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Lin Z, Ji X, Tian N, Gan Y, Ke L. APOB is a potential prognostic biomarker in hepatocellular carcinoma. Discov Oncol 2024; 15:28. [PMID: 38310202 PMCID: PMC10838261 DOI: 10.1007/s12672-024-00877-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 01/30/2024] [Indexed: 02/05/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is significantly associated with adverse prognostic outcomes. The development and progression of different types of human tumors are significantly influenced by APOB. Nevertheless, the significance and pathomechanisms of APOB in HCC have not been conclusively determined. We assessed APOB expression levels in HCC using three publicly available databases of TIMER2.0, UALCAN and Human Protein Atlas. To identify the biological function of APOB, we conducted enrichment analysis via LinkedOmics. Moreover, UALCAN was employed to assess the relationship between APOB expression and clinicopathological features among HCC patients. Additionally, the Kaplan-Meier plotter was utilized to investigate the prognostic relevance of APOB in HCC. To explore potential regulatory ncRNAs that could bind to APOB, we utilized StarBase and GEPIA. Furthermore, the correlation between APOB expression and immune cell infiltration, as well as immune checkpoint genes, was investigated using Spearman's correlation analysis in TISIDB, GEPIA, and TIMER2.0. The findings of our investigation showed a notable decrease in the expression levels of APOB among individuals diagnosed with HCC. Moreover, a noteworthy correlation was observed between the expression of APOB and immune checkpoint genes, alongside the occurrence of immune cell infiltration. The levels of APOB expression in HCC tissues also showed correlations with various clinicopathological features. According to Cox regression analysis, decreased APOB expression emerged as a potential autonomous predictor for OS, RFS, DSS, and PFS among HCC patients. Furthermore, we identified six potential pathways associated with non-coding RNA (ncRNA) as the most promising pathway for APOB in HCC. Our results illuminate the possible involvement of APOB in HCC and offer understanding into its governing mechanisms and medical importance.
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Affiliation(s)
- Zhifeng Lin
- Department of Medical Record; Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology; Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
| | - Xiaohui Ji
- Department of Obstetrics and Gynaecology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Nana Tian
- Department of Medical Record, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yu Gan
- Department of Medical Record, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Li Ke
- Department of Medical Record; Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology; Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
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Alves ES, Henriques AD, Tonet-Furioso AC, Paula RS, Gomes LO, Moraes CF, Nóbrega OT. The APOB rs693 polymorphism impacts the lipid profile of Brazilian older adults. ACTA ACUST UNITED AC 2020; 53:e9102. [PMID: 32130292 PMCID: PMC7057931 DOI: 10.1590/1414-431x20199102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 12/20/2019] [Indexed: 01/17/2023]
Abstract
The apolipoprotein B (APOB) gene contains several polymorphic sites described as risk modifiers for cardiovascular events. The objective of this study was to verify the association of the classic APOB Xba I polymorphism (rs693) with atherosclerotic risk factors in a segment of the Brazilian elderly population considering their usual dietary intake. Clinical and biochemical characteristics as well as total caloric and fat intake data were determined from 644 elderly individuals. Polymorphism analysis was performed by conventional polymerase chain reaction followed by enzyme restriction. Statistical analyses compared measures and proportions according to different APOB genotypic combinations. Statistically significant association was found between Xba I polymorphism and serum LDL, total cholesterol, and total lipid levels, with important elevations among T homozygotes compared to the other genotypes. There was homogeneity in all other parameters analyzed (including intake pattern), with a tendency for reduced levels of circulating apolipoprotein B among TT individuals. Our results pointed out that genetic variation in APOB affected the lipemic profile of elderly individuals in a context not biased by diet, generating a pattern suggestive of secretory disorder of lipoprotein particles, with possible implication in atherosclerotic risk.
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Affiliation(s)
- E S Alves
- Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Ciências da Saúde, Universidade de Brasília, Brasília, DF, Brasil
| | - A D Henriques
- Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Ciências da Saúde, Universidade de Brasília, Brasília, DF, Brasil
| | - A C Tonet-Furioso
- Programa de Pós-Graduação em Ciências Médicas, Faculdade de Medicina, Universidade de Brasília, Brasília, DF, Brasil.,Programa de Pós-Graduação em Gerontologia, Escola de Saúde e Medicina, Universidade Católica de Brasília, Brasília, DF, Brasil
| | - R S Paula
- Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Ciências da Saúde, Universidade de Brasília, Brasília, DF, Brasil
| | - L O Gomes
- Programa de Pós-Graduação em Gerontologia, Escola de Saúde e Medicina, Universidade Católica de Brasília, Brasília, DF, Brasil
| | - C F Moraes
- Programa de Pós-Graduação em Ciências Médicas, Faculdade de Medicina, Universidade de Brasília, Brasília, DF, Brasil.,Programa de Pós-Graduação em Gerontologia, Escola de Saúde e Medicina, Universidade Católica de Brasília, Brasília, DF, Brasil
| | - O T Nóbrega
- Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Ciências da Saúde, Universidade de Brasília, Brasília, DF, Brasil.,Programa de Pós-Graduação em Ciências Médicas, Faculdade de Medicina, Universidade de Brasília, Brasília, DF, Brasil.,Research Centre, Institut Universitaire de Gériatrie de Montréal, Montreal, Quebec, Canada
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Wippel HH, Santos MDM, Clasen MA, Kurt LU, Nogueira FCS, Carvalho CE, McCormick TM, Neto GPB, Alves LR, da Gloria da Costa Carvalho M, Carvalho PC, Fischer JDSDG. Comparing intestinal versus diffuse gastric cancer using a PEFF-oriented proteomic pipeline. J Proteomics 2017; 171:63-72. [PMID: 29032071 DOI: 10.1016/j.jprot.2017.10.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 09/29/2017] [Accepted: 10/06/2017] [Indexed: 12/19/2022]
Abstract
Gastric cancer is the fifth most common malignant neoplasia and the third leading cause of cancer death worldwide. Mac-Cormick et al. recently showed the importance of considering the anatomical region of the tumor in proteomic gastric cancer studies; more differences were found between distinct anatomical regions than when comparing healthy versus diseased tissue. Thus, failing to consider the anatomical region could lead to differential proteins that are not disease specific. With this as motivation, we compared the proteomic profiles of intestinal and diffuse adenocarcinoma from the same anatomical region, the corpus. To achieve this, we used isobaric labeling (iTRAQ) of peptides, a 10-step HILIC fractionation, and reversed-phase nano-chromatography coupled online with a Q-Exactive Plus mass spectrometer. We updated PatternLab to take advantage of the new Comet-PEFF search engine that enables identifying post-translational modifications and mutations included in neXtProt's PSI Extended FASTA Format (PEFF) metadata. Our pipeline then uses a text-mining tool that automatically extracts PubMed IDs from the proteomic result metadata and drills down keywords from manuscripts related with the biological processes at hand. Our results disclose important proteins such as apolipoprotein B-100, S100 and 14-3-3 proteins, among many others, highlighting the different pathways enriched by each cancer type. SIGNIFICANCE Gastric cancer is a heterogeneous and multifactorial disease responsible for a significant number of deaths every year. Despite the constant improvement of surgical techniques and multimodal treatments, survival rates are low, mostly due to limited diagnostic techniques and late symptoms. Intestinal and diffuse types of gastric cancer have distinct clinical and pathological characteristics; yet little is known about the molecular mechanisms regulating these two types of gastric tumors. Here we compared the proteomic profile of diffuse and intestinal types of gastric cancer from the same anatomical location, the corpus, from four male patients. This methodological design aimed to eliminate proteomic variations resulting from comparison of tumors from distinct anatomical regions. Our PEFF-tailored proteomic pipeline significantly increased the identifications as when compared to previous versions of PatternLab.
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Affiliation(s)
- Helisa Helena Wippel
- Computational Mass Spectrometry & Proteomics Group, Carlos Chagas Institute, Fiocruz - Paraná, Brazil
| | | | - Milan Avila Clasen
- Computational Mass Spectrometry & Proteomics Group, Carlos Chagas Institute, Fiocruz - Paraná, Brazil
| | - Louise Ulrich Kurt
- Computational Mass Spectrometry & Proteomics Group, Carlos Chagas Institute, Fiocruz - Paraná, Brazil
| | - Fabio Cesar Sousa Nogueira
- Laboratory of Proteomics, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; Laboratory of Protein Chemistry, Proteomic Unit, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Carlos Eduardo Carvalho
- Pathology Service of the Clementino Fraga Filho University Hospital (HUCFF-UFRJ), Rio de Janeiro, Brazil
| | | | - Guilherme Pinto Bravo Neto
- Division of Esophageal and Gastric Surgery, General Surgery Service of the HUCFF-UFRJ, Rio de Janeiro, Brazil
| | | | | | - Paulo Costa Carvalho
- Computational Mass Spectrometry & Proteomics Group, Carlos Chagas Institute, Fiocruz - Paraná, Brazil.
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Gu W, Zhang M, Wen S. Association between the APOB XbaI and EcoRI polymorphisms and lipids in Chinese: a meta-analysis. Lipids Health Dis 2015; 14:123. [PMID: 26446158 PMCID: PMC4596460 DOI: 10.1186/s12944-015-0125-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 09/29/2015] [Indexed: 11/17/2022] Open
Abstract
Background No previous meta-analysis was to report the association between the apolipoprotein B (APOB) XbaI and EcoRI polymorphisms and serum lipids in Chinese. We performed the study to investigate their potentially association. Methods and Results Studies in English and Chinese were found via a systematic search of Pubmed, Embase, CNKI and Wanfang databases. The dominant genetic model and random-effects model were used to pool data from individual studies. As a result, a total of 30 articles with 5611 subjects for XbaI and 2653 subjects for EcoRI were included in the current study. For the XbaI polymorphism, overall, subjects carrying X+ allele were significantly associated with higher TC,TG and LDL compared with X-X- genotype (Pvalue =0.0006, OR (95 %) = -0.55 (-0.86,-0.23); Pvalue = 0.0004, OR (95 %) = -0.30 (-0.47,-0.14); (Pvalue = 0.05, OR (95 %) = -0.23(-0.46,-0.00), respectively). Similar results were observed in the subgroups of Han, healthy individuals (HT), coronary heart disease (CHD), cerebral infarction (CI), and cholelithiasis. For HDL, positive association between X+ allele with Lower lipid value was found in CHD and CI subgroups. For EcoRI polymorphism, overall, the E- allele carriers were found to be obviously linked with elevated LDL and lower HDL compared with E + E+ genotype (Pvalue = 0.02,OR (95 %) = -0.27 (-0.49,-0.05); Pvalue = 0.01, OR (95 %) = 0.17 (0.03, 0.30), respectively). TC was significantly high in subjects carrying E- allele in the subgroup of hyperlipidemia. No evidence of publication bias was observed. Conclusions The two genetic variants of APOB may be associated with serum lipids in Chinese.
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Affiliation(s)
- Wei Gu
- Department of Hypertension Research, Beijing Anzhen Hospital, Capital Medical University and Beijing Institute of Heart Lung and Blood Vessel Diseases, 2 Anzhen Road, Beijing, 100029, People's Republic of China
| | - Mingduo Zhang
- Department of cardiology, Beijing Anzhen Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Shaojun Wen
- Department of Hypertension Research, Beijing Anzhen Hospital, Capital Medical University and Beijing Institute of Heart Lung and Blood Vessel Diseases, 2 Anzhen Road, Beijing, 100029, People's Republic of China.
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Bogari NM, Abdel-Latif AM, Hassan MA, Ramadan A, Fawzy A. No association of apolipoprotein B gene polymorphism and blood lipids in obese Egyptian subjects. J Negat Results Biomed 2015; 14:7. [PMID: 25889118 PMCID: PMC4389411 DOI: 10.1186/s12952-015-0026-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 02/27/2015] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Several environmental and genetic factors are associated with high levels of lipids in obese patients. Apolipoprotein B (ApoB) is the major protein component of low-density lipoproteins (LDL), very-low density lipoproteins (VLDL) and chylomicrons and plays a central role in lipid metabolism. Several apoB restriction fragment length polymorphisms (XbaI, EcoRI, MspI) have been reported to be associated with variation in lipid levels and obesity. To date, no data are available on the relationship between XbaI polymorphism and lipid levels in Egyptian populations. Following clinical profiling, 178 obese (body mass index [BMI] >25 kg/m(2)) and 178 age-matched non-obese (BMI ≤ 25 kg/m(2)) subjects were included in this case-control study. All samples were analysed for total cholesterol, triglycerides and HDL-cholesterol. Genetic analysis of apoB XbaI (X) was performed using Polymerase Chain Reaction-Restriction Fragment Length polymorphism (PCR-RFLP). The aim of this study was to assess the association of apoB XbaI gene polymorphism (X) and lipid profiles in obese and non-obese Egyptian populations. RESULTS Obese subjects demonstrated significantly higher values of waist-to-hip ratio, blood pressure, and total lipid. However, in our sample we did not find significant differences in apoB XbaI gene polymorphism (X) genotype or allele frequencies. Moreover, none of the studied lipid parameters showed any association with the gene polymorphism. CONCLUSION This study reveals no significant association of apoB XbaI gene polymorphism (X) with obesity or lipid profiles in an Egyptian population.
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Affiliation(s)
- Neda M Bogari
- Faculty of Medicine, Department of Medical Genetics, Umm Al-Qura University, Makkah, Kingdom of Saudi Arabia.
| | - Azza M Abdel-Latif
- Division of Human Genetics & Genome Researches, Department of Molecular Genetics and Enzymology, National Research Centre, 33 Bohouth St. Dokki, Giza, Egypt.
| | - Maha A Hassan
- Holding Company for Biological products and Vaccines (VACSERA-Egypt), Cairo, Egypt.
| | - Abeer Ramadan
- Division of Human Genetics & Genome Researches, Department of Molecular Genetics and Enzymology, National Research Centre, 33 Bohouth St. Dokki, Giza, Egypt.
| | - Ahmed Fawzy
- Division of Human Genetics & Genome Researches, Department of Molecular Genetics and Enzymology, National Research Centre, 33 Bohouth St. Dokki, Giza, Egypt.
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Srivastava N, Prakash J, Srivastava A, Agarwal CG, Pant DC, Mittal B. Association of apolipoprotein B XbaI gene polymorphism and lipid profile in northern Indian obese. INDIAN JOURNAL OF HUMAN GENETICS 2013; 19:26-31. [PMID: 23901190 PMCID: PMC3722626 DOI: 10.4103/0971-6866.112880] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
BACKGROUND: Over the last few decades, obesity, diabetes, and hypertension have become main health evils. The health problems of obesity are well-recognized. However, the fact that all obese individuals are not at the same risk of developing a disease is also recognized. The apolipoprotein B (APOB) plays a central role in lipid metabolism. So we compare the association of APOB XbaI gene polymorphism and lipid profile total in obese north Indian population. MATERIALS AND METHODS: A total of 132 obese (body mass index [BMI] >25 kg/m2) and 132 age matched non-obese (BMI ≤ 25 kg/m2) subjects were studied after taking detailed clinical profile. Lipid profile in serum/plasma was done using commercial kits. Genetic analysis of APOB XbaI was done using Polymerase Chain Reaction-Restriction Fragment Leanth polymorphism (PCR-RFLP). STATISTICAL ANALYSIS: Statistical analysis was performed by Statistical Package for the Social Sciences (SPSS) (version 11.5) software (IBM Corporation). All continuous variables were expressed as mean ± SD and tested by analysis of variance test. Comparisons of categorical variables were assessed using χ2 tests or Fisher's exact test. P < 0.05 was considered as significant. RESULTS: Analysis showed that obese subjects had significantly higher value of the waist-to-hip ratio, blood pressure (systolic and diastolic), and lipid profile. In APOB XbaI gene polymorphism, we did not find significant differences in genotype or allele frequencies. Moreover, none of the studied metabolic parameters (lipid profile) showed any association with the gene polymorphism. CONCLUSIONS: Study reveals no considerable association of APOB XbaI gene polymorphism with obesity and lipid profile in north Indians.
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Affiliation(s)
- Neena Srivastava
- Department of Physiology, KGMU UP, Lucknow, India (Formerly Chatrapati Shahuji Maharaj Medical University, Lucknow, Uttar Pradesh, India)
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Liu X, Wang Y, Qu H, Hou M, Cao W, Ma Z, Wang H. Associations of polymorphisms of rs693 and rs1042031 in apolipoprotein B gene with risk of breast cancer in Chinese. Jpn J Clin Oncol 2013; 43:362-8. [PMID: 23444115 DOI: 10.1093/jjco/hyt018] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Lipid synthesis is an integrated result of genetic, epigenetic and environmental factors, and also can promote growth and survival of cancer cells. Apolipoprotein B plays a central role in lipid metabolism as the major protein component of very-low-density lipoprotein and low-density lipoprotein. METHODS We investigated the associations of polymorphisms of rs693 (-7673C>T) and rs1042031 (-12669 G>A) in the APOB gene with risk of breast cancer in 675 blood-unrelated Chinese patients with breast cancer and 712 healthy controls. RESULTS Polymorphisms of -12669 G>A and -7673C>T in the APOB gene were significantly associated with an increased risk of breast cancer (P = 0.000), especially for postmenopausal women (P = 0.000, 0.023). The positive associations still remained after further analysis of the two polymorphisms' distribution according to body mass index. However, no statistical associations were found between -12669 G>A and -7673C>T polymorphisms and other clinical characteristics, including tumor size, lymph node metastasis, histological grade, estrogen and progesterone receptor status and Her-2 status. CONCLUSIONS rs693 and rs1042031 polymorphisms in the APOB gene increased the risk of breast cancer in Chinese, and this role of the two polymorphisms in connection with breast cancer was not dependent on body mass index.
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Affiliation(s)
- Xiaoyi Liu
- Department of Galactophore, Qingdao University, Qingdao, China
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