCID: PMC9553900 DOI: 10.26508/lsa.202201518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 09/23/2022] [Accepted: 09/26/2022] [Indexed: 11/24/2022] Open
Abstract
Gene expression studies are intrinsically biased, with many studies influenced by concomitant information such as gene-disease associations. This limitation can be overcome using a data-driven analysis approach without relying on ancillary information. The FANTOM CAGE-Associated Transcriptome project provides a comprehensive meta-assembly of the human transcriptome using coding and noncoding genes. Hypoxia strongly influences gene expression; in addition, noncoding RNA (ncRNA) metabolism is down-regulated in response to hypoxic stimuli. We evaluated the differential response of various transcripts to hypoxia by determining their hypoxia responsiveness scores. Enrichment analysis revealed that several genes associated with ncRNA metabolism, particularly those involved in ribosomal RNA processing, were down-regulated in response to hypoxia. Previously published information from the FANTOM CAGE-Associated Transcriptome project was suitable for meta-analysis of the transcriptome sequencing data from both coding and ncRNAs and to evaluate the hypoxia responsiveness of target transcripts and relationship between sense-antisense transcripts from the same locus. Our results may facilitate functional annotation of various transcripts including ncRNAs, allowing for both sense and antisense and coding and noncoding evaluations.
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Affiliation(s)
- Yoko Ono
- Laboratory of Genome Informatics, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Japan
| | - Hidemasa Bono
- Laboratory of Genome Informatics, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Japan .,Laboratory of Bio-DX, Genome Editing Innovation Center, Hiroshima University, Higashihiroshima, Japan
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11
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Formal Meta-Analysis of Hypoxic Gene Expression Profiles Reveals a Universal Gene Signature. Biomedicines 2022; 10:biomedicines10092229. [PMID: 36140330 PMCID: PMC9496516 DOI: 10.3390/biomedicines10092229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 08/29/2022] [Accepted: 09/02/2022] [Indexed: 11/16/2022] Open
Abstract
Integrating transcriptional profiles results in identifying gene expression signatures that are more robust than those obtained for individual datasets. However, a direct comparison of datasets derived from heterogeneous experimental conditions is problematic, hence their integration requires applying of specific meta-analysis techniques. The transcriptional response to hypoxia has been the focus of intense research due to its central role in tissue homeostasis and prevalent diseases. Accordingly, many studies have determined the gene expression profile of hypoxic cells. Yet, despite this wealth of information, little effort has been made to integrate these datasets to produce a robust hypoxic signature. We applied a formal meta-analysis procedure to datasets comprising 430 RNA-seq samples from 43 individual studies including 34 different cell types, to derive a pooled estimate of the effect of hypoxia on gene expression in human cell lines grown ingin vitro. This approach revealed that a large proportion of the transcriptome is significantly regulated by hypoxia (8556 out of 20,888 genes identified across studies). However, only a small fraction of the differentially expressed genes (1265 genes, 15%) show an effect size that, according to comparisons to gene pathways known to be regulated by hypoxia, is likely to be biologically relevant. By focusing on genes ubiquitously expressed, we identified a signature of 291 genes robustly and consistently regulated by hypoxia. Overall, we have developed a robust gene signature that characterizes the transcriptomic response of human cell lines exposed to hypoxia in vitro by applying a formal meta-analysis to gene expression profiles.
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12
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Tamura K, Bono H. Meta-Analysis of RNA Sequencing Data of Arabidopsis and Rice under Hypoxia. Life (Basel) 2022; 12:1079. [PMID: 35888167 PMCID: PMC9317734 DOI: 10.3390/life12071079] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/16/2022] [Accepted: 07/18/2022] [Indexed: 11/30/2022] Open
Abstract
Hypoxia is an abiotic stress in plants. Flooding resulting from climate change is a major crop threat that increases the risk of hypoxic stress. The molecular mechanisms underlying hypoxia in plants were elucidated in recent years, but new genes related to this stress remain to be discovered. Thus, we aimed to perform a meta-analysis of the RNA sequencing (RNA-Seq) data of Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) under hypoxia. We collected 29 (Arabidopsis) and 26 (rice) pairs of RNA-Seq data involving hypoxic (including submergence) and normoxic (control) treatments and extracted the genes that were commonly upregulated or downregulated in the majority of the experiments. The meta-analysis revealed 40 and 19 commonly upregulated and downregulated genes, respectively, in the two species. Several WRKY transcription factors and cinnamate-4-hydroxylase were commonly upregulated, but their involvement in hypoxia remains unclear. Our meta-analysis identified candidate genes for novel molecular mechanisms in plants under hypoxia.
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Affiliation(s)
- Keita Tamura
- Laboratory of Genome Informatics, Graduate School of Integrated Sciences for Life, Hiroshima University, 3-10-23 Kagamiyama, Higashi-Hiroshima 739-0046, Hiroshima, Japan;
- Laboratory of BioDX, Genome Editing Innovation Center, Hiroshima University, 3-10-23 Kagamiyama, Higashi-Hiroshima 739-0046, Hiroshima, Japan
| | - Hidemasa Bono
- Laboratory of Genome Informatics, Graduate School of Integrated Sciences for Life, Hiroshima University, 3-10-23 Kagamiyama, Higashi-Hiroshima 739-0046, Hiroshima, Japan;
- Laboratory of BioDX, Genome Editing Innovation Center, Hiroshima University, 3-10-23 Kagamiyama, Higashi-Hiroshima 739-0046, Hiroshima, Japan
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13
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Kiessling E, Peters F, Ebner LJ, Merolla L, Samardzija M, Baumgartner MR, Grimm C, Froese DS. HIF1 and DROSHA are involved in MMACHC repression in hypoxia. Biochim Biophys Acta Gen Subj 2022; 1866:130175. [DOI: 10.1016/j.bbagen.2022.130175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 05/03/2022] [Accepted: 05/23/2022] [Indexed: 11/25/2022]
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14
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Katsman M, Azriel A, Horev G, Reizel Y, Levi BZ. N-VEGF, the Autoregulatory Arm of VEGF-A. Cells 2022; 11:cells11081289. [PMID: 35455969 PMCID: PMC9024919 DOI: 10.3390/cells11081289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/05/2022] [Accepted: 04/09/2022] [Indexed: 02/04/2023] Open
Abstract
Vascular endothelial growth factor A (VEGF-A) is a secreted protein that stimulates angiogenesis in response to hypoxia. Under hypoxic conditions, a non-canonical long isoform called L-VEGF is concomitantly expressed with VEGF-A. Once translated, L-VEGF is proteolytically cleaved to generate N-VEGF and VEGF-A. Interestingly, while VEGF-A is secreted and affects the surrounding cells, N-VEGF is mobilized to the nucleus. This suggests that N-VEGF participates in transcriptional response to hypoxia. In this study, we performed a series of complementary experiments to examine the functional role of N-VEGF. Strikingly, we found that the mere expression of N-VEGF followed by its hypoxia-independent mobilization to the nucleus was sufficient to induce key genes associated with angiogenesis, such as Hif1α,VEGF-A isoforms, as well as genes associated with cell survival under hypoxia. Complementarily, when N-VEGF was genetically depleted, key hypoxia-induced genes were downregulated and cells were significantly susceptible to hypoxia-mediated apoptosis. This is the first report of N-VEGF serving as an autoregulatory arm of VEGF-A. Further experiments will be needed to determine the role of N-VEGF in cancer and embryogenesis.
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Affiliation(s)
- Marina Katsman
- Faculty of Biotechnology and Food Engineering, Technion-Israel, Institute of Technology, Haifa 3200003, Israel; (M.K.); (A.A.)
| | - Aviva Azriel
- Faculty of Biotechnology and Food Engineering, Technion-Israel, Institute of Technology, Haifa 3200003, Israel; (M.K.); (A.A.)
| | - Guy Horev
- Bioinformatics Knowledge Unit, The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering, Technion-Israel, Institute of Technology, Haifa 3200003, Israel;
| | - Yitzhak Reizel
- Faculty of Biotechnology and Food Engineering, Technion-Israel, Institute of Technology, Haifa 3200003, Israel; (M.K.); (A.A.)
- Correspondence: (Y.R.); (B.-Z.L.)
| | - Ben-Zion Levi
- Faculty of Biotechnology and Food Engineering, Technion-Israel, Institute of Technology, Haifa 3200003, Israel; (M.K.); (A.A.)
- Correspondence: (Y.R.); (B.-Z.L.)
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15
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Ajouaou Y, Azouz A, Taquin A, Denanglaire S, Hussein H, Krayem M, Andris F, Moser M, Goriely S, Leo O. The oxygen sensor Prolyl hydroxylase domain 2 regulates the in vivo suppressive capacity of regulatory T cells. eLife 2022; 11:70555. [PMID: 35192456 PMCID: PMC8896828 DOI: 10.7554/elife.70555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 02/18/2022] [Indexed: 11/26/2022] Open
Abstract
The oxygen sensor prolyl hydroxylase domain 2 (PHD2) plays an important role in cell hypoxia adaptation by regulating the stability of HIF proteins (HIF1α and HIF2α) in numerous cell types, including T lymphocytes. The role of oxygen sensor on immune cells, particularly on regulatory T cell (Treg) function, has not been fully elucidated. The purpose of our study was to evaluate the role of PHD2 in the regulation of Treg phenotype and function. We demonstrate herein that selective ablation of PHD2 expression in Treg (PHD2ΔTreg mice) leads to a spontaneous systemic inflammatory syndrome, as evidenced by weight loss, development of a rectal prolapse, splenomegaly, shortening of the colon, and elevated expression of IFN-γ in the mesenteric lymph nodes, intestine, and spleen. PHD2 deficiency in Tregs led to an increased number of activated CD4 conventional T cells expressing a Th1-like effector phenotype. Concomitantly, the expression of innate-type cytokines such as Il1b, Il12a, Il12b, and Tnfa was found to be elevated in peripheral (gut) tissues and spleen. PHD2ΔTreg mice also displayed an enhanced sensitivity to dextran sodium sulfate-induced colitis and toxoplasmosis, suggesting that PHD2-deficient Tregs did not efficiently control inflammatory response in vivo, particularly those characterized by IFN-γ production. Further analysis revealed that Treg dysregulation was largely prevented in PHD2-HIF2α (PHD2-HIF2αΔTreg mice), but not in PHD2-HIF1α (PHD2-HIF1αΔTreg mice) double KOs, suggesting an important and possibly selective role of the PHD2-HIF2α axis in the control of Treg function. Finally, the transcriptomic analysis of PHD2-deficient Tregs identified the STAT1 pathway as a target of the PHD2-HIF2α axis in regulatory T cell phenotype and in vivo function.
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Affiliation(s)
| | | | | | | | - Hind Hussein
- Université Libre de Bruxelles, Gosselies, Belgium
| | - Mohammad Krayem
- Department of Radiation Oncology, Université Libre de Bruxelles, Brussels, Belgium
| | | | - Muriel Moser
- Université Libre de Bruxelles, Gosselies, Belgium
| | | | - Oberdan Leo
- Université Libre de Bruxelles, Gosselies, Belgium
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16
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Batie M, Kenneth NS, Rocha S. Systems approaches to understand oxygen sensing: how multi-omics has driven advances in understanding oxygen-based signalling. Biochem J 2022; 479:245-257. [PMID: 35119457 PMCID: PMC8883490 DOI: 10.1042/bcj20210554] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/06/2022] [Accepted: 01/10/2022] [Indexed: 12/11/2022]
Abstract
Hypoxia is a common denominator in the pathophysiology of a variety of human disease states. Insight into how cells detect, and respond to low oxygen is crucial to understanding the role of hypoxia in disease. Central to the hypoxic response is rapid changes in the expression of genes essential to carry out a wide range of functions to adapt the cell/tissue to decreased oxygen availability. These changes in gene expression are co-ordinated by specialised transcription factors, changes to chromatin architecture and intricate balances between protein synthesis and destruction that together establish changes to the cellular proteome. In this article, we will discuss the advances of our understanding of the cellular oxygen sensing machinery achieved through the application of 'omics-based experimental approaches.
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Affiliation(s)
- Michael Batie
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool L697ZB, U.K
| | - Niall S. Kenneth
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool L697ZB, U.K
| | - Sonia Rocha
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool L697ZB, U.K
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17
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Hirota K. Special Issue: Hypoxia-Inducible Factors: Regulation and Therapeutic Potential. Biomedicines 2021; 9:biomedicines9121768. [PMID: 34944583 PMCID: PMC8698262 DOI: 10.3390/biomedicines9121768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 10/29/2021] [Indexed: 11/19/2022] Open
Affiliation(s)
- Kiichi Hirota
- Department of Human Stress Response Science, Institute of Biomedical Science, Kansai Medical University, Hirakata 573-1010, Osaka, Japan
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18
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Barthelson K, Pederson SM, Newman M, Lardelli M. Brain Transcriptome Analysis of a Protein-Truncating Mutation in Sortilin-Related Receptor 1 Associated With Early-Onset Familial Alzheimer's Disease Indicates Early Effects on Mitochondrial and Ribosome Function. J Alzheimers Dis 2021; 79:1105-1119. [PMID: 33386808 DOI: 10.3233/jad-201383] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND The early cellular stresses leading to Alzheimer's disease (AD) remain poorly understood because we cannot access living, asymptomatic human AD brains for detailed molecular analyses. Sortilin-related receptor 1 (SORL1) encodes a multi-domain receptor protein genetically associated with both rare, early-onset familial AD (EOfAD) and common, sporadic, late-onset AD (LOAD). SORL1 protein has been shown to act in the trafficking of the amyloid β A4 precursor protein (AβPP) that is proteolysed to form one of the pathological hallmarks of AD, amyloid-β (Aβ) peptide. However, other functions of SORL1 in AD are less well understood. OBJECTIVE To investigate the effects of heterozygosity for an EOfAD-like mutation in SORL1 on the brain transcriptome of young-adult mutation carriers using zebrafish as a model organism. METHODS We performed targeted mutagenesis to generate an EOfAD-like mutation in the zebrafish orthologue of SORL1 and performed RNA-sequencing on mRNA isolated from the young adult brains of siblings in a family of fish either wild type (non-mutant) or heterozygous for the EOfAD-like mutation. RESULTS We identified subtle differences in gene expression indicating changes in mitochondrial and ribosomal function in the mutant fish. These changes appear to be independent of changes in mitochondrial content or the expression of AβPP-related proteins in zebrafish. CONCLUSION These findings provided evidence supporting that EOfAD mutations in SORL1 affect mitochondrial and ribosomal function and provide the basis for future investigation elucidating the nature of these effects.
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Affiliation(s)
- Karissa Barthelson
- Alzheimer's Disease Genetics Laboratory, School of Biological Sciences, University of Adelaide, North Terrace, Adelaide, SA, Australia
| | - Stephen Martin Pederson
- Bioinformatics Hub, School of Biological Sciences, University of Adelaide, North Terrace, Adelaide, SA, Australia
| | - Morgan Newman
- Alzheimer's Disease Genetics Laboratory, School of Biological Sciences, University of Adelaide, North Terrace, Adelaide, SA, Australia
| | - Michael Lardelli
- Alzheimer's Disease Genetics Laboratory, School of Biological Sciences, University of Adelaide, North Terrace, Adelaide, SA, Australia
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19
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Gene Expression Profile of Human Mesenchymal Stromal Cells Exposed to Hypoxic and Pseudohypoxic Preconditioning-An Analysis by RNA Sequencing. Int J Mol Sci 2021; 22:ijms22158160. [PMID: 34360925 PMCID: PMC8348678 DOI: 10.3390/ijms22158160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/24/2021] [Accepted: 07/26/2021] [Indexed: 12/31/2022] Open
Abstract
Mesenchymal stromal cell (MSC) therapy is making its way into clinical practice, accompanied by research into strategies improving their therapeutic potential. Preconditioning MSCs with hypoxia-inducible factors-α (HIFα) stabilizers is an alternative to hypoxic priming, but there remains insufficient data evaluating its transcriptomic effect. Herein, we determined the gene expression profile of 6 human bone marrow-derived MSCs preconditioned for 6 h in 2% O2 (hypoxia) or with 40 μM Vadadustat, compared to control cells and each other. RNA-Sequencing was performed using the Illumina platform, quality control with FastQC and adapter-trimming with BBDUK2. Transcripts were mapped to the Homo_sapiens. GRCh37 genome and converted to relative expression using Salmon. Differentially expressed genes (DEGs) were generated using DESeq2 while functional enrichment was performed in GSEA and g:Profiler. Comparison of hypoxia versus control resulted in 250 DEGs, Vadadustat versus control 1071, and Vadadustat versus hypoxia 1770. The terms enriched in both phenotypes referred mainly to metabolism, in Vadadustat additionally to vesicular transport, chromatin modifications and interaction with extracellular matrix. Compared with hypoxia, Vadadustat upregulated autophagic, phospholipid metabolism, and TLR cascade genes, downregulated those of cytoskeleton and GG-NER pathway and regulated 74 secretory factor genes. Our results provide valuable insight into the transcriptomic effects of these two methods of MSCs preconditioning.
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20
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Uba T, Matsuo Y, Sumi C, Shoji T, Nishi K, Kusunoki M, Harada H, Kimura H, Bono H, Hirota K. Polysulfide inhibits hypoxia-elicited hypoxia-inducible factor activation in a mitochondria-dependent manner. Mitochondrion 2021; 59:255-266. [PMID: 34133955 DOI: 10.1016/j.mito.2021.06.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 05/20/2021] [Accepted: 06/11/2021] [Indexed: 11/27/2022]
Abstract
In cellular signaling, the diverse physiological actions of biological gases, including O2, CO, NO, and H2S, have attracted much interest. Hypoxia-inducible factors (HIFs), including HIF-1 and HIF-2, are transcription factors that respond to reduced intracellular O2 availability. Polysulfides are substances containing varying numbers of sulfur atoms (H2Sn) that are generated endogenously from H2S by 3-mercaptopyruvate sulfurtransferase in the presence of O2, and regulate ion channels, specific tumor suppressors, and protein kinases. However, the effect of polysulfides on HIF activation in hypoxic mammalian cells is largely unknown. Here, we have investigated the effect of polysulfide on cells in vitro. In established cell lines, polysulfide donors reversibly reduced cellular O2 consumption and inhibited hypoxia-induced HIF-1α protein accumulation and the expression of genes downstream of HIFs; however, these effects were not observed in anoxia. In Von Hippel-Lindau tumor suppressor (VHL)- and mitochondria-deficient cells, polysulfides did not affect HIF-1α protein synthesis but destabilized it in a VHL- and mitochondria-dependent manner. For the first time, we show that polysulfides modulate intracellular O2 homeostasis and regulate HIF activation and subsequent hypoxia-induced gene expression in a VHL- and mitochondria-dependent manner.
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Affiliation(s)
- Takeo Uba
- Department of Human Stress Response Science, Institute of Biomedical Science, Kansai Medical University, Hirakata 573-1010, Japan; Department of Anesthesiology, Kansai Medical University, Hirakata 573-1010, Japan
| | - Yoshiyuki Matsuo
- Department of Human Stress Response Science, Institute of Biomedical Science, Kansai Medical University, Hirakata 573-1010, Japan
| | - Chisato Sumi
- Department of Human Stress Response Science, Institute of Biomedical Science, Kansai Medical University, Hirakata 573-1010, Japan
| | - Tomohiro Shoji
- Department of Human Stress Response Science, Institute of Biomedical Science, Kansai Medical University, Hirakata 573-1010, Japan; Department of Anesthesiology, Kansai Medical University, Hirakata 573-1010, Japan
| | - Kenichiro Nishi
- Department of Human Stress Response Science, Institute of Biomedical Science, Kansai Medical University, Hirakata 573-1010, Japan
| | - Munenori Kusunoki
- Department of Human Stress Response Science, Institute of Biomedical Science, Kansai Medical University, Hirakata 573-1010, Japan
| | - Hiroshi Harada
- Laboratory of Cancer Cell Biology, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
| | - Hideo Kimura
- Department of Pharmacology, Faculty of Pharmaceutical Science, Sanyo-Onoda City University, Sanyo-Onoda 756-0884, Japan
| | - Hidemasa Bono
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima 739-0046, Japan
| | - Kiichi Hirota
- Department of Human Stress Response Science, Institute of Biomedical Science, Kansai Medical University, Hirakata 573-1010, Japan.
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21
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Rao VKS, Eipper BA, Mains RE. Multiple roles for peptidylglycine α-amidating monooxygenase in the response to hypoxia. J Cell Physiol 2021; 236:7745-7758. [PMID: 34061983 DOI: 10.1002/jcp.30457] [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: 02/25/2021] [Revised: 05/10/2021] [Accepted: 05/19/2021] [Indexed: 11/11/2022]
Abstract
The biosynthesis of many of the peptides involved in homeostatic control requires peptidylglycine α-amidating monooxygenase (PAM), an ancient, highly conserved copper- and ascorbate-dependent enzyme. Using the production of amidated chromogranin A to monitor PAM function in tumor cells, physiologically relevant levels of hypoxia were shown to inhibit this monooxygenase. The ability of primary pituitary cells exposed to hypoxic conditions for 4 h to produce amidated chromogranin A was similarly inhibited. The affinity of the purified monooxygenase for oxygen (Km = 99 ± 19 μM) was consistent with this result. The ability of PAM to alter secretory pathway behavior under normoxic conditions required its monooxygenase activity. Under normoxic conditions, hypoxia-inducible factor 1a levels in dense cultures of corticotrope tumor cells expressing high levels of PAM exceeded those in control cells; expression of inactive monooxygenase did not have this effect. The effects of hypoxia on levels of two PAM-regulated genes (activating transcription factor 3 [Atf3] and FK506 binding protein 2 [Fkbp2]) differed in cells expressing high versus low levels of PAM. Putative hypoxia response elements occur in both human and mouse PAM, and hPAM has consistently been identified as one of the genes upregulated in response to hypoxia. Expression of PAM is also known to alter gene expression. A quarter of the genes consistently upregulated in response to hypoxia were downregulated following increased expression of PAM. Taken together, our data suggest roles for PAM and amidated peptide secretion in the coordination of tissue-specific responses to hypoxia.
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Affiliation(s)
- Vishwanatha K S Rao
- Department of Neuroscience, University of Connecticut Health Center, Farmington, Connecticut, USA
| | - Betty A Eipper
- Department of Neuroscience, University of Connecticut Health Center, Farmington, Connecticut, USA.,Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, Connecticut, USA
| | - Richard E Mains
- Department of Neuroscience, University of Connecticut Health Center, Farmington, Connecticut, USA
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22
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Multi-Omic Meta-Analysis of Transcriptomes and the Bibliome Uncovers Novel Hypoxia-Inducible Genes. Biomedicines 2021; 9:biomedicines9050582. [PMID: 34065451 PMCID: PMC8160971 DOI: 10.3390/biomedicines9050582] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/15/2021] [Accepted: 05/19/2021] [Indexed: 12/30/2022] Open
Abstract
Hypoxia is a condition in which cells, tissues, or organisms are deprived of sufficient oxygen supply. Aerobic organisms have a hypoxic response system, represented by hypoxia-inducible factor 1-α (HIF1A), to adapt to this condition. Due to publication bias, there has been little focus on genes other than well-known signature hypoxia-inducible genes. Therefore, in this study, we performed a meta-analysis to identify novel hypoxia-inducible genes. We searched publicly available transcriptome databases to obtain hypoxia-related experimental data, retrieved the metadata, and manually curated it. We selected the genes that are differentially expressed by hypoxic stimulation, and evaluated their relevance in hypoxia by performing enrichment analyses. Next, we performed a bibliometric analysis using gene2pubmed data to examine genes that have not been well studied in relation to hypoxia. Gene2pubmed data provides information about the relationship between genes and publications. We calculated and evaluated the number of reports and similarity coefficients of each gene to HIF1A, which is a representative gene in hypoxia studies. In this data-driven study, we report that several genes that were not known to be associated with hypoxia, including the G protein-coupled receptor 146 gene, are upregulated by hypoxic stimulation.
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23
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Hirota K. Hypoxia-dependent signaling in perioperative and critical care medicine. J Anesth 2021; 35:741-756. [PMID: 34003375 PMCID: PMC8128984 DOI: 10.1007/s00540-021-02940-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 04/24/2021] [Indexed: 12/14/2022]
Abstract
A critical goal of patient management for anesthesiologists and intensivists is to maintain oxygen homeostasis in patients admitted to operation theaters and intensive care units. For this purpose, it is imperative to understand the strategies of the body against oxygen imbalance—especially oxygen deficiency (hypoxia). Adaptation to hypoxia and maintenance of oxygen homeostasis involve a wide range of responses that occur at different organizational levels in the body. These responses are greatly influenced by perioperative patient management including factors such as perioperative drugs. Herein, the influence of perioperative patient management on the body's response to oxygen imbalance was reviewed with a special emphasis on hypoxia-inducible factors (HIFs), transcription factors whose activity are regulated by the perturbation of oxygen metabolism. The 2019 Nobel Prize in Physiology or Medicine was awarded to three researchers who made outstanding achievements in this field. While previous studies have reported the effect of perioperatively used drugs on hypoxia-induced gene expression mediated by HIFs, this review focused on effects of subacute or chronic hypoxia changes in gene expression that are mediated by the transcriptional regulator HIFs. The clinical implications and perspectives of these findings also will be discussed. Understanding the basic biology of the transcription factor HIF can be informative for us since anesthesiologists manage patients during the perioperative period facing the imbalances the oxygen metabolism in organ and tissue. The clinical implications of hypoxia-dependent signaling in critical illness, including Coronavirus disease (COVID-19), in which disturbances in oxygen metabolism play a major role in its pathogenesis will also be discussed.
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Affiliation(s)
- Kiichi Hirota
- Department of Human Stress Response Science, Institute of Biomedical Science, Kansai Medical University, Hirakata, Japan.
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24
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Bono H. Meta-Analysis of Oxidative Transcriptomes in Insects. Antioxidants (Basel) 2021; 10:antiox10030345. [PMID: 33669076 PMCID: PMC7996572 DOI: 10.3390/antiox10030345] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 02/17/2021] [Accepted: 02/22/2021] [Indexed: 11/29/2022] Open
Abstract
Data accumulation in public databases has resulted in extensive use of meta-analysis, a statistical analysis that combines the results of multiple studies. Oxidative stress occurs when there is an imbalance between free radical activity and antioxidant activity, which can be studied in insects by transcriptome analysis. This study aimed to apply a meta-analysis approach to evaluate insect oxidative transcriptomes using publicly available data. We collected oxidative stress response-related RNA sequencing (RNA-seq) data for a wide variety of insect species, mainly from public gene expression databases, by manual curation. Only RNA-seq data of Drosophila melanogaster were found and were systematically analyzed using a newly developed RNA-seq analysis workflow for species without a reference genome sequence. The results were evaluated by two metric methods to construct a reference dataset for oxidative stress response studies. Many genes were found to be downregulated under oxidative stress and related to organ system process (GO:0003008) and adherens junction organization (GO:0034332) by gene enrichment analysis. A cross-species analysis was also performed. RNA-seq data of Caenorhabditis elegans were curated, since no RNA-seq data of insect species are currently available in public databases. This method, including the workflow developed, represents a powerful tool for deciphering conserved networks in oxidative stress response.
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Affiliation(s)
- Hidemasa Bono
- Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, 3-10-23 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-0046, Japan; ; Tel.: +81-82-424-4013
- Database Center for Life Science (DBCLS), Joint Support-Center for Data Science Research, Research Organization of Information and Systems, 178-4-4 Wakashiba, Kashiwa, Chiba 277-0871, Japan
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25
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Lim N, Tesar S, Belmadani M, Poirier-Morency G, Mancarci BO, Sicherman J, Jacobson M, Leong J, Tan P, Pavlidis P. Curation of over 10 000 transcriptomic studies to enable data reuse. Database (Oxford) 2021; 2021:6143045. [PMID: 33599246 PMCID: PMC7904053 DOI: 10.1093/database/baab006] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 12/09/2020] [Accepted: 01/28/2021] [Indexed: 01/07/2023]
Abstract
Vast amounts of transcriptomic data reside in public repositories, but effective reuse remains challenging. Issues include unstructured dataset metadata, inconsistent data processing and quality control, and inconsistent probe-gene mappings across microarray technologies. Thus, extensive curation and data reprocessing are necessary prior to any reuse. The Gemma bioinformatics system was created to help address these issues. Gemma consists of a database of curated transcriptomic datasets, analytical software, a web interface and web services. Here we present an update on Gemma's holdings, data processing and analysis pipelines, our curation guidelines, and software features. As of June 2020, Gemma contains 10 811 manually curated datasets (primarily human, mouse and rat), over 395 000 samples and hundreds of curated transcriptomic platforms (both microarray and RNA sequencing). Dataset topics were represented with 10 215 distinct terms from 12 ontologies, for a total of 54 316 topic annotations (mean topics/dataset = 5.2). While Gemma has broad coverage of conditions and tissues, it captures a large majority of available brain-related datasets, accounting for 34% of its holdings. Users can access the curated data and differential expression analyses through the Gemma website, RESTful service and an R package. Database URL: https://gemma.msl.ubc.ca/home.html.
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Affiliation(s)
- Nathaniel Lim
- Genome Science and Technology Graduate Program, University of British Columbia, Vancouver, BC V6T1Z4, Canada,Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T1Z4, Canada
| | - Stepan Tesar
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T1Z4, Canada
| | - Manuel Belmadani
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T1Z4, Canada
| | - Guillaume Poirier-Morency
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T1Z4, Canada
| | - Burak Ogan Mancarci
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T1Z4, Canada,Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC V6T1Z4, Canada
| | - Jordan Sicherman
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T1Z4, Canada,Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC V6T1Z4, Canada
| | - Matthew Jacobson
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T1Z4, Canada
| | - Justin Leong
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T1Z4, Canada
| | - Patrick Tan
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T1Z4, Canada
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Meta-Analysis of Hypoxic Transcriptomes from Public Databases. Biomedicines 2020; 8:biomedicines8010010. [PMID: 31936636 PMCID: PMC7168238 DOI: 10.3390/biomedicines8010010] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 12/26/2019] [Accepted: 01/08/2020] [Indexed: 12/16/2022] Open
Abstract
Hypoxia is the insufficiency of oxygen in the cell, and hypoxia-inducible factors (HIFs) are central regulators of oxygen homeostasis. In order to obtain functional insights into the hypoxic response in a data-driven way, we attempted a meta-analysis of the RNA-seq data from the hypoxic transcriptomes archived in public databases. In view of methodological variability of archived data in the databases, we first manually curated RNA-seq data from appropriate pairs of transcriptomes before and after hypoxic stress. These included 128 human and 52 murine transcriptome pairs. We classified the results of experiments for each gene into three categories: upregulated, downregulated, and unchanged. Hypoxic transcriptomes were then compared between humans and mice to identify common hypoxia-responsive genes. In addition, meta-analyzed hypoxic transcriptome data were integrated with public ChIP-seq data on the known human HIFs, HIF-1 and HIF-2, to provide insights into hypoxia-responsive pathways involving direct transcription factor binding. This study provides a useful resource for hypoxia research. It also demonstrates the potential of a meta-analysis approach to public gene expression databases for selecting candidate genes from gene expression profiles generated under various experimental conditions.
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