1
|
Baquero J, Tang XH, Ferrotta A, Zhang T, DiKun KM, Gudas LJ. The transcription factor BMI1 increases hypoxic signaling in oral cavity epithelia. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167161. [PMID: 38599260 DOI: 10.1016/j.bbadis.2024.167161] [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: 11/29/2023] [Revised: 03/07/2024] [Accepted: 04/04/2024] [Indexed: 04/12/2024]
Abstract
The tongue epithelium is maintained by a proliferative basal layer. This layer contains long-lived stem cells (SCs), which produce progeny cells that move up to the surface as they differentiate. B-lymphoma Mo-MLV insertion region 1 (BMI1), a protein in mammalian Polycomb Repressive Complex 1 (PRC1) and a biomarker of oral squamous cell carcinoma, is expressed in almost all basal epithelial SCs of the tongue, and single, Bmi1-labelled SCs give rise to cells in all epithelial layers. We previously developed a transgenic mouse model (KrTB) containing a doxycycline- (dox) controlled, Tet-responsive element system to selectively overexpress Bmi1 in the tongue basal epithelial SCs. Here, we used this model to assess BMI1 actions in tongue epithelia. Genome-wide transcriptomics revealed increased levels of transcripts involved in the cellular response to hypoxia in Bmi1-overexpressing (KrTB+DOX) oral epithelia even though these mice were not subjected to hypoxia conditions. Ectopic Bmi1 expression in tongue epithelia increased the levels of hypoxia inducible factor-1 alpha (HIF1α) and HIF1α targets linked to metabolic reprogramming during hypoxia. We used chromatin immunoprecipitation (ChIP) to demonstrate that Bmi1 associates with the promoters of HIF1A and HIF1A-activator RELA (p65) in tongue epithelia. We also detected increased SC proliferation and oxidative stress in Bmi1-overexpressing tongue epithelia. Finally, using a human oral keratinocyte line (OKF6-TERT1R), we showed that ectopic BMI1 overexpression decreases the oxygen consumption rate while increasing the extracellular acidification rate, indicative of elevated glycolysis. Thus, our data demonstrate that high BMI1 expression drives hypoxic signaling, including metabolic reprogramming, in normal oral cavity epithelia.
Collapse
Affiliation(s)
- Jorge Baquero
- Department of Pharmacology, Weill Cornell Medical College, New York, NY, USA; Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Xiao-Han Tang
- Department of Pharmacology, Weill Cornell Medical College, New York, NY, USA; Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Annalisa Ferrotta
- Department of Pharmacology, Weill Cornell Medical College, New York, NY, USA; Department of Pharmacology, Weill Cornell Graduate School of Biomedical Sciences, New York, NY, USA
| | - Tuo Zhang
- Weill Cornell Genomics Core Facility, Weill Cornell Medical College, New York, NY, USA
| | - Krysta M DiKun
- Department of Pharmacology, Weill Cornell Medical College, New York, NY, USA; Department of Pharmacology, Weill Cornell Graduate School of Biomedical Sciences, New York, NY, USA
| | - Lorraine J Gudas
- Department of Pharmacology, Weill Cornell Medical College, New York, NY, USA; Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA; Department of Pharmacology, Weill Cornell Graduate School of Biomedical Sciences, New York, NY, USA.
| |
Collapse
|
2
|
Papadopoulos KI, Papadopoulou A, Aw TC. Anexelekto (AXL) no more: microRNA-155 (miR-155) controls the "Uncontrolled" in SARS-CoV-2. Hum Cell 2024; 37:582-592. [PMID: 38472734 DOI: 10.1007/s13577-024-01041-6] [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: 11/22/2023] [Accepted: 01/30/2024] [Indexed: 03/14/2024]
Abstract
AXL is the gene that encodes the Anexelekto (AXL) receptor tyrosine kinase that demonstrates significant roles in various cellular processes, including cell growth, survival, and migration. Anexelekto is a Greek word meaning excessive and uncontrolled, semantically implying the crucial involvement of AXL in cancer and immune biology, and in promoting cancer metastasis. AXL overexpression appears to drive epithelial to mesenchymal transition, tumor angiogenesis, decreased antitumor immune response, and resistance to therapeutic agents. Recently, AXL has been reported to play important roles in several viral infections, including SARS-CoV-2. We have previously outlined the importance of microRNAs (miRNAs, miRs) and especially miR-155 in SARS-CoV-2 pathophysiology through regulation of the Renin-Angiotensin Aldosterone System (RAAS) and influence on several aspects of host innate immunity. MiRNAs are negative regulators of gene expression, decreasing the stability of target RNAs or limiting their translation and, enthrallingly, miR-155 is also involved in AXL homeostasis-both endogenously and pharmaceutically using repurposed drugs (e.g., metformin)-highlighting thrifty evolutionary host innate immunity mechanisms that successfully can thwart viral entry and replication. Cancer, infections, and immune system disturbances will increasingly involve miRNA diagnostics and therapeutics in the future.
Collapse
Affiliation(s)
- K I Papadopoulos
- THAI StemLife, 566/3 Soi Ramkhamhaeng 39 (Thepleela 1), Prachaouthit Rd, Wangthonglang, Bangkok, 10310, Thailand.
| | - A Papadopoulou
- Feelgood Lund, Occupational and Environmental Health Services, Ideon Science Park, Scheelevägen 17, 223 63, Lund, Sweden
| | - T C Aw
- Department of Laboratory Medicine, Changi General Hospital, 2 Simei Street 3, Singapore, 529889, Singapore
- Department of Medicine, National University of Singapore, Singapore, 119228, Singapore
| |
Collapse
|
3
|
Troise D, Infante B, Mercuri S, Piccoli C, Lindholm B, Stallone G. Hypoxic Inducible Factor Stabilization in Pericytes beyond Erythropoietin Production: The Good and the Bad. Antioxidants (Basel) 2024; 13:537. [PMID: 38790642 PMCID: PMC11118908 DOI: 10.3390/antiox13050537] [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: 03/26/2024] [Revised: 04/22/2024] [Accepted: 04/25/2024] [Indexed: 05/26/2024] Open
Abstract
The paracrine signaling pathways for the crosstalk between pericytes and endothelial cells are essential for the coordination of cell responses to challenges such as hypoxia in both healthy individuals and pathological conditions. Ischemia-reperfusion injury (IRI), one of the causes of cellular dysfunction and death, is associated with increased expression of genes involved in cellular adaptation to a hypoxic environment. Hypoxic inducible factors (HIFs) have a central role in the response to processes initiated by IRI not only linked to erythropoietin production but also because of their participation in inflammation, angiogenesis, metabolic adaptation, and fibrosis. While pericytes have an essential physiological function in erythropoietin production, a lesser-known role of HIF stabilization during IRI is that pericytes' HIF expression could influence vascular remodeling, cell loss and organ fibrosis. Better knowledge of mechanisms that control functions and consequences of HIF stabilization in pericytes beyond erythropoietin production is advisable for the development of therapeutic strategies to influence disease progression and improve treatments. Thus, in this review, we discuss the dual roles-for good or bad-of HIF stabilization during IRI, focusing on pericytes, and consequences in particular for the kidneys.
Collapse
Affiliation(s)
- Dario Troise
- Nephrology, Dialysis and Transplantation Unit, Advanced Research Center on Kidney Aging (A.R.K.A.), Department of Medical and Surgical Sciences, University of Foggia, 71122 Foggia, Italy
- Renal Medicine and Baxter Novum, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, 141 52 Stockholm, Sweden
| | - Barbara Infante
- Nephrology, Dialysis and Transplantation Unit, Advanced Research Center on Kidney Aging (A.R.K.A.), Department of Medical and Surgical Sciences, University of Foggia, 71122 Foggia, Italy
| | - Silvia Mercuri
- Nephrology, Dialysis and Transplantation Unit, Advanced Research Center on Kidney Aging (A.R.K.A.), Department of Medical and Surgical Sciences, University of Foggia, 71122 Foggia, Italy
| | - Claudia Piccoli
- Department of Clinical and Experimental Medicine, University of Foggia, 71122 Foggia, Italy
| | - Bengt Lindholm
- Renal Medicine and Baxter Novum, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, 141 52 Stockholm, Sweden
| | - Giovanni Stallone
- Nephrology, Dialysis and Transplantation Unit, Advanced Research Center on Kidney Aging (A.R.K.A.), Department of Medical and Surgical Sciences, University of Foggia, 71122 Foggia, Italy
| |
Collapse
|
4
|
Niu R, Zhang X, Yu Y, Bao Z, Yang J, Yuan J, Li F. Identification of Growth-Related Gene BAMBI and Analysis of Gene Structure and Function in the Pacific White Shrimp Litopenaeus vannamei. Animals (Basel) 2024; 14:1074. [PMID: 38612313 PMCID: PMC11011141 DOI: 10.3390/ani14071074] [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: 02/19/2024] [Revised: 03/30/2024] [Accepted: 03/30/2024] [Indexed: 04/14/2024] Open
Abstract
As one of the most important aquaculture species in the world, the improvement of growth traits of the Pacific white shrimp (Litopenaeus vannamei), has always been a primary focus. In this study, we conducted SNP-specific locus analysis and identified a growth-related gene, BAMBI, in L. vannamei. We analyzed the structure and function of LvBAMBI using genomic, transcriptomic, metabolomic, and RNA interference (RNAi) assays. The LvBAMBI possessed highly conserved structural domains and widely expressed in various tissues. Knockdown of LvBAMBI significantly inhibited the gain of body length and weight of the shrimp, underscoring its role as a growth-promoting factor. Specifically, knockdown of LvBAMBI resulted in a significant downregulation of genes involved in lipid metabolism, protein synthesis, catabolism and transport, and immunity. Conversely, genes related to glucose metabolism exhibited significant upregulations. Analysis of differential metabolites (DMs) in metabolomics further revealed that LvBAMBI knockdown may primarily affect shrimp growth by regulating biological processes related to lipid and glucose metabolism. These results suggested that LvBAMBI plays a crucial role in regulating lipid metabolism, glucose metabolism, and protein transport in shrimp. This study provides valuable insights for future research and utilization of BAMBI genes in shrimp and crustaceans.
Collapse
Affiliation(s)
- Ruigang Niu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (R.N.); (Y.Y.); (Z.B.); (J.Y.); (J.Y.); (F.L.)
- College of Earth Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaojun Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (R.N.); (Y.Y.); (Z.B.); (J.Y.); (J.Y.); (F.L.)
- College of Earth Science, University of Chinese Academy of Sciences, Beijing 100049, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan 430072, China
| | - Yang Yu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (R.N.); (Y.Y.); (Z.B.); (J.Y.); (J.Y.); (F.L.)
- College of Earth Science, University of Chinese Academy of Sciences, Beijing 100049, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan 430072, China
| | - Zhenning Bao
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (R.N.); (Y.Y.); (Z.B.); (J.Y.); (J.Y.); (F.L.)
- College of Earth Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Junqing Yang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (R.N.); (Y.Y.); (Z.B.); (J.Y.); (J.Y.); (F.L.)
- College of Earth Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianbo Yuan
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (R.N.); (Y.Y.); (Z.B.); (J.Y.); (J.Y.); (F.L.)
- College of Earth Science, University of Chinese Academy of Sciences, Beijing 100049, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan 430072, China
| | - Fuhua Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (R.N.); (Y.Y.); (Z.B.); (J.Y.); (J.Y.); (F.L.)
- College of Earth Science, University of Chinese Academy of Sciences, Beijing 100049, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan 430072, China
| |
Collapse
|
5
|
Motlagh PE, Jamali E, Karimi N, Eslami S, Sharifi G, Ghafouri-Fard S. Integrated bioinformatics approaches and expression assays identified new markers in pituitary adenomas. Pathol Res Pract 2024; 255:155193. [PMID: 38364650 DOI: 10.1016/j.prp.2024.155193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 02/01/2024] [Accepted: 02/03/2024] [Indexed: 02/18/2024]
Abstract
Pituitary adenomas (PA) include about one third of primary central nervous tumors in adolescent and young adult. Despite extensive research, the underlying mechanism of PA tumorigenesis is still unknown. In the present study, through bioinformatics analysis of a PA-related dataset downloaded from GEO database, we attempted to identify pair(s) of lncRNA/target mRNA whose expression changes may be involved in the tumorigenesis of PAs. For this end, we evaluated expression of a set of bioinformatically obtained genes in 46 PA tissues against adjacent non-tumor pituitary tissues. The bioinformatics step led to selection of four genes for validation through expression assays. Expression levels of HIF1A and MAPK1 were increased in NFPA tissues (P < 0.0001 and =0.0042, respectively). Expression level of BANCR was significantly decreased in tumor tissues (P < 0.0001). However, expression of STAT3 was not meaningfully different between the two tissue types (P = 0.56). Since there was no significant correlation between MAPK1 and BANCR expressions in either tumor or adjacent normal tissues, the regulatory effect of BANCR on MAPK1 was not confirmed. In conclusion, this study offers information about deregulation of bioinformatically identified genes in PA tumors and indicates that further studies in this field is needed to understand the involved molecular mechanisms.
Collapse
Affiliation(s)
- Parisa Esmaeili Motlagh
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Islamic Republic of Iran
| | - Elena Jamali
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
| | - Nastaran Karimi
- School of Medicine, Sari Branch, Islamic Azad University, Sari, Islamic Republic of Iran
| | - Solat Eslami
- Department of Medical Biotechnology, School of Medicine, Alborz University of Medical Sciences, Karaj, Islamic Republic of Iran; Non-communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Islamic Republic of Iran
| | - Guive Sharifi
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Islamic Republic of Iran
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Islamic Republic of Iran.
| |
Collapse
|
6
|
Liu W, Huang K, Yang XZ, Wang P. Transcriptomic and network analysis identifies shared and unique pathways and immune changes across fibrotic interstitial lung diseases. Aging (Albany NY) 2024; 16:3200-3230. [PMID: 38349858 PMCID: PMC10929820 DOI: 10.18632/aging.205530] [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: 08/07/2023] [Accepted: 12/01/2023] [Indexed: 02/15/2024]
Abstract
BACKGROUND Interstitial lung disease (ILD) encompasses a diverse group of disorders characterized by chronic inflammation and fibrosis of the pulmonary interstitium. Three ILDs, namely idiopathic pulmonary fibrosis (IPF), fibrotic hypersensitivity pneumonitis (fHP), and connective tissue disease-associated ILD (CTD-ILD), exhibit similar progressive fibrosis phenotypes, yet possess distinct etiologies, encouraging us to explore their different underlying mechanisms. METHODS Transcriptome data of fibrotic lung tissues from patients with IPF, fHP, and CTD-ILD were subjected to functional annotation, network, and pathway analyses. Additionally, we employed the xCell deconvolution algorithm to predict immune cell infiltration in patients with fibrotic ILDs and healthy controls. RESULTS We identified a shared progressive fibrosis-related module in these diseases which was related to extracellular matrix (ECM) degradation and production and potentially regulated by the p53 family transcription factors. In IPF, neuron-related processes emerged as a critical specific mechanism in functional enrichment. In fHP, we observed that B cell signaling and immunoglobulin A (IgA) production may act as predominant processes, which was further verified by B cell infiltration and the central role of CD19 gene. In CTD-ILD, active chemokine processes were enriched, and active dendritic cells (aDCs) were predicted to infiltrate the lung tissues. CONCLUSIONS This study revealed shared and specific molecular and cellular pathways among IPF, fHP, and CTD-ILD, providing a basis for understanding their pathogenesis and identifying potential therapeutic targets.
Collapse
Affiliation(s)
- Wenhao Liu
- Eight-Year Program of Clinical Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Kangping Huang
- Eight-Year Program of Clinical Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Xin-Zhuang Yang
- Center for Bioinformatics, National Infrastructures for Translational Medicine, Institute of Clinical Medicine and Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Ping Wang
- Department of Pulmonary and Critical Care Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China
| |
Collapse
|
7
|
Troise D, Infante B, Mercuri S, Netti GS, Ranieri E, Gesualdo L, Stallone G, Pontrelli P. Hypoxic State of Cells and Immunosenescence: A Focus on the Role of the HIF Signaling Pathway. Biomedicines 2023; 11:2163. [PMID: 37626660 PMCID: PMC10452839 DOI: 10.3390/biomedicines11082163] [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: 06/08/2023] [Revised: 07/20/2023] [Accepted: 07/27/2023] [Indexed: 08/27/2023] Open
Abstract
Hypoxia activates hypoxia-related signaling pathways controlled by hypoxia-inducible factors (HIFs). HIFs represent a quick and effective detection system involved in the cellular response to insufficient oxygen concentration. Activation of HIF signaling pathways is involved in improving the oxygen supply, promoting cell survival through anaerobic ATP generation, and adapting energy metabolism to meet cell demands. Hypoxia can also contribute to the development of the aging process, leading to aging-related degenerative diseases; among these, the aging of the immune system under hypoxic conditions can play a role in many different immune-mediated diseases. Thus, in this review we aim to discuss the role of HIF signaling pathways following cellular hypoxia and their effects on the mechanisms driving immune system senescence.
Collapse
Affiliation(s)
- Dario Troise
- Nephrology, Dialysis and Transplantation Unit, Advanced Research Center on Kidney Aging (A.R.K.A.), Department of Medical and Surgical Science, University of Foggia, 71122 Foggia, Italy; (D.T.); (B.I.); (S.M.); (G.S.)
| | - Barbara Infante
- Nephrology, Dialysis and Transplantation Unit, Advanced Research Center on Kidney Aging (A.R.K.A.), Department of Medical and Surgical Science, University of Foggia, 71122 Foggia, Italy; (D.T.); (B.I.); (S.M.); (G.S.)
| | - Silvia Mercuri
- Nephrology, Dialysis and Transplantation Unit, Advanced Research Center on Kidney Aging (A.R.K.A.), Department of Medical and Surgical Science, University of Foggia, 71122 Foggia, Italy; (D.T.); (B.I.); (S.M.); (G.S.)
| | - Giuseppe Stefano Netti
- Clinical Pathology Unit, Department of Medical and Surgical Sciences, University of Foggia, 71122 Foggia, Italy; (G.S.N.); (E.R.)
| | - Elena Ranieri
- Clinical Pathology Unit, Department of Medical and Surgical Sciences, University of Foggia, 71122 Foggia, Italy; (G.S.N.); (E.R.)
| | - Loreto Gesualdo
- Nephrology, Dialysis and Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari “Aldo Moro”, Policlinico, Piazza Giulio Cesare 11, 70124 Bari, Italy;
| | - Giovanni Stallone
- Nephrology, Dialysis and Transplantation Unit, Advanced Research Center on Kidney Aging (A.R.K.A.), Department of Medical and Surgical Science, University of Foggia, 71122 Foggia, Italy; (D.T.); (B.I.); (S.M.); (G.S.)
| | - Paola Pontrelli
- Nephrology, Dialysis and Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari “Aldo Moro”, Policlinico, Piazza Giulio Cesare 11, 70124 Bari, Italy;
| |
Collapse
|
8
|
Strauss E, Gotz-Więckowska A, Sobaniec A, Chmielarz-Czarnocińska A, Szpecht D, Januszkiewicz-Lewandowska D. Hypoxia-Inducible Pathway Polymorphisms and Their Role in the Complications of Prematurity. Genes (Basel) 2023; 14:genes14050975. [PMID: 37239335 DOI: 10.3390/genes14050975] [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: 02/28/2023] [Revised: 04/18/2023] [Accepted: 04/24/2023] [Indexed: 05/28/2023] Open
Abstract
Excessive oxidative stress resulting from hyperoxia or hypoxia is a recognized risk factor for diseases of prematurity. However, the role of the hypoxia-related pathway in the development of these diseases has not been well studied. Therefore, this study aimed to investigate the association between four functional single nucleotide polymorphisms (SNPs) in the hypoxia-related pathway, and the development of complications of prematurity in relation to perinatal hypoxia. A total of 334 newborns born before or on the 32nd week of gestation were included in the study. The SNPs studied were HIF1A rs11549465 and rs11549467, VEGFA rs2010963, and rs833061. The findings suggest that the HIF1A rs11549465T allele is an independent protective factor against necrotizing enterocolitis (NEC), but may increase the risk of diffuse white matter injury (DWMI) in newborns exposed to hypoxia at birth and long-term oxygen supplementation. In addition, the rs11549467A allele was found to be an independent protective factor against respiratory distress syndrome (RDS). No significant associations with VEGFA SNPs were observed. These findings indicate the potential involvement of the hypoxia-inducible pathway in the pathogenesis of complications of prematurity. Studies with larger sample sizes are needed to confirm these results and explore their clinical implications.
Collapse
Affiliation(s)
- Ewa Strauss
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszynska 32, 60-479 Poznan, Poland
| | - Anna Gotz-Więckowska
- Department of Ophthalmology, Poznan University of Medical Sciences, Szamarzewskiego 84, 60-569 Poznan, Poland
| | - Alicja Sobaniec
- Department of Neonatology, Poznan University of Medical Sciences, Polna 33, 60-535 Poznan, Poland
| | - Anna Chmielarz-Czarnocińska
- Department of Ophthalmology, Poznan University of Medical Sciences, Szamarzewskiego 84, 60-569 Poznan, Poland
| | - Dawid Szpecht
- Department of Neonatology, Poznan University of Medical Sciences, Polna 33, 60-535 Poznan, Poland
| | - Danuta Januszkiewicz-Lewandowska
- Department of Medical Diagnostics, Poznan University of Medical Sciences, Dobra Street 38a, 60-595 Poznan, Poland
- Department of Pediatric Oncology, Hematology and Transplantology, Poznan University of Medical Sciences, Szpitalna 27/33, 60-572 Poznan, Poland
| |
Collapse
|
9
|
Šimon M, Mikec Š, Morton NM, Atanur SS, Konc J, Horvat S, Kunej T. Genome-wide screening for genetic variants in polyadenylation signal (PAS) sites in mouse selection lines for fatness and leanness. Mamm Genome 2023; 34:12-31. [PMID: 36414820 PMCID: PMC9684942 DOI: 10.1007/s00335-022-09967-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 10/31/2022] [Indexed: 11/23/2022]
Abstract
Alternative polyadenylation (APA) determines mRNA stability, localisation, translation and protein function. Several diseases, including obesity, have been linked to APA. Studies have shown that single nucleotide polymorphisms in polyadenylation signals (PAS-SNPs) can influence APA and affect phenotype and disease susceptibility. However, these studies focussed on associations between single PAS-SNP alleles with very large effects and phenotype. Therefore, we performed a genome-wide screening for PAS-SNPs in the polygenic mouse selection lines for fatness and leanness by whole-genome sequencing. The genetic variants identified in the two lines were overlapped with locations of PAS sites obtained from the PolyASite 2.0 database. Expression data for selected genes were extracted from the microarray expression experiment performed on multiple tissue samples. In total, 682 PAS-SNPs were identified within 583 genes involved in various biological processes, including transport, protein modifications and degradation, cell adhesion and immune response. Moreover, 63 of the 583 orthologous genes in human have been previously associated with human diseases, such as nervous system and physical disorders, and immune, endocrine, and metabolic diseases. In both lines, PAS-SNPs have also been identified in genes broadly involved in APA, such as Polr2c, Eif3e and Ints11. Five PAS-SNPs within 5 genes (Car, Col4a1, Itga7, Lat, Nmnat1) were prioritised as potential functional variants and could contribute to the phenotypic disparity between the two selection lines. The developed PAS-SNPs catalogue presents a key resource for planning functional studies to uncover the role of PAS-SNPs in APA, disease susceptibility and fat deposition.
Collapse
Affiliation(s)
- Martin Šimon
- grid.8954.00000 0001 0721 6013Biotechnical Faculty, Department of Animal Science, University of Ljubljana, Domžale, Slovenia
| | - Špela Mikec
- grid.8954.00000 0001 0721 6013Biotechnical Faculty, Department of Animal Science, University of Ljubljana, Domžale, Slovenia
| | - Nicholas M. Morton
- grid.511172.10000 0004 0613 128XUniversity of Edinburgh, The Queen’s Medical Research Institute, Centre for Cardiovascular Science, Edinburgh, UK
| | - Santosh S. Atanur
- grid.7445.20000 0001 2113 8111Faculty of Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- grid.4305.20000 0004 1936 7988Centre for Genomic and Experimental Medicine, University of Edinburgh, Edinburgh, UK
| | - Janez Konc
- grid.454324.00000 0001 0661 0844Laboratory for Molecular Modeling, National Institute of Chemistry, Ljubljana, Slovenia
| | - Simon Horvat
- grid.8954.00000 0001 0721 6013Biotechnical Faculty, Department of Animal Science, University of Ljubljana, Domžale, Slovenia
| | - Tanja Kunej
- grid.8954.00000 0001 0721 6013Biotechnical Faculty, Department of Animal Science, University of Ljubljana, Domžale, Slovenia
| |
Collapse
|
10
|
Kang H, Liu Q, Seim I, Zhang W, Li H, Gao H, Lin W, Lin M, Zhang P, Zhang Y, Gao H, Wang Y, Qin Y, Liu M, Dong L, Yang Z, Zhang Y, Han L, Fan G, Li S. A genome and single-nucleus cerebral cortex transcriptome atlas of the short-finned pilot whale Globicephala macrorhynchus. Mol Ecol Resour 2023. [PMID: 36826393 DOI: 10.1111/1755-0998.13775] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 02/09/2023] [Accepted: 02/22/2023] [Indexed: 02/25/2023]
Abstract
Cetaceans (dolphins, whales, and porpoises) have large and anatomically sophisticated brains. To expand our understanding of the cellular makeup of cetacean brains and the similarities and divergence between the brains of cetaceans and terrestrial mammals, we report a short-finned pilot whale (Globicephala macrorhynchus) single-nucleus transcriptome atlas. To achieve this goal, we assembled a chromosome-scale reference genome spanning 2.25 Gb on 22 chromosomes and profiled the gene expression of five major anatomical cortical regions of the short-finned pilot whale by single-nucleus RNA-sequencing (snRNA-seq). We identified six major cell lineages in the cerebral cortex (excitatory neurons, inhibitory neurons, oligodendrocytes, oligodendrocyte precursor cells, astrocytes, and endothelial cells), eight molecularly distinct subclusters of excitatory neurons, and four subclusters of inhibitory neurons. Finally, a comparison of snRNA-seq data from the short-finned pilot whale, human, and rhesus macaque revealed a broadly conserved cellular makeup of brain cell types. Our study provides genomic resources and molecular insights into cetacean brain evolution.
Collapse
Affiliation(s)
- Hui Kang
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Qun Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China.,Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China.,Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Qingdao Key Laboratory of Marine Genomics, BGI-Qingdao, Qingdao, China
| | - Inge Seim
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Wenwei Zhang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Hanbo Li
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China.,Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China
| | - Haiyu Gao
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wenzhi Lin
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Mingli Lin
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Peijun Zhang
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | | | | | - Yang Wang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China
| | - Yating Qin
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China
| | - Mingming Liu
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Lijun Dong
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Zixin Yang
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | | | - Lei Han
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China.,State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Songhai Li
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| |
Collapse
|
11
|
Kosim MY, Fukazawa T, Miyauchi M, Hirohashi N, Tanimoto K. p53 status modifies cytotoxic activity of lactoferrin under hypoxic conditions. Front Pharmacol 2022; 13:988335. [PMID: 36199689 PMCID: PMC9527284 DOI: 10.3389/fphar.2022.988335] [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: 07/07/2022] [Accepted: 09/01/2022] [Indexed: 11/13/2022] Open
Abstract
Lactoferrin (LF) is an iron binding glycoprotein of the transferrin family with a wide spectrum of biological effects, including anti-cancer activity. However, the detailed molecular mechanisms of anti-cancer activity of LF have not been fully determined. In this study, we tried to clarify cytotoxic functions of LF on various cell lines under hypoxic conditions and elucidate those molecular mechanisms. Cytotoxic activity of LF on cell lines was found to have a range of sensitivities. Hypoxia decreased sensitivity to LF in KD (lip fibroblast) but increased that in HSC2 (oral squamous cell carcinoma). Expression analyses further revealed that LF treatments increased hypoxic HIF-1α, -2α and p53 proteins in KD but attenuated them in HSC2 cells, and decreased HIF-1 target gene, DEC2, in KD but increased it in HSC2, suggesting a possible relationship between LF-modified DEC2 expression and HIF-α protein. MTT assay strikingly demonstrated that cells expressing mutant-type p53 (MT5) were more sensitive to LF than control HepG2 (hepatoma), suggesting an important role of the p53 signal. Knock-down of TP53 (p53 gene) interestingly reduced sensitivity to LF in HepG2, suggesting that p53 may be a target of LF cytotoxic activity. Further analyses with a ferroptosis promoter or inhibitor demonstrated that LF increased ACSL4 in hypoxic MT5, suggesting LF-induced ferroptosis in cells expressing mutant-type p53. In conclusion, hypoxia was found to regulate cytotoxic activities of LF differently among various cell lines, possibly through the p53 signaling pathway. LF further appeared to regulate ferroptosis through a modification of ACSL4 expression.
Collapse
Affiliation(s)
- Maryami Yuliana Kosim
- Department of Radiation Disaster Medicine, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Takahiro Fukazawa
- Natural Science Center for Basic Research and Development, Hiroshima University, Hiroshima, Japan
| | - Mutsumi Miyauchi
- Department of Oral and Maxillofacial Pathology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima , Japan
| | - Nobuyuki Hirohashi
- Department of Radiation Disaster Medicine, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Keiji Tanimoto
- Department of Radiation Disaster Medicine, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
- *Correspondence: Keiji Tanimoto,
| |
Collapse
|
12
|
Dzhalilova DS, Makarova OV. The Role of Hypoxia-Inducible Factor in the Mechanisms of Aging. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:995-1014. [PMID: 36180993 DOI: 10.1134/s0006297922090115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/17/2022] [Accepted: 08/17/2022] [Indexed: 06/16/2023]
Abstract
Aging is accompanied by a reduction in the oxygen delivery to all organs and tissues and decrease in the oxygen partial pressure in them, resulting in the development of hypoxia. The lack of oxygen activates cell signaling pathway mediated by the hypoxia-inducible transcription factor (HIF), which exists in three isoforms - HIF-1, HIF-2, and HIF-3. HIF regulates expression of several thousand genes and is a potential target for the development of new drugs for the treatment of many diseases, including those associated with age. Human organism and organisms of laboratory animals differ in their tolerance to hypoxia and expression of HIF and HIF-dependent genes, which may contribute to the development of inflammatory, tumor, and cardiovascular diseases. Currently, the data on changes in the HIF expression with age are contradictory, which is mostly due to the fact that such studies are conducted in different age groups, cell types, and model organisms, as well as under different hypoxic conditions and mainly in vitro. Furthermore, the observed discrepancies can be due to the individual tolerance of the studied organisms to hypoxia, which is typically not taken into account. Therefore, the purpose of this review was to analyze the published data on the connection between the mechanisms of aging, basal tolerance to hypoxia, and changes in the level of HIF expression with age. Here, we summarized the data on the age-related changes in the hypoxia tolerance, HIF expression and the role of HIF in aging, which is associated with its involvement in the molecular pathways mediated by insulin and IGF-1 (IIS), sirtuins (SIRTs), and mTOR. HIF-1 interacts with many components of the IIS pathway, in particular with FOXO, the activation of which reduces production of reactive oxygen species (ROS) and increases hypoxia tolerance. Under hypoxic conditions, FOXO is activated via both HIF-dependent and HIF-independent pathways, which contributes to a decrease in the ROS levels. The activity of HIF-1 is regulated by all members of the sirtuin family, except SIRT5, while the mechanisms of SIRT interaction with HIF-2 and HIF-3 are poorly understood. The connection between HIF and mTOR and its inhibitor, AMPK, has been identified, but its exact mechanism has yet to be studied. Understanding the role of HIF and hypoxia in aging and pathogenesis of age-associated diseases is essential for the development of new approaches to the personalized therapy of these diseases, and requires further research.
Collapse
Affiliation(s)
- Dzhuliia Sh Dzhalilova
- Avtsyn Research Institute of Human Morphology, Petrovsky National Research Centre of Surgery, Moscow, 117418, Russia.
| | - Olga V Makarova
- Avtsyn Research Institute of Human Morphology, Petrovsky National Research Centre of Surgery, Moscow, 117418, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| |
Collapse
|
13
|
Mikec Š, Šimon M, Morton NM, Atanur SS, Konc J, Dovč P, Horvat S, Kunej T. Genetic variants of the hypoxia-inducible factor 3 alpha subunit (Hif3a) gene in the Fat and Lean mouse selection lines. Mol Biol Rep 2022; 49:4619-4631. [PMID: 35347545 DOI: 10.1007/s11033-022-07309-0] [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: 01/10/2022] [Accepted: 02/25/2022] [Indexed: 10/18/2022]
Abstract
BACKGROUND Adipose tissue hypoxia and members of the hypoxia-inducible factor alpha (HIFA) are involved in development of obesity. However, the mechanism and functions of HIF3A, one of three HIFA paralogs, in fat deposition have not been sufficiently studied. METHODS AND RESULTS In the present study, we investigated whether Hif3a sequence variants are associated with divergent fat deposition in mouse selection lines for fatness and leanness. Sequencing and RFLP were used to analyse sequence variants within Hif3a. To identify candidate regulatory variants, we performed literature screening and used databases and bioinformatics tools like Ensembl, MethPrimer, TargetScanMouse, miRDB, PolyAsite, RISE, LncRRIsearch, RNAfold, PredictProtein, CAIcal, and switches.ELM Resource. There are 90 sequence variants in Hif3a between the two mouse lines. While most Fat line variants locate within intronic regions, Lean line variants are mainly in 3' UTR. We constructed a map of Hif3a potential regulatory regions and identified 39 regulatory variants by integrating data on constrained and regulatory elements, CpGs, and miRNAs and lncRNAs binding sites. Moreover, 3' UTR and two exonic variants may influence mRNA stability, translation rate and protein functionality. We propose as priority candidates for further functional studies a missense (rs37398126) and synonymous (rs37739792) variants, and intronic (rs47471302) variant that overlap conserved element in promoter region and predicted lncRNAs binding site. CONCLUSION The results indicate a potential involvement of Hif3a in fat deposition. Additionally, approach used in the present study may serve as a general guideline for constructing an integrative gene map for prioritizing candidate gene variants with phenotypic effects.
Collapse
Affiliation(s)
- Špela Mikec
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, Slovenia
| | - Martin Šimon
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, Slovenia
| | - Nicholas M Morton
- The Queen's Medical Research Institute, Centre for Cardiovascular Science, University of Edinburgh, Edinburgh, UK
| | - Santosh S Atanur
- Centre for Genomic and Experimental Medicine, University of Edinburgh, Edinburgh, UK.,Department of Metabolism, Digestion, and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - Janez Konc
- Laboratory for Molecular Modeling, National Institute of Chemistry, Ljubljana, Slovenia
| | - Peter Dovč
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, Slovenia
| | - Simon Horvat
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, Slovenia.
| | - Tanja Kunej
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, Slovenia.
| |
Collapse
|
14
|
Kristan A, Debeljak N, Kunej T. Integration and Visualization of Regulatory Elements and Variations of the EPAS1 Gene in Human. Genes (Basel) 2021; 12:genes12111793. [PMID: 34828399 PMCID: PMC8620933 DOI: 10.3390/genes12111793] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/05/2021] [Accepted: 11/09/2021] [Indexed: 01/15/2023] Open
Abstract
Endothelial PAS domain-containing protein 1 (EPAS1), also HIF2α, is an alpha subunit of hypoxia-inducible transcription factor (HIF), which mediates cellular and systemic response to hypoxia. EPAS1 has an important role in the transcription of many hypoxia-responsive genes, however, it has been less researched than HIF1α. The aim of this study was to integrate an increasing number of data on EPAS1 into a map of diverse OMICs elements. Publications, databases, and bioinformatics tools were examined, including Ensembl, MethPrimer, STRING, miRTarBase, COSMIC, and LOVD. The EPAS1 expression, stability, and activity are tightly regulated on several OMICs levels to maintain complex oxygen homeostasis. In the integrative EPAS1 map we included: 31 promoter-binding proteins, 13 interacting miRNAs and one lncRNA, and 16 post-translational modifications regulating EPAS1 protein abundance. EPAS1 has been associated with various cancer types and other diseases. The development of neuroendocrine tumors and erythrocytosis was shown to be associated with 11 somatic and 20 germline variants. The integrative map also includes 12 EPAS1 target genes and 27 interacting proteins. The study introduced the first integrative map of diverse genomics, transcriptomics, proteomics, regulomics, and interactomics data associated with EPAS1, to enable a better understanding of EPAS1 activity and regulation and support future research.
Collapse
Affiliation(s)
- Aleša Kristan
- Medical Centre for Molecular Biology, Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia; (A.K.); (N.D.)
| | - Nataša Debeljak
- Medical Centre for Molecular Biology, Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia; (A.K.); (N.D.)
| | - Tanja Kunej
- Department for Animal Science, Biotechnical Faculty, University of Ljubljana, 1230 Domžale, Slovenia
- Correspondence:
| |
Collapse
|