1
|
Wu Y, Jiang D, Liu Q, Yan S, Liu X, Wu T, Sun W, Li G. Cathepsin L induces cellular senescence by upregulating CUX1 and p16 INK4a. Aging (Albany NY) 2024; 16:205955. [PMID: 38944813 DOI: 10.18632/aging.205955] [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: 09/19/2023] [Accepted: 04/18/2024] [Indexed: 07/01/2024]
Abstract
Cathepsin L (CTSL) has been implicated in aging and age-related diseases, such as cardiovascular diseases, specifically atherosclerosis. However, the underlying mechanism(s) is not well documented. Recently, we demonstrated a role of CUT-like homeobox 1 (CUX1) in regulating the p16INK4a-dependent cellular senescence in human endothelial cells (ECs) and vascular smooth muscle cells (VSMCs) via its binding to an atherosclerosis-associated functional SNP (fSNP) rs1537371 on the CDKN2A/B locus. In this study, to determine if CTSL, which was reported to proteolytically activate CUX1, regulates cellular senescence via CUX1, we measured the expression of CTSL, together with CUX1 and p16INK4a, in human ECs and VSMCs undergoing senescence. We discovered that CUX1 is not a substrate that is cleaved by CTSL. Instead, CTSL is an upstream regulator that activates CUX1 transcription indirectly in a process that requires the proteolytic activity of CTSL. Our findings suggest that there is a transcription factor in between CTSL and CUX1, and cleavage of this factor by CTSL can activate CUX1 transcription, inducing endothelial senescence. Thus, our findings provide new insights into the signal transduction pathway that leads to atherosclerosis-associated cellular senescence.
Collapse
Affiliation(s)
- Yuwei Wu
- Department of Cardiology, Third Xiangya Hospital, Central South University, Changsha, China
- Aging Institute, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Danli Jiang
- Aging Institute, University of Pittsburgh, Pittsburgh, PA 15260, USA
- International Center for Aging and Cancer Hainan Medical University, Hainan, China
| | - Qing Liu
- Aging Institute, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Shaoyang Yan
- Aging Institute, University of Pittsburgh, Pittsburgh, PA 15260, USA
- Tsinghua Medicine, Tsinghua University, Peking, China
| | - Xiuzhen Liu
- Aging Institute, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Ting Wu
- Department of Cardiology, Third Xiangya Hospital, Central South University, Changsha, China
- Aging Institute, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Wei Sun
- Department of Medicine, Division of Cardiology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
- Vascular Medicine Institute, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, PA 15213, USA
| | - Gang Li
- Aging Institute, University of Pittsburgh, Pittsburgh, PA 15260, USA
- Department of Medicine, Division of Cardiology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
- Vascular Medicine Institute, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, PA 15213, USA
| |
Collapse
|
2
|
Yue RZ, Wang J, Lin F, Li CJ, Su BH, Zeng R. CUX1 attenuates the apoptosis of renal tubular epithelial cells induced by contrast media through activating the PI3K/AKT signaling pathway. BMC Nephrol 2024; 25:192. [PMID: 38849771 PMCID: PMC11162042 DOI: 10.1186/s12882-024-03625-8] [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: 06/29/2023] [Accepted: 05/28/2024] [Indexed: 06/09/2024] Open
Abstract
OBJECTIVE Contrast media (CM) is a commonly applied drug in medical examination and surgery. However, contrast-induced acute kidney injury (CIAKI) poses a severe threat to human life and health. Notably, the CUT-like homeobox 1 (CUX1) gene shows protective effects in a variety of cells. Therefore, the objective of this study was to provide a new target for the treatment of CIAKI through exploring the role and possible molecular mechanism of CUX1 in CIAKI. METHOD Blood samples were collected from 20 patients with CIAKI and healthy volunteers. Human kidney 2 (HK-2) cells were incubated with 200 mg/mL iohexol for 6 h to establish a contrast-induced injury model of HK-2 cells. Subsequently, qRT-PCR was used to detect the relative mRNA expression of CUX1; CCK-8 and flow cytometry to assess the proliferation and apoptosis of HK-2 cells; the levels of IL(interleukin)-1β, tumor necrosis factor alpha (TNF-α) and malondialdehyde (MDA) in cells and lactate dehydrogenase (LDH) activity in cell culture supernatant were detect; and western blot to observe the expression levels of CUX1 and the PI3K/AKT signaling pathway related proteins [phosphorylated phosphoinositide 3-kinase (p-PI3K), PI3K, phosphorylated Akt (p-AKT), AKT]. RESULTS CUX1 expression was significantly downregulated in blood samples of patients with CIAKI and contrast-induced HK-2 cells. Contrast media (CM; iohexol) treatment significantly reduced the proliferation of HK-2 cells, promoted apoptosis, stimulated inflammation and oxidative stress that caused cell damage. CUX1 overexpression alleviated cell damage by significantly improving the proliferation level of HK-2 cells induced by CM, inhibiting cell apoptosis, and reducing the level of LDH in culture supernatant and the expression of IL-1β, TNF-α and MDA in cells. CM treatment significantly inhibited the activity of PI3K/AKT signaling pathway activity. Nevertheless, up-regulating CUX1 could activate the PI3K/AKT signaling pathway activity in HK-2 cells induced by CM. CONCLUSION CUX1 promotes cell proliferation, inhibits apoptosis, and reduces inflammation and oxidative stress in CM-induced HK-2 cells to alleviate CM-induced damage. The mechanism of CUX1 may be correlated with activation of the PI3K/AKT signaling pathway.
Collapse
Affiliation(s)
- Rong-Zheng Yue
- Department of Nephrology, Kindey Research Institute, West China Hospital of Sichuan University, Chengdu, Sichuan, 610041, China
| | - Jing Wang
- Department of Nephrology, Kindey Research Institute, West China Hospital of Sichuan University, Chengdu, Sichuan, 610041, China
| | - Feng Lin
- Department of Nephrology, Kindey Research Institute, West China Hospital of Sichuan University, Chengdu, Sichuan, 610041, China
| | - Cong-Jun Li
- Department of Nephrology, Kindey Research Institute, West China Hospital of Sichuan University, Chengdu, Sichuan, 610041, China
| | - Bai-Hai Su
- Department of Nephrology, Kindey Research Institute, West China Hospital of Sichuan University, Chengdu, Sichuan, 610041, China
| | - Rui Zeng
- Department of Cardiovascular diseases, West China Hospital, School of Clinic Medicine, Sichuan University, Chengdu, Sichuan, 610041, China.
| |
Collapse
|
3
|
Cai P, Fu X, Li X, Zhao W. Upregulation of circ_0076684 in osteosarcoma facilitates malignant processes by mediating miRNAs/CUX1. J Orthop Surg Res 2024; 19:260. [PMID: 38659042 PMCID: PMC11044396 DOI: 10.1186/s13018-024-04742-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 04/16/2024] [Indexed: 04/26/2024] Open
Abstract
Circular RNAs (circRNAs) are a newly appreciated type of endogenous noncoding RNAs that play vital roles in the development of various human cancers, including osteosarcoma (OS). In this study, we investigated three circRNAs (circ_0076684, circ_0003563, circ_0076691) from the RUNX Family Transcription Factor 2 (RUNX2) gene locus in OS. We found that the expression of circ_0076684, circ_0003563, circ_0076691, and RUNX2 mRNA is upregulated in OS, which is a consequence of CBX4-mediated transcriptional activation. Among these three RUNX2-circRNAs, only circ_0076684 is significantly associated with the clinical features and prognosis of OS patients. Functional experiments indicate that circ_0076684 promotes OS progression in vitro and in vivo. Circ_0076684 acts as a sponge for miR-370-3p, miR-140-3p, and miR-193a-5p, raising Cut Like Homeobox 1 (CUX1) expression by sponging these three miRNAs. Furthermore, we presented that circ_0076684 facilitates OS progression via CUX1. In conclusion, this study found that the expression of three circRNAs and RUNX2 mRNA from the RUNX2 gene locus is significantly upregulated in OS, as a result of CBX4-mediated transcriptional activation. Circ_0076684 raises CUX1 expression by sponging miR-370-3p, miR-140-3p, and miR-193a-5p, and facilitates OS progression via CUX1.
Collapse
Affiliation(s)
- Pengfei Cai
- Department of Orthopeadics, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, No. 365 Renmin East Road, Jinhua City, 321000, Zhejiang Province, China
| | - Xin Fu
- Department of Orthopeadics, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, No. 365 Renmin East Road, Jinhua City, 321000, Zhejiang Province, China
| | - Xiaofei Li
- Department of Orthopeadics, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, No. 365 Renmin East Road, Jinhua City, 321000, Zhejiang Province, China.
| | - Wei Zhao
- Department of Orthopeadics, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, No. 365 Renmin East Road, Jinhua City, 321000, Zhejiang Province, China.
| |
Collapse
|
4
|
Goel K, Chhetri A, Ludhiadch A, Munshi A. Current Update on Categorization of Migraine Subtypes on the Basis of Genetic Variation: a Systematic Review. Mol Neurobiol 2023:10.1007/s12035-023-03837-3. [PMID: 38135854 DOI: 10.1007/s12035-023-03837-3] [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: 09/26/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023]
Abstract
Migraine is a complex neurovascular disorder that is characterized by severe behavioral, sensory, visual, and/or auditory symptoms. It has been labeled as one of the ten most disabling medical illnesses in the world by the World Health Organization (Aagaard et al Sci Transl Med 6(237):237ra65, 2014). According to a recent report by the American Migraine Foundation (Shoulson et al Ann Neurol 25(3):252-9, 1989), around 148 million people in the world currently suffer from migraine. On the basis of presence of aura, migraine is classified into two major subtypes: migraine with aura (Aagaard et al Sci Transl Med 6(237):237ra65, 2014) and migraine without aura. (Aagaard K et al Sci Transl Med 6(237):237ra65, 2014) Many complex genetic mechanisms have been proposed in the pathophysiology of migraine but specific pathways associated with the different subtypes of migraine have not yet been explored. Various approaches including candidate gene association studies (CGAS) and genome-wide association studies (Fan et al Headache: J Head Face Pain 54(4):709-715, 2014). have identified the genetic markers associated with migraine and its subtypes. Several single nucleotide polymorphisms (Kaur et al Egyp J Neurol, Psychiatry Neurosurg 55(1):1-7, 2019) within genes involved in ion homeostasis, solute transport, synaptic transmission, cortical excitability, and vascular function have been associated with the disorder. Currently, the diagnosis of migraine is majorly behavioral with no focus on the genetic markers and thereby the therapeutic intervention specific to subtypes. Therefore, there is a need to explore genetic variants significantly associated with MA and MO as susceptibility markers in the diagnosis and targets for therapeutic interventions in the specific subtypes of migraine. Although the proper characterization of pathways based on different subtypes is yet to be studied, this review aims to make a first attempt to compile the information available on various genetic variants and the molecular mechanisms involved with the development of MA and MO. An attempt has also been made to suggest novel candidate genes based on their function to be explored by future research.
Collapse
Affiliation(s)
- Kashish Goel
- Complex Disease Genomics and Precision Medicine Laboratory, Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, Punjab, India, 151401
| | - Aakash Chhetri
- Complex Disease Genomics and Precision Medicine Laboratory, Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, Punjab, India, 151401
| | - Abhilash Ludhiadch
- Complex Disease Genomics and Precision Medicine Laboratory, Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, Punjab, India, 151401
| | - Anjana Munshi
- Complex Disease Genomics and Precision Medicine Laboratory, Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, Punjab, India, 151401.
| |
Collapse
|
5
|
Lv X, Li Y, Chen W, Wang S, Cao X, Yuan Z, Getachew T, Mwacharo J, Haile A, Li Y, Sun W. Association between DNA Methylation in the Core Promoter Region of the CUT-like Homeobox 1 ( CUX1) Gene and Lambskin Pattern in Hu Sheep. Genes (Basel) 2023; 14:1873. [PMID: 37895221 PMCID: PMC10606103 DOI: 10.3390/genes14101873] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/18/2023] [Accepted: 09/25/2023] [Indexed: 10/29/2023] Open
Abstract
CUT-like homeobox 1 (CUX1) has been proven to be a key regulator in sheep hair follicle development. In our previous study, CUX1 was identified as a differential expressed gene between Hu sheep lambskin with small wave patterns (SM) and straight wool patterns (ST); however, the exact molecular mechanism of CUX1 expression has been obscure. As DNA methylation can regulate the gene expression, the potential association between CUX1 core promotor region methylation and lambskin pattern in Hu sheep was explored in the present study. The results show that the core promoter region of CUX1 was present at (-1601-(-1) bp) upstream of the transcription start site. A repressive region (-1151-(-751) bp) was also detected, which had a strong inhibitory effect on CUX1 promoter activity. Bisulfite amplicon sequencing revealed that no significant difference was detected between the methylation levels of CUX1 core promoter region in SM tissues and ST tissues. Although the data demonstrated the differential expression of CUX1 between SM and ST probably has no association with DNA methylation, the identification of the core region and a potential repressive region of CUX1 promoter can enrich the role of CUX1 in Hu sheep hair follicle development.
Collapse
Affiliation(s)
- Xiaoyang Lv
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou 225009, China
| | - Yue Li
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Animal Husbandry and Veterinary Station, Zhuba Street, Hongze District, Huai’an 223100, China
| | - Weihao Chen
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou 225009, China
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Shanhe Wang
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou 225009, China
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Xiukai Cao
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou 225009, China
| | - Zehu Yuan
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou 225009, China
| | - Tesfaye Getachew
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou 225009, China
- International Centre for Agricultural Research in the Dry Areas, Addis Ababa 999047, Ethiopia
| | - Joram Mwacharo
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou 225009, China
- International Centre for Agricultural Research in the Dry Areas, Addis Ababa 999047, Ethiopia
| | - Aynalem Haile
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou 225009, China
- International Centre for Agricultural Research in the Dry Areas, Addis Ababa 999047, Ethiopia
| | - Yutao Li
- CSIRO Agriculture and Food, 306 Carmody Rd., Saint Lucia, QLD 4067, Australia;
| | - Wei Sun
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou 225009, China
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- “Innovative China” “Belt and Road” International Agricultural Technology Innovation Institute for Evaluation, Protection, and Improvement on Sheep Genetic Resource, Yangzhou 225009, China
| |
Collapse
|
6
|
Cheng J, Li G, Wang W, Stovall DB, Sui G, Li D. Circular RNAs with protein-coding ability in oncogenesis. Biochim Biophys Acta Rev Cancer 2023; 1878:188909. [PMID: 37172651 DOI: 10.1016/j.bbcan.2023.188909] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 05/08/2023] [Accepted: 05/08/2023] [Indexed: 05/15/2023]
Abstract
As ubiquitously expressed transcripts in eukaryotes, circular RNAs (circRNAs) are covalently closed and lack a 5'-cap and 3'-polyadenylation (poly (A)) tail. Initially, circRNAs were considered non-coding RNA (ncRNA), and their roles as sponging molecules to adsorb microRNAs have been extensively reported. However, in recent years, accumulating evidence has demonstrated that circRNAs could encode functional polypeptides through the initiation of translation mediated by internal ribosomal entry sites (IRESs) or N6-methyladenosine (m6A). In this review, we collectively discuss the biogenesis, cognate mRNA products, regulatory mechanisms, aberrant expression and biological phenotypes or clinical relevance of all currently reported, cancer-relevant protein-coding circRNAs. Overall, we provide a comprehensive overview of circRNA-encoded proteins and their physiological and pathological functions.
Collapse
Affiliation(s)
- Jiahui Cheng
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Guangyue Li
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Wenmeng Wang
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Daniel B Stovall
- College of Arts and Sciences, Winthrop University, Rock Hill, SC 29733, United States
| | - Guangchao Sui
- College of Life Science, Northeast Forestry University, Harbin 150040, China.
| | - Dangdang Li
- College of Life Science, Northeast Forestry University, Harbin 150040, China.
| |
Collapse
|
7
|
Campos Segura AV, Velásquez Sotomayor MB, Gutiérrez Román AIF, Ortiz Rojas CA, Murillo Carrasco AG. Impact of mini-driver genes in the prognosis and tumor features of colorectal cancer samples: a novel perspective to support current biomarkers. PeerJ 2023; 11:e15410. [PMID: 37214090 PMCID: PMC10198153 DOI: 10.7717/peerj.15410] [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: 12/14/2022] [Accepted: 04/23/2023] [Indexed: 05/24/2023] Open
Abstract
Background Colorectal cancer (CRC) is the second leading cause of cancer-related deaths, and its development is associated with the gains and/or losses of genetic material, which leads to the emergence of main driver genes with higher mutational frequency. In addition, there are other genes with mutations that have weak tumor-promoting effects, known as mini-drivers, which could aggravate the development of oncogenesis when they occur together. The aim of our work was to use computer analysis to explore the survival impact, frequency, and incidence of mutations of possible mini-driver genes to be used for the prognosis of CRC. Methods We retrieved data from three sources of CRC samples using the cBioPortal platform and analyzed the mutational frequency to exclude genes with driver features and those mutated in less than 5% of the original cohort. We also observed that the mutational profile of these mini-driver candidates is associated with variations in the expression levels. The candidate genes obtained were subjected to Kaplan-Meier curve analysis, making a comparison between mutated and wild-type samples for each gene using a p-value threshold of 0.01. Results After gene filtering by mutational frequency, we obtained 159 genes of which 60 were associated with a high accumulation of total somatic mutations with Log2 (fold change) > 2 and p values < 10-5. In addition, these genes were enriched to oncogenic pathways such as epithelium-mesenchymal transition, hsa-miR-218-5p downregulation, and extracellular matrix organization. Our analysis identified five genes with possible implications as mini-drivers: DOCK3, FN1, PAPPA2, DNAH11, and FBN2. Furthermore, we evaluated a combined classification where CRC patients with at least one mutation in any of these genes were separated from the main cohort obtaining a p-value < 0.001 in the evaluation of CRC prognosis. Conclusion Our study suggests that the identification and incorporation of mini-driver genes in addition to known driver genes could enhance the accuracy of prognostic biomarkers for CRC.
Collapse
Affiliation(s)
- Anthony Vladimir Campos Segura
- Biochemistry and Molecular Biology Research Laboratory. Faculty of Natural Sciences and Mathematics, Universidad Nacional Federico Villarreal, Lima, Peru
- Research Group in Biochemistry and Synthetic Biology (GIBBS-UNFV), Lima, Peru
- Research Group in Immunology and Cancer (IMMUCA), Lima, Peru
| | - Mariana Belén Velásquez Sotomayor
- Research Group in Immunology and Cancer (IMMUCA), Lima, Peru
- School of Human Medicine, Faculty of Health Sciences, Universidad Cientifica del Sur, Lima, Peru
| | - Ana Isabel Flor Gutiérrez Román
- Biochemistry and Molecular Biology Research Laboratory. Faculty of Natural Sciences and Mathematics, Universidad Nacional Federico Villarreal, Lima, Peru
- Research Group in Biochemistry and Synthetic Biology (GIBBS-UNFV), Lima, Peru
| | - César Alexander Ortiz Rojas
- Research Group in Immunology and Cancer (IMMUCA), Lima, Peru
- Hematology Division, LIM31, Medical School, Universidade de São Paulo, Sao Paulo, Brazil
| | - Alexis Germán Murillo Carrasco
- Research Group in Immunology and Cancer (IMMUCA), Lima, Peru
- Centro de Investigação Translacional em Oncologia (LIM24), Departamento de Radiologia e Oncologia, Faculdade de Medicina, Universidade de São Paulo, Sao Paulo, Brazil
| |
Collapse
|
8
|
Gu L, Xia C, Yang S, Yang G. The adaptive evolution of cancer driver genes. BMC Genomics 2023; 24:215. [PMID: 37098512 PMCID: PMC10131384 DOI: 10.1186/s12864-023-09301-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 04/08/2023] [Indexed: 04/27/2023] Open
Abstract
BACKGROUND Cancer is a life-threatening disease in humans; yet, cancer genes are frequently reported to be under positive selection. This suggests an evolutionary-genetic paradox in which cancer evolves as a secondary product of selection in human beings. However, systematic investigation of the evolution of cancer driver genes is sparse. RESULTS Using comparative genomics analysis, population genetics analysis and computational molecular evolutionary analysis, the evolution of 568 cancer driver genes of 66 cancer types were evaluated at two levels, selection on the early evolution of humans (long timescale selection in the human lineage during primate evolution, i.e., millions of years), and recent selection in modern human populations (~ 100,000 years). Results showed that eight cancer genes covering 11 cancer types were under positive selection in the human lineage (long timescale selection). And 35 cancer genes covering 47 cancer types were under positive selection in modern human populations (recent selection). Moreover, SNPs associated with thyroid cancer in three thyroid cancer driver genes (CUX1, HERC2 and RGPD3) were under positive selection in East Asian and European populations, consistent with the high incidence of thyroid cancer in these populations. CONCLUSIONS These findings suggest that cancer can be evolved, in part, as a by-product of adaptive changes in humans. Different SNPs at the same locus can be under different selection pressures in different populations, and thus should be under consideration during precision medicine, especially for targeted medicine in specific populations.
Collapse
Affiliation(s)
- Langyu Gu
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, 510275, China.
| | - Canwei Xia
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Shiyu Yang
- The Affiliated Brain Hospital, Guangzhou Medical University, Guangzhou, 510180, Guangdong, China
| | - Guofen Yang
- Department of Gynecology, First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510060, Guangdong, China.
| |
Collapse
|
9
|
Pahl MC, Grant SFA, Leibel RL, Stratigopoulos G. Technologies, strategies, and cautions when deconvoluting genome-wide association signals: FTO in focus. Obes Rev 2023; 24:e13558. [PMID: 36882962 DOI: 10.1111/obr.13558] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 10/08/2022] [Accepted: 01/31/2023] [Indexed: 03/09/2023]
Abstract
Genome-wide association studies have revealed a plethora of genetic variants that correlate with polygenic conditions. However, causal molecular mechanisms have proven challenging to fully define. Without such information, the associations are not physiologically useful or clinically actionable. By reviewing studies of the FTO locus in the genetic etiology of obesity, we wish to highlight advances in the field fueled by the evolution of technical and analytic strategies in assessing the molecular bases for genetic associations. Particular attention is drawn to extrapolating experimental findings from animal models and cell types to humans, as well as technical aspects used to identify long-range DNA interactions and their biological relevance with regard to the associated trait. A unifying model is proposed by which independent obesogenic pathways regulated by multiple FTO variants and genes are integrated at the primary cilium, a cellular antenna where signaling molecules that control energy balance convene.
Collapse
Affiliation(s)
- Matthew C Pahl
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Struan F A Grant
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Division of Diabetes and Endocrinology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, The University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA.,Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Rudolph L Leibel
- Department of Pediatrics, College of Physicians and Surgeons, Columbia University, New York, New York, USA.,Naomi Berrie Diabetes Center, Columbia University Medical Center, New York, New York, USA
| | - George Stratigopoulos
- Department of Pediatrics, College of Physicians and Surgeons, Columbia University, New York, New York, USA.,Naomi Berrie Diabetes Center, Columbia University Medical Center, New York, New York, USA
| |
Collapse
|
10
|
Teng S, Liu G, Li L, Ou J, Yu Y. CUX1 promotes epithelial-mesenchymal transition (EMT) in renal fibrosis of UUO model by targeting MMP7. Biochem Biophys Res Commun 2022; 608:128-134. [PMID: 35397425 DOI: 10.1016/j.bbrc.2022.03.097] [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: 03/18/2022] [Accepted: 03/18/2022] [Indexed: 11/16/2022]
Abstract
Epithelial-to-mesenchymal transition (EMT) displays a critical role in the development of renal fibrosis, an important pathological process of chronic kidney disease (CKD). Transcription factor Cut-like homeobox 1 (CUX1) has shown profound effects on several kidney diseases. However, its role in CKD has not been understood yet. In this study, unilateral ureteric obstruction (UUO) surgery was performed on male C57BL/6 mice to simulate CKD in vivo. Renal fibrosis was further induced in human proximal tubular epithelial cell (HK-2) by TGF-β1 stimulation. CUX1 and MMP7 were found to be over-expressed in renal tissue of UUO mice. Renal functional analyses and histological assessment indicated that CUX1 knockdown alleviated renal injury in UUO mice. Mitochondrial dysfunction was determined in UUO group and improved after CUX1 silencing. Besides, CUX1 knockdown suppressed EMT in UUO mice and TGF-β1 treated HK-2 cells, as evidenced by reduced expressions of α-SMA, vimentin, fibronectin and augmented abundance of E-cadherin. Furthermore, CUX1 knockdown decreased MMP7 expression by targeting at its promoter region. MMP7 was responsible for the inhibitory effect of CUX1 knockdown on EMT in HK-2 cells. In summary, our findings suggest that CUX1 promotes EMT in CKD by targeting MMP7, and highlight the crucial role of CUX1 in CKD pathogenesis.
Collapse
Affiliation(s)
- Siyuan Teng
- Department of Nephrology, The Second Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China.
| | - Ge Liu
- Department of Nephrology, The Second Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Liangjun Li
- Department of Laboratory Medicine, The Second Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Jun Ou
- Department of Nephrology, Affiliated Hospital of Guilin Medical University, Guilin, Guangxi, China
| | - Yang Yu
- Department of Urology, The Second Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| |
Collapse
|
11
|
Bian W, Wang Z, Li X, Jiang X, Zhang H, Liu Z, Zhang D. Identification of vital modules and genes associated with heart failure based on weighted gene coexpression network analysis. ESC Heart Fail 2022; 9:1370-1379. [PMID: 35128826 PMCID: PMC8934958 DOI: 10.1002/ehf2.13827] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 01/11/2022] [Accepted: 01/14/2022] [Indexed: 12/04/2022] Open
Abstract
Aims Heart failure (HF) is a chronic heart disease with a high incidence and mortality. Due to the regulatory complexity of gene coexpression networks, the underlying hub genes regulation in HF remain incompletely appreciated. We aimed to explore potential key modules and genes for HF using weighted gene coexpression network analysis (WGCNA). Methods and results The expression profiles by high throughput sequencing of heart tissues samples from HF and non‐HF samples were obtained from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) between HF and non‐HF samples were firstly identified. Then, a coexpression network was constructed to identify key modules and potential hub genes. The biological functions of potential hub genes were analysed by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses. Finally, a protein–protein interaction (PPI) network was constructed using the STRING online tool. A total of 135 DEGs (133 up‐regulated and 2 down‐regulated DEGs) between HF and non‐HF samples were identified in the GSE135055 and GSE123976 datasets. Moreover, a total of 38 modules were screened based on WGCNA in the GSE135055 dataset, and six potential hub genes (UCK2, ASB1, CCNI, CUX1, IRX6, and STX16) were screened from the key module by setting the gene significance over 0.2 and the module membership over 0.8. Furthermore, 78 potential hub genes were obtained by taking the intersection of the 135 DEGs and all genes in the key module, and enrichment analysis revealed that they were mainly involved in the MAPK and PI3K‐AKT signalling pathways. Finally, in a PPI network constructed with the 78 potential hub genes, CUX1 and ASB1 were identified as hub genes in HF because they were also identified as potential hub genes in the WGCNA. Conclusions To the best of our knowledge, our study is the first to employ WGCNA to identify the key module and hub genes for HF. Our study identified a module and two genes that might play important roles in HF, which may provide potential biomarkers for the diagnosis of HF and improve our knowledge of the molecular mechanisms underlying HF.
Collapse
Affiliation(s)
- Weikang Bian
- Department of Cardiology Nanjing First Hospital, Nanjing Medical University 68 Changle Road Nanjing 210006 China
| | - Zhicheng Wang
- Department of Cardiology Nanjing First Hospital, Nanjing Medical University 68 Changle Road Nanjing 210006 China
| | - Xiaobo Li
- Department of Cardiology Nanjing First Hospital, Nanjing Medical University 68 Changle Road Nanjing 210006 China
| | - Xiao‐Xin Jiang
- Department of Cardiology Nanjing First Hospital, Nanjing Medical University 68 Changle Road Nanjing 210006 China
| | - Hongsong Zhang
- Department of Cardiology Nanjing First Hospital, Nanjing Medical University 68 Changle Road Nanjing 210006 China
| | - Zhizhong Liu
- Department of Cardiology Nanjing First Hospital, Nanjing Medical University 68 Changle Road Nanjing 210006 China
| | - Dai‐Min Zhang
- Department of Cardiology Nanjing First Hospital, Nanjing Medical University 68 Changle Road Nanjing 210006 China
- Department of Cardiology Sir Run Run Hospital, Nanjing Medical University Nanjing China
| |
Collapse
|
12
|
Jiang D, Sun W, Wu T, Zou M, Vasamsetti SB, Zhang X, Zhao Y, Phillippi JA, Sawalha AH, Tavakoli S, Dutta P, Florentin J, Chan SY, Tollison TS, Di Wu, Cui J, Huntress I, Peng X, Finkel T, Li G. Post-GWAS functional analysis identifies CUX1 as a regulator of p16 INK4a and cellular senescence. NATURE AGING 2022; 2:140-154. [PMID: 37117763 PMCID: PMC10154215 DOI: 10.1038/s43587-022-00177-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 12/21/2021] [Indexed: 04/30/2023]
Abstract
Accumulation of senescent cells with age is an important driver of aging and age-related diseases. However, the mechanisms and signaling pathways that regulate senescence remain elusive. In this report, we performed post-genome-wide association studies (GWAS) functional studies on the CDKN2A/B locus, a locus known to be associated with multiple age-related diseases and overall human lifespan. We demonstrate that transcription factor CUX1 (Cut-Like Homeobox 1) specifically binds to an atherosclerosis-associated functional single-nucleotide polymorphism (fSNP) (rs1537371) within the locus and regulates the CDKN2A/B-encoded proteins p14ARF, p15INK4b and p16INK4a and the antisense noncoding RNA in the CDK4 (INK4) locus (ANRIL) in endothelial cells (ECs). Endothelial CUX1 expression correlates with telomeric length and is induced by both DNA-damaging agents and oxidative stress. Moreover, induction of CUX1 expression triggers both replicative and stress-induced senescence via activation of p16INK4a expression. Thus, our studies identify CUX1 as a regulator of p16INK4a-dependent endothelial senescence and a potential therapeutic target for atherosclerosis and other age-related diseases.
Collapse
Affiliation(s)
- Danli Jiang
- Aging Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Wei Sun
- Center for Pulmonary Vascular Biology and Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Ting Wu
- Aging Institute, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Medicine, Xiangya School of Medicine, Central South University, Changsha, China
| | - Meijuan Zou
- Aging Institute, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Pharmacology, Nanjing Medical University, Nanjing, China
| | - Sathish Babu Vasamsetti
- Center for Pulmonary Vascular Biology and Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Xiaoyu Zhang
- Aging Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yihan Zhao
- Aging Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Julie A Phillippi
- Department of Cardiothoracic Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Amr H Sawalha
- Departments of Pediatrics Medicine, and Immunology & Lupus Center of Excellence, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Sina Tavakoli
- Departments of Radiology and Medicine, University of Pittsburgh, UPMC Presbyterian Hospital, Pittsburg, PA, USA
| | - Partha Dutta
- Center for Pulmonary Vascular Biology and Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Jonathan Florentin
- Center for Pulmonary Vascular Biology and Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, PA, USA
- Department of Medicine, Division of Cardiology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Stephen Y Chan
- Center for Pulmonary Vascular Biology and Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Tammy S Tollison
- Department of Molecular Biomedical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, NC, USA
| | - Di Wu
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Division of Oral and Craniofacial Health Sciences, Adam School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jing Cui
- Department of Medicine, Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA, USA
| | - Ian Huntress
- Department of Molecular Biomedical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, NC, USA
- Bioinformatics Graduate Program, North Carolina State University, Raleigh, NC, USA
| | - Xinxia Peng
- Department of Molecular Biomedical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, NC, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Toren Finkel
- Aging Institute, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Medicine, Division of Cardiology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Gang Li
- Aging Institute, University of Pittsburgh, Pittsburgh, PA, USA.
- Department of Medicine, Division of Cardiology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA.
| |
Collapse
|
13
|
Zhang L, Cao W. Histone deacetylase 3 (HDAC3) as an important epigenetic regulator of kidney diseases. J Mol Med (Berl) 2021; 100:43-51. [PMID: 34698870 DOI: 10.1007/s00109-021-02141-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 08/18/2021] [Accepted: 09/09/2021] [Indexed: 12/18/2022]
Abstract
Development and progression of many kidney diseases are substantially influenced by aberrant protein acetylation modifications of gene expression crucial for kidney functions. Histone deacetylase (HDAC) expression alterations are detected from renal samples of patients and animal models of various kidney diseases, and the administrations of HDAC inhibitors display impressive renal protective effects in vitro and in vivo. However, when the expression alterations of multiple HDACs occur, not all the HDACs causally affect the disease onset or progression. Identification of a single HDAC as a disease-causing factor will allow subtype-targeted intervention with less side effect. HDAC3 is a unique HDAC with distinct structural and subcellular distribution features and co-repressor dependency. HDAC3 is required for kidney development and its aberrations actively participate in many pathological processes, such as cancer, cardiovascular diseases, diabetes, and neurodegenerative disorders, and contribute significantly to the pathogenesis of kidney diseases. This review will discuss the recent studies that investigate the critical roles of HDAC3 aberrations in kidney development, renal aging, renal cell carcinoma, renal fibrosis, chronic kidney disease, polycystic kidney disease, glomerular podocyte injury, and diabetic nephropathy. These studies reveal the distinct characters of HDAC3 aberrations that act on different molecules/signaling pathways under various renal pathological conditions, which might shed lights into the epigenetic mechanisms of renal diseases and the potentially therapeutic strategies.
Collapse
Affiliation(s)
- Lijun Zhang
- Department of Nephrology, Northern Jiangsu People's Hospital, Nanjing University School of Medicine, Yangzhou, 225001, China
- Jiangsu Key Lab of Molecular Medicine, Nanjing University School of Medicine, Nanjing, 210093, China
| | - Wangsen Cao
- Department of Nephrology, Northern Jiangsu People's Hospital, Nanjing University School of Medicine, Yangzhou, 225001, China.
- Jiangsu Key Lab of Molecular Medicine, Nanjing University School of Medicine, Nanjing, 210093, China.
| |
Collapse
|
14
|
Feng F, Zhao Z, Zhou Y, Cheng Y, Wu X, Heng X. CUX1 Facilitates the Development of Oncogenic Properties Via Activating Wnt/β-Catenin Signaling Pathway in Glioma. Front Mol Biosci 2021; 8:705008. [PMID: 34422906 PMCID: PMC8377541 DOI: 10.3389/fmolb.2021.705008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 07/26/2021] [Indexed: 11/30/2022] Open
Abstract
Background: Homeobox cut like 1 (CUX1), which often presents aberrated expression in many cancer cells, exerts a crucial role in tumorigenesis. Evidence describing CUX1 in gliomagenesis is scarce, and the effects of CUX1 on the Wnt/β-catenin pathway have not been reported. Our study aimed to explore the biological functions and molecular mechanisms involved in CUX1 activity in glioma. Methods: Datasets for bioinformatics analysis were obtained from the GEO, TCGA, CGGA, GTEX and CCLE databases. qRT-PCR, western blotting (WB), and immunohistochemistry (IHC) assays were used to investigate the expression patterns of CUX1 among glioma and brain tissues. CUX1 knockdown and overexpression vectors were transfected into glioma cell lines, the CCK-8, clone formation assay, wound healing, Transwell assay, and flow cytometry were performed to detect changes in cell viability, invasiveness, and the cell cycle. WB and immunofluorescence (IF) assays were used to explore changes in cell cycle-related and Wnt/β-catenin signaling protein levels. Results: Overexpression of CUX1 was identified in glioma tissues, and especially in glioblastoma (GBM), when compared to normal controls and correlated with poor prognosis. In comparison with untreated cells, TJ905 glioma cells overexpressing CUX1 showed higher proliferation and invasion abilities and S phase cell-cycle arrest, while the knockdown of CUX1 suppressed cell invasive ability and induced G1 phase arrest. Active Wnt/β-catenin signaling was enriched and clustered in a CUX1-associated GSEA/GSVA analysis. IF and WB assays indicated that CUX1 regulated the distribution of Axin2/β-catenin in glioma cells and regulated the expression of proteins downstream of the Wnt/β-catenin signaling pathway, suggesting that CUX1 served as an upstream positive regulator of the Wnt/β-catenin pathway. Finally, the knockdown of Axin2 or β-catenin could reverse the tumor-promoting effects caused by CUX1 overexpression, suggesting that CUX1 induced gliomagenesis and malignant phenotype by activating the Wnt/β-catenin signaling pathway. Conclusion: Our data suggested that the transcription factor CUX1 could be a novel therapeutic target for glioma with gene therapy.
Collapse
Affiliation(s)
- Fan Feng
- Institute of Clinical Medicine College, Guangzhou University of Chinese Medicine, Guangzhou, China.,Institute of Brain Science and Brain-Like Intelligence, Linyi People's Hospital, Linyi, China.,Department of Neurosurgery, Linyi People's Hospital, Linyi, China
| | - Zongqing Zhao
- Institute of Brain Science and Brain-Like Intelligence, Linyi People's Hospital, Linyi, China.,Department of Neurosurgery, Linyi People's Hospital, Linyi, China
| | - Yunfei Zhou
- Department of Neurosurgery, Linyi People's Hospital, Linyi, China
| | - Yanhao Cheng
- Institute of Brain Science and Brain-Like Intelligence, Linyi People's Hospital, Linyi, China.,Department of Neurosurgery, Linyi People's Hospital, Linyi, China
| | - Xiujie Wu
- Institute of Brain Science and Brain-Like Intelligence, Linyi People's Hospital, Linyi, China.,Department of Neurosurgery, Linyi People's Hospital, Linyi, China
| | - Xueyuan Heng
- Institute of Brain Science and Brain-Like Intelligence, Linyi People's Hospital, Linyi, China.,Department of Neurosurgery, Linyi People's Hospital, Linyi, China
| |
Collapse
|
15
|
Tsai CK, Liang CS, Lin GY, Tsai CL, Lee JT, Sung YF, Lin YK, Hung KS, Chen WL, Yang FC. Identifying genetic variants for age of migraine onset in a Han Chinese population in Taiwan. J Headache Pain 2021; 22:89. [PMID: 34380431 PMCID: PMC8356430 DOI: 10.1186/s10194-021-01301-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 07/21/2021] [Indexed: 12/23/2022] Open
Abstract
Background Considering the involvement of genetics in migraine pathogenesis in diverse ethnic populations, genome-wide association studies (GWAS) are being conducted to identify migraine-susceptibility genes. However, limited surveys have focused on the onset age of migraine (AoM) in Asians. Therefore, in this study, we aimed to identify the susceptibility loci of migraine considering the AoM in an Asian population. Methods We conducted a GWAS in 715 patients with migraine of Han Chinese ethnicity, residing in Taiwan, to identify the susceptibility genes associated with AoM. Based on our standard demographic questionnaire, the population was grouped into different subsets. Single-nucleotide polymorphism (SNP) associations were examined using PLINK in different AoM onset groups. Results We discovered eight novel susceptibility loci correlated with AoM that reached the GWAS significance level in the Han Chinese population. First, rs146094041 in ESRRG was associated with AoM \documentclass[12pt]{minimal}
\usepackage{amsmath}
\usepackage{wasysym}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsbsy}
\usepackage{mathrsfs}
\usepackage{upgreek}
\setlength{\oddsidemargin}{-69pt}
\begin{document}$$\le$$\end{document}≤ 12 years. The other SNPs including rs77630941 in CUX1, rs146778855 in CDH18, rs117608715 in NOL3, rs150592309 in PRAP1, and rs181024055 in NRAP were associated with the later AoM. Conclusions To our knowledge, this is the first GWAS to investigate the AoM in an Asian Han Chinese population. Our newly discovered susceptibility genes may have prospective associations with migraine pathogenesis. Supplementary Information The online version contains supplementary material available at 10.1186/s10194-021-01301-y.
Collapse
Affiliation(s)
- Chia-Kuang Tsai
- Department of Neurology, Tri-Service General Hospital, National Defense Medical Center, No. 325, Section 2, Cheng-Kung Road, Neihu 114, Taipei, Taiwan
| | - Chih-Sung Liang
- Department of Psychiatry, Beitou Branch, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Guan-Yu Lin
- Department of Neurology, Tri-Service General Hospital, National Defense Medical Center, No. 325, Section 2, Cheng-Kung Road, Neihu 114, Taipei, Taiwan.,Department of Neurology, Songshan Branch, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Chia-Lin Tsai
- Department of Neurology, Tri-Service General Hospital, National Defense Medical Center, No. 325, Section 2, Cheng-Kung Road, Neihu 114, Taipei, Taiwan
| | - Jiunn-Tay Lee
- Department of Neurology, Tri-Service General Hospital, National Defense Medical Center, No. 325, Section 2, Cheng-Kung Road, Neihu 114, Taipei, Taiwan
| | - Yueh-Feng Sung
- Department of Neurology, Tri-Service General Hospital, National Defense Medical Center, No. 325, Section 2, Cheng-Kung Road, Neihu 114, Taipei, Taiwan
| | - Yu-Kai Lin
- Department of Neurology, Tri-Service General Hospital, National Defense Medical Center, No. 325, Section 2, Cheng-Kung Road, Neihu 114, Taipei, Taiwan
| | - Kuo-Sheng Hung
- Center for Precision Medicine and Genomics, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Wei-Liang Chen
- Division of Family Medicine, Department of Family and Community Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan.,Division of Geriatric Medicine, Department of Family and Community Medicine, School of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Fu-Chi Yang
- Department of Neurology, Tri-Service General Hospital, National Defense Medical Center, No. 325, Section 2, Cheng-Kung Road, Neihu 114, Taipei, Taiwan.
| |
Collapse
|
16
|
Chen Q, Yin Q, Song J, Liu C, Chen H, Li S. Identification of monocyte-associated genes as predictive biomarkers of heart failure after acute myocardial infarction. BMC Med Genomics 2021; 14:44. [PMID: 33563285 PMCID: PMC7871627 DOI: 10.1186/s12920-021-00890-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 01/31/2021] [Indexed: 12/21/2022] Open
Abstract
Background Acute myocardial infarction (AMI) is a major contributor of heart failure (HF). Peripheral blood mononuclear cells (PBMCs), mainly monocytes, are the essential initiators of AMI-induced HF. The powerful biomarkers for early identification of AMI patients at risk of HF remain elusive. We aimed to identify monocyte-related critical genes as predictive biomarkers for post-AMI HF. Methods We performed weighted gene co-expression network analysis (WGCNA) on transcriptomics of PBMCs from AMI patients who developed HF or did not. Functional enrichment analysis of genes in significant modules was performed via Metascape. Then we obtained the single-cell RNA-sequencing data of recruited monocytes/macrophages from AMI and control mice using the Scanpy and screened 381 differentially expressed genes (DEGs) between the two groups. We validated the expression changes of the 25 genes in cardiac macrophages from AMI mice based on bulk RNA-sequencing data and PBMCs data mentioned above. Results In our study, the results of WGCNA showed that two modules containing 827 hub genes were most significantly associated with post-AMI HF, which mainly participated in cell migration, inflammation, immunity, and apoptosis. There were 25 common genes between DEGs and hub genes, showing close relationship with inflammation and collagen metabolism. CUX1, CTSD and ADD3 exhibited consistent changes in three independent studies. Receiver operating characteristic curve analysis showed that each of the three genes had excellent performance in recognizing post-AMI HF patients. Conclusion Our findings provided a set of three monocyte-related biomarkers for the early prediction of HF development after AMI as well as potential therapeutic targets of post-AMI HF.
Collapse
Affiliation(s)
- Qixin Chen
- Department of Cardiology, Beijing Key Laboratory of Early Prediction and Intervention of Acute Myocardial Infarction, Center for Cardiovascular Translational Research, Peking University People's Hospital, No 11. Xizhimen South Street, Xicheng District, Beijing, 100044, China
| | - Qijin Yin
- Ministry of Education Key Laboratory of Bioinformatics, Research Department of Bioinformatics at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University, Beijing, 100084, China
| | - Junxian Song
- Department of Cardiology, Beijing Key Laboratory of Early Prediction and Intervention of Acute Myocardial Infarction, Center for Cardiovascular Translational Research, Peking University People's Hospital, No 11. Xizhimen South Street, Xicheng District, Beijing, 100044, China
| | - Chuanfen Liu
- Department of Cardiology, Beijing Key Laboratory of Early Prediction and Intervention of Acute Myocardial Infarction, Center for Cardiovascular Translational Research, Peking University People's Hospital, No 11. Xizhimen South Street, Xicheng District, Beijing, 100044, China
| | - Hong Chen
- Department of Cardiology, Beijing Key Laboratory of Early Prediction and Intervention of Acute Myocardial Infarction, Center for Cardiovascular Translational Research, Peking University People's Hospital, No 11. Xizhimen South Street, Xicheng District, Beijing, 100044, China.
| | - Sufang Li
- Department of Cardiology, Beijing Key Laboratory of Early Prediction and Intervention of Acute Myocardial Infarction, Center for Cardiovascular Translational Research, Peking University People's Hospital, No 11. Xizhimen South Street, Xicheng District, Beijing, 100044, China.
| |
Collapse
|
17
|
Wei R, Chen L, Qin D, Guo Q, Zhu S, Li P, Min L, Zhang S. Liquid Biopsy of Extracellular Vesicle-Derived miR-193a-5p in Colorectal Cancer and Discovery of Its Tumor-Suppressor Functions. Front Oncol 2020; 10:1372. [PMID: 33014778 PMCID: PMC7461920 DOI: 10.3389/fonc.2020.01372] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 06/29/2020] [Indexed: 12/27/2022] Open
Abstract
Previously, abnormal extracellular vesicle (EV) sorting of miR-193a was identified in colorectal cancer (CRC) progression. Although a reduced level of miR-193a-5p in plasma/serum has been reported in many different types of cancer, the EV-derived miR-193a-5p level in CRC and its potential application as a minimally invasive biomarker are still unknown. Here, we evaluated the circulating EV-derived miR-193a-5p expression levels in a cohort of 101 participants by real-time quantitative polymerase chain reaction (RT-qPCR). We found that plasma EV-miR-193a-5p decreased significantly in CRC patients as compared with precancerous colorectal adenoma (CA) and non-cancerous control (NC) individuals. The circulating EV-miR-193a-5p showed an area under the receiver operating characteristic curve (AUC) of 0.740 in distinguishing CRC from CA and an AUC of 0.759 in distinguishing CRC from NC. Furthermore, the suppression on CRC cells of miR-193a-5p was verified by transwell, MTS (3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium), EdU, RT-qPCR, and western blotting. Bioinformatic analysis predicted 32 genes, which were the most likely miR-193a-5p targeted and mainly focused on tumor progression. Among them, we revealed that miR-193a-5p could inhibit CRC migration and invasion via targeting tumor-associated genes like CUT-like homeobox 1 (CUX1) and intersectin 1 (ITSN1). In conclusion, miR-193a-5p could suppress CRC development, and decreased plasma EV-miR-193a-5p could be a promising biomarker for human CRC detection.
Collapse
Affiliation(s)
- Rui Wei
- Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Department of Gastroenterology, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Lei Chen
- Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Department of Gastroenterology, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Da Qin
- Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Department of Gastroenterology, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Qingdong Guo
- Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Department of Gastroenterology, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Shengtao Zhu
- Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Department of Gastroenterology, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Peng Li
- Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Department of Gastroenterology, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Li Min
- Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Department of Gastroenterology, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Shutian Zhang
- Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Department of Gastroenterology, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| |
Collapse
|