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Wang X, Zhang Y, Song N, Li K, Lei S, Wang J, Wang Z, Zhang W. CILP2: A prognostic biomarker associated with immune infiltration in colorectal cancer. Heliyon 2023; 9:e15535. [PMID: 37144183 PMCID: PMC10151353 DOI: 10.1016/j.heliyon.2023.e15535] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/04/2023] [Accepted: 04/13/2023] [Indexed: 05/06/2023] Open
Abstract
The function played by cartilage intermediate layer protein 2 (CILP2) between colorectal cancer (CRC) progression and immune response remains unclear, especially with respect to immune cell infiltration and checkpoints. Materials and Methods: We examined CILP2 expression in The Cancer Genome Atlas (TCGA) COAD-READ cohort and analyzed its relationship with clinicopathological features, mutations, survival, and immunity. Gene ontology, Kyoto Encyclopedia of Genes and Genomes pathway analysis, and gene set enrichment analyses (GSEA) were performed to determine CILP2 related pathways. To further investigate the results of TCGA analysis, validation was performed using CRC cell lines, fresh pathological tissues, and a CRC tissue microarray (TMA). Results: In both TCGA and TMA cohorts, CILP2 expression was increased in CRC tissues and was associated with patient T stage (T3 and T4), N stage (N1), pathological stage (III and IV), and overall survival. Immune cell infiltration and checkpoint analysis revealed that CILP2 expression is highly correlated with multiple immune marker genes, including PD-1. In addition, results of enrichment analysis indicated that CILP2 related genes was mainly enriched in extracellular matrix related functions. Conclusion: Elevated CILP2 expression is associated with adverse CRC clinical features and immune cells, it has potential as a biomarker detrimental to CRC survival.
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Affiliation(s)
- Xueli Wang
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310032, China
| | - Yu Zhang
- Department of Gastroenterology, Zhejiang Provincial People’s Hospital, People’s Hospital of Hangzhou Medical College, Hangzhou, China
| | - Niping Song
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Kaiqiang Li
- Center for Laboratory Medicine, Allergy Center, Department of Transfusion Medicine, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, Zhejiang 310014, China
| | - Siyun Lei
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310032, China
| | - Jianwei Wang
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310032, China
| | - Zhen Wang
- Center for Laboratory Medicine, Allergy Center, Department of Transfusion Medicine, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, Zhejiang 310014, China
- Corresponding author.
| | - Wei Zhang
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310032, China
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou 310005, China
- Corresponding author. Department of Gastrointestinal surgery, The Second Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou 310005, China.
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Lee Y, Yoon JW, Kim YA, Choi HJ, Yoon BW, Seo JH. A Genome-Wide Association Study of Genetic Variants of Apolipoprotein A1 Levels and Their Association with Vitamin D in Korean Cohorts. Genes (Basel) 2022; 13:genes13091553. [PMID: 36140721 PMCID: PMC9498618 DOI: 10.3390/genes13091553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/17/2022] [Accepted: 08/26/2022] [Indexed: 12/02/2022] Open
Abstract
Dyslipidemia is an important independent risk factor for cardiovascular disease (CVD). Specifically, apolipoprotein A1 (ApoA1), apolipoprotein B (ApoB), and the ApoB/A1 ratio have been linked to CVD. We conducted a genome-wide association study meta-analysis of two Korean cohorts containing a total of 12,924 patients to identify novel single nucleotide polymorphisms (SNPs) associated with ApoA1 and ApoB levels and the ApoB/A1 ratio. Additionally, an expression quantitative trait locus (eQTL) and differentially expressed genes (DEGs) analysis were performed. The statistically significant eQTL, DEG, and Gene Ontology (GO) results were used to explore the predicted interaction networks and retrieve the interacting genes and proteins. We identified three novel SNPs (rs11066280, p = 3.46 × 10−21; rs1227162, p = 2.98 × 10−15; rs73216931, p = 5.62 × 10−9) associated with ApoA1. SNP rs73216931 was an eQTL for KMT5A in the pancreas and whole blood. The network analysis revealed that HECTD4 and MYL2:LINC1405 are associated with AKT1. Our in silico analysis of ApoA1 genetic variants revealed heart muscle-related signals. ApoA1 also correlated positively with vitamin D, and genes associated with ApoA1 and vitamin D were found. Our data imply that more research into ApoA1 is needed to understand the links between dyslipidemia and CVD and vitamin D and CVD.
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Affiliation(s)
- Young Lee
- Veterans Medical Research Institute, Veterans Health Service Medical Center, Seoul 05368, Korea
- Department of Applied Statistics, Chung-Ang University, Seoul 06974, Korea
| | - Ji Won Yoon
- Healthcare System Gangnam Center, Seoul National University Hospital, Seoul 06236, Korea
| | - Ye An Kim
- Division of Endocrinology, Department of Internal Medicine, Veterans Health Service Medical Center, Seoul 05368, Korea
| | - Hyuk Jin Choi
- Healthcare System Gangnam Center, Seoul National University Hospital, Seoul 06236, Korea
| | - Byung Woo Yoon
- Department of Internal Medicine, College of Medicine, Chung-Ang University, Seoul 06974, Korea
| | - Je Hyun Seo
- Veterans Medical Research Institute, Veterans Health Service Medical Center, Seoul 05368, Korea
- Correspondence: ; Tel.: +82-2-2225-1445; Fax: +82-2-2225-3950
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Identifying the Potential Roles of PBX4 in Human Cancers Based on Integrative Analysis. Biomolecules 2022; 12:biom12060822. [PMID: 35740947 PMCID: PMC9221482 DOI: 10.3390/biom12060822] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/09/2022] [Accepted: 06/11/2022] [Indexed: 02/05/2023] Open
Abstract
PBX4 belongs to the pre-B-cell leukemia homeobox (PBX) transcription factors family and acts as a transcriptional cofactor of HOX proteins participating in several pathophysiological processes. Recent studies have revealed that the dysregulation of PBX4 is closely related to multiple diseases, especially cancers. However, the research on PBX4’s potential roles in 33 cancers from the Cancer Genome Atlas (TCGA) is still insufficient. Therefore, we performed a comprehensive pan-cancer analysis to explore the roles of PBX4with multiple public databases. Our results showed that PBX4 was differentially expressed in 17 types of human cancer and significantly correlated to the pathological stage, tumor grade, and immune and molecular subtypes. We used the Kaplan–Meier plotter and PrognoScan databases to find the significant associations between PBX4 expression and prognostic values of multiple cancers. It was also found that PBX4 expression was statistically related to mutation status, DNA methylation, immune infiltration, drug sensitivity, and immune checkpoint blockade (ICB) therapy. Additionally, we found that PBX4 was involved in different functional states of multiple cancers from the single-cell resolution perspective. Enrichment analysis results showed that PBX4-related genes were enriched in the cell cycle process, MAPK cascade, ncRNA metabolic process, positive regulation of GTPase activity, and regulation of lipase activity and mainly participated in the pathways of cholesterol metabolism, base excision repair, herpes simplex virus 1 infection, transcriptional misregulation in cancer, and Epstein–Barr virus infection. Altogether, our integrative analysis could help in better understanding the potential roles of PBX4 in different human cancers.
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PCSK9: A Multi-Faceted Protein That Is Involved in Cardiovascular Biology. Biomedicines 2021; 9:biomedicines9070793. [PMID: 34356856 PMCID: PMC8301306 DOI: 10.3390/biomedicines9070793] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/02/2021] [Accepted: 07/05/2021] [Indexed: 12/29/2022] Open
Abstract
Pro-protein convertase subtilisin/kexin type 9 (PCSK9) is secreted mostly by hepatocytes and to a lesser extent by the intestine, pancreas, kidney, adipose tissue, and vascular cells. PCSK9 has been known to interact with the low-density lipoprotein receptor (LDLR) and chaperones the receptor to its degradation. In this manner, targeting PCSK9 is a novel attractive approach to reduce hyperlipidaemia and the risk for cardiovascular diseases. Recently, it has been recognised that the effects of PCSK9 in relation to cardiovascular complications are not only LDLR related, but that various LDLR-independent pathways and processes are also influenced. In this review, the various LDLR dependent and especially independent effects of PCSK9 on the cardiovascular system are discussed, followed by an overview of related PCSK9-polymorphisms and currently available and future therapeutic approaches to manipulate PCSK9 expression.
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Khan AA, Sundar P, Natarajan B, Gupta V, Arige V, Reddy SS, Barthwal MK, Mahapatra NR. An evolutionarily-conserved promoter allele governs HMG-CoA reductase expression in spontaneously hypertensive rat. J Mol Cell Cardiol 2021; 158:140-152. [PMID: 34081950 DOI: 10.1016/j.yjmcc.2021.05.017] [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: 11/20/2019] [Revised: 04/27/2021] [Accepted: 05/25/2021] [Indexed: 11/18/2022]
Abstract
3-Hydroxy-3-methyl glutaryl-coenzyme A reductase (Hmgcr) encodes the rate-limiting enzyme in the cholesterol biosynthesis pathway. The regulation of Hmgcr in rat models of genetic hypertension (viz. Spontaneously Hypertensive Rat [SHR] and its normotensive control Wistar/Kyoto [WKY] strain) is unclear. Interestingly, Hmgcr transcript and protein levels are diminished in liver tissues of SHR as compared to WKY. This observation is consistent with the diminished plasma cholesterol level in SHR animals. However, the molecular basis of these apparently counter-intuitive findings remains completely unknown. Sequencing of the Hmgcr promoter in SHR and WKY strains reveals three variations: A-405G, C-62T and a 11 bp insertion (-398_-388insTGCGGTCCTCC) in SHR. Among these variations, A-405G occurs at an evolutionarily-conserved site among many mammals. Moreover, SHR-Hmgcr promoter displays lower activity than WKY-Hmgcr promoter in various cell lines. Transient transfections of Hmgcr-promoter mutants and in silico analysis suggest altered binding of Runx3 and Srebf1 across A-405G site. On the other hand, C-62T and -398_-388insTGCGGTCCTCC variations do not appear to contribute to the reduced Hmgcr promoter activity in SHR as compared to WKY. Indeed, chromatin immunoprecipitation assays confirm differential binding of Runx3 and Srebf1 to Hmgcr promoter leading to reduced expression of Hmgcr in SHR as compared to WKY under basal as well as cholesterol-modulated conditions. Taken together, this study provides, for the first time, molecular basis for diminished Hmgcr expression in SHR animals, which may account for the reduced circulating cholesterol level in this widely-studied model for cardiovascular diseases.
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Affiliation(s)
- Abrar A Khan
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Poovitha Sundar
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Bhargavi Natarajan
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Vinayak Gupta
- Bennett University, Plot No. 8-11, Techzone II, Greater Noida 201310, India
| | - Vikas Arige
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - S Santosh Reddy
- Pharmacology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India; Academy of Scientific and Innovative Research (AcSIR), New Delhi 110025, India
| | - Manoj K Barthwal
- Pharmacology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Nitish R Mahapatra
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India.
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Zamarrón-Licona E, Rodríguez-Pérez JM, Posadas-Sánchez R, Vargas-Alarcón G, Baños-González MA, Borgonio-Cuadra VM, Pérez-Hernández N. Variants of PCSK9 Gene Are Associated with Subclinical Atherosclerosis and Cardiometabolic Parameters in Mexicans. The GEA Project. Diagnostics (Basel) 2021; 11:diagnostics11050774. [PMID: 33925815 PMCID: PMC8145882 DOI: 10.3390/diagnostics11050774] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 04/17/2021] [Accepted: 04/23/2021] [Indexed: 12/20/2022] Open
Abstract
Background: Coronary artery disease (CAD) is a chronic, inflammatory, and complex disease associated with vascular risk factors. Nowadays, the coronary artery calcium (CAC) is a specific marker of the presence and extent of atherosclerosis. Additionally, CAC is a predictor of future coronary events in asymptomatic individuals diagnosed with subclinical atherosclerosis (CAC > 0). In this study, our aim is to evaluate the participation of two polymorphisms of the PCSK9 gene as genetic markers for developing subclinical atherosclerosis and cardiometabolic risk factors in asymptomatic individuals. Methods: We analyzed two PCSK9 polymorphisms (rs2479409 and rs615563) in 394 individuals with subclinical atherosclerosis and 1102 healthy controls using real time- polymerase chain reaction (PCR). Results: Under various inheritance models adjusted for different confounding factors, the rs2479409 polymorphism was associated with an increased risk of developing subclinical atherosclerosis (OR = 1.53, P recessive = 0.041). Both polymorphisms were significantly associated with several cardiometabolic parameters. Conclusions: Our data suggest that rs2479409 polymorphism could be envisaged as a risk marker for subclinical atherosclerosis.
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Affiliation(s)
- Erasmo Zamarrón-Licona
- Departamento de Biología Molecular, Instituto Nacional de Cardiología Ignacio Chávez, Ciudad de México 14080, Mexico; (E.Z.-L.); (J.M.R.-P.); (G.V.-A.)
| | - José Manuel Rodríguez-Pérez
- Departamento de Biología Molecular, Instituto Nacional de Cardiología Ignacio Chávez, Ciudad de México 14080, Mexico; (E.Z.-L.); (J.M.R.-P.); (G.V.-A.)
| | - Rosalinda Posadas-Sánchez
- Departamento de Endocrinología, Instituto Nacional de Cardiología Ignacio Chávez, Ciudad de México 14080, Mexico;
| | - Gilberto Vargas-Alarcón
- Departamento de Biología Molecular, Instituto Nacional de Cardiología Ignacio Chávez, Ciudad de México 14080, Mexico; (E.Z.-L.); (J.M.R.-P.); (G.V.-A.)
| | - Manuel Alfonso Baños-González
- Centro de Investigación y Posgrado, División Académica de Ciencias de la Salud, Universidad Juárez Autónoma de Tabasco, Villahermosa 86150, Mexico;
| | | | - Nonanzit Pérez-Hernández
- Departamento de Biología Molecular, Instituto Nacional de Cardiología Ignacio Chávez, Ciudad de México 14080, Mexico; (E.Z.-L.); (J.M.R.-P.); (G.V.-A.)
- Correspondence: ; Tel.: +52-55-55732911 (ext. 26301)
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Huang Z, Xu Z, Xu R, Huang L, Xu X, Lai X. Whole exome sequencing identifies three novel gene mutations in patients with the triad of diabetic ketoacidosis, hypertriglyceridemia, and acute pancreatitis. J Diabetes 2021; 13:200-210. [PMID: 32734598 DOI: 10.1111/1753-0407.13100] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 07/05/2020] [Accepted: 07/24/2020] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND This study aimed to analyze the genetics and treatments of the patients with the triad of diabetic ketoacidosis (DKA), hypertriglyceridemia, and acute pancreatitis (AP). METHODS We conducted a retrospective study of six patients with the triad of AP, hypertriglyceridemia, and DKA at our hospital. All patients underwent plasmapheresis as part of their treatment. The clinical characteristics of the patients were obtained from the hospital information system and analyzed. Whole exome sequencing was performed using samples of one patient (case 6) and his family members. RESULTS The average triglyceride level before plasmapheresis was 3282.17 ± 2975.43 mg/dL (range: 1646-9332 mg/dL). The triglyceride levels dropped by approximately 80% after plasmapheresis. None of the patients developed complications related from plasmapheresis. During follow-up, patients 5 and 6 developed recurrent pancreatitis for several times and showed the formation of pancreatic pseudocysts. We identified three novel heterozygous missense mutations in the family of patient 6, including c.12614C > T (p.Pro4205Leu) in APOB, c.160G > C (p.Glu54Gln) in CILP2, and c.1199C > A (p.Ala400Glu) in PEPD. CONCLUSIONS Three novel heterozygous missense mutations, including c.12614C > T (p.Pro4205Leu) in APOB, c.160G > C (p.Glu54Gln) in CILP2, and c.1199C > A (p.Ala400Glu) in PEPD were first identified in a patient with the triad of DKA, hypertriglyceridemia, and AP. The combination of plasmapheresis, hydration, and insulin therapy may have the greatest clinical benefits for these patients.
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Affiliation(s)
- Zixi Huang
- Department of General Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, China
- Department of Endocrinology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zhenyan Xu
- Department of Cardiovascular Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Ruoqing Xu
- Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lin Huang
- Department of Cardiovascular Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xiang Xu
- Department of Ultrasound Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xiaoyang Lai
- Department of Endocrinology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
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