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Li M, Zhao Z, Mak TK, Wang X, Chen J, Ren H, Yu Z, Zhang C. Neutrophil extracellular traps-related signature predicts the prognosis and immune infiltration in gastric cancer. Front Med (Lausanne) 2023; 10:1174764. [PMID: 37636564 PMCID: PMC10447905 DOI: 10.3389/fmed.2023.1174764] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 07/27/2023] [Indexed: 08/29/2023] Open
Abstract
Introduction Gastric cancer (GC) is the fifth most prevalent cancer globally, with the third highest case fatality rate. Neutrophil extracellular traps (NETs) are a reticulated structure of DNA, histones, and antimicrobial peptides produced by active neutrophils that trap pathogens. Even though NETs are associated with poorer recurrence-free survival (RFS) and overall survival (OS), the specifics of this interaction between NETs and cancer cells are yet unknown. Methods The keywords "neutrophil extracellular traps and gastric cancer" were used in the GEO database for retrieval, and the GSE188741 dataset was selected to obtain the NETs-related gene. 27 NETs-related genes were screened by univariate Cox regression analysis (p < 0.05). 27 NETs-related genes were employed to identify and categorize NETs-subgroups of GC patients under the Consensus clustering analysis. 808 GC patients in TCGA-STAD combined with GES84437 were randomly divided into a training group (n = 403) and a test group (n = 403) at a ratio of 1:1 to validate the NETs-related signature. Results Based on Multivariate Cox regression and LASSO regression analysis to develop a NETs-related prognosis model. We developed a very specific nomogram to improve the NETs-clinical score's usefulness. Similarly, we also performed a great result in pan-cancer study with NETs-score. Low NETs scores were linked to higher MSI-H (microsatellite instability-high), mutation load, and immune activity. The cancer stem cell (CSC) index and chemotherapeutic treatment sensitivity were also connected to the NET score. Our comprehensive analysis of NETs in GC suggests that NETs have a role in the tumor microenvironment, clinicopathological features, and prognosis. Discussion The NETs-score risk model provides a basis for better prognosis and therapy outcomes in GC patients.
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Affiliation(s)
- Mingzhe Li
- Digestive Diseases Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Zidan Zhao
- Digestive Diseases Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Tsz Kin Mak
- Digestive Diseases Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Xiaoqun Wang
- Digestive Diseases Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Jingyao Chen
- Digestive Diseases Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Hui Ren
- Digestive Diseases Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Zhiwei Yu
- Digestive Diseases Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Changhua Zhang
- Digestive Diseases Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong, China
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Zhang TP, Li R, Wang LJ, Tang F, Li HM. Clinical relevance of vitamin B12 level and vitamin B12 metabolic gene variation in pulmonary tuberculosis. Front Immunol 2022; 13:947897. [PMID: 36275653 PMCID: PMC9583150 DOI: 10.3389/fimmu.2022.947897] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 09/09/2022] [Indexed: 11/14/2022] Open
Abstract
The aim of this study was to assess the association of vitamin B12 level and single nucleotide polymorphisms (SNPs) in vitamin B12 metabolic genes with pulmonary tuberculosis (PTB) in Chinese Han population. The plasma vitamin B12 expression level was detected using ELISA. Ten SNPs in six key genes (TCN1, TCN2, CUBN, MMACHC, FUT6, and MUT) of vitamin B12 metabolic pathway were included for genotyping by the SNPscan technique among 454 PTB patients and 467 controls. Our results found that vitamin B12 level was significantly reduced in PTB patients when compared with controls. There was no significant association between TCN1 rs526934, TCN2 rs1801198, CUBN rs7906242, rs10904861, rs1801222, MMACHC rs10789465, FUT6 rs3760776, rs3760775, MUT rs9473555, rs9381784 variants, and PTB susceptibility. TCN2 rs1801198 CC genotype, C allele was significantly associated with hypoproteinemia in PTB patients. In CUBN, rs7906242 GG genotype, G allele, rs10904861 TT genotype, and T allele were significantly related to the decreased frequency of sputum smear-positive, and rs10904861 variant affected the occurrence of drug resistance in PTB patients. In addition, the increased frequency of CUBN rs1801222 AA genotype was significantly associated with leukopenia. The decreased frequency of MUT rs9473555 CC genotype was found in the PTB patients with hypoproteinemia. However, vitamin B12 expression was not associated with the genotype distribution of above SNPs. In conclusion, vitamin B12 level was significantly decreased in PTB patients and genetic variants in vitamin B12 metabolic genes were not contributed to PTB susceptibility. Several SNPs in TCN2, CUBN, and MUT gene might associate with multiple clinical manifestations in PTB.
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Affiliation(s)
- Tian-Ping Zhang
- Department of Rheumatology and Immunology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Rui Li
- Department of Nosocomial Infection Management, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Li-Jun Wang
- Department of Infectious Diseases, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Fei Tang
- Department of Interventional Pulmonology and Endoscopic Diagnosis and Treatment Center, Anhui Chest Hospital, Hefei, China
- *Correspondence: Hong-Miao Li, ; Fei Tang,
| | - Hong-Miao Li
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China
- *Correspondence: Hong-Miao Li, ; Fei Tang,
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Lacombe V, Lenaers G, Urbanski G. Diagnostic and Therapeutic Perspectives Associated to Cobalamin-Dependent Metabolism and Transcobalamins' Synthesis in Solid Cancers. Nutrients 2022; 14:2058. [PMID: 35631199 PMCID: PMC9145230 DOI: 10.3390/nu14102058] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 05/11/2022] [Indexed: 02/01/2023] Open
Abstract
Cobalamin or vitamin B12 (B12) is a cofactor for methionine synthase and methylmalonyl-CoA mutase, two enzymes implicated in key pathways for cell proliferation: methylation, purine synthesis, succinylation and ATP production. Ensuring these functions in cancer cells therefore requires important cobalamin needs and its uptake through the transcobalamin II receptor (TCII-R). Thus, both the TCII-R and the cobalamin-dependent metabolic pathways constitute promising therapeutic targets to inhibit cancer development. However, the link between cobalamin and solid cancers is not limited to cellular metabolism, as it also involves the circulating transcobalamins I and II (TCI or haptocorrin and TCII) carrier proteins, encoded by TCN1 and TCN2, respectively. In this respect, elevations of B12, TCI and TCII concentrations in plasma are associated with cancer onset and relapse, and with the presence of metastases and worse prognosis. In addition, TCN1 and TCN2 overexpressions are associated with chemoresistance and a proliferative phenotype, respectively. Here we review the involvement of cobalamin and transcobalamins in cancer diagnosis and prognosis, and as potential therapeutic targets. We further detail the relationship between cobalamin-dependent metabolic pathways in cancer cells and the transcobalamins' abundancies in plasma and tumors, to ultimately hypothesize screening and therapeutic strategies linking these aspects.
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Affiliation(s)
- Valentin Lacombe
- MitoLab Team, MitoVasc Institut, CNRS UMR6015, INSERM U1083, Angers University, 49000 Angers, France; (G.L.); (G.U.)
- Department of Internal Medicine and Clinical Immunology, Angers University Hospital, 49000 Angers, France
| | - Guy Lenaers
- MitoLab Team, MitoVasc Institut, CNRS UMR6015, INSERM U1083, Angers University, 49000 Angers, France; (G.L.); (G.U.)
- Department of Neurology, Angers University Hospital, 49000 Angers, France
| | - Geoffrey Urbanski
- MitoLab Team, MitoVasc Institut, CNRS UMR6015, INSERM U1083, Angers University, 49000 Angers, France; (G.L.); (G.U.)
- Department of Internal Medicine and Clinical Immunology, Angers University Hospital, 49000 Angers, France
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Kozyraki R, Verroust P, Cases O. Cubilin, the intrinsic factor-vitamin B12 receptor. VITAMINS AND HORMONES 2022; 119:65-119. [PMID: 35337634 DOI: 10.1016/bs.vh.2022.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Cubilin (CUBN), the intrinsic factor-vitamin B12 receptor is a large endocytic protein involved in various physiological functions: vitamin B12 uptake in the gut; reabsorption of albumin and maturation of vitamin D in the kidney; nutrient delivery during embryonic development. Cubilin is an atypical receptor, peripherally associated to the plasma membrane. The transmembrane proteins amnionless (AMN) and Lrp2/Megalin are the currently known molecular partners contributing to plasma membrane transport and internalization of Cubilin. The role of Cubilin/Amn complex in the handling of vitamin B12 in health and disease has extensively been studied and so is the role of the Cubilin-Lrp2 tandem in renal pathophysiology. Accumulating evidence strongly supports a role of Cubilin in some developmental defects including impaired closure of the neural tube. Are these defects primarily caused by the dysfunction of a specific Cubilin ligand or are they secondary to impaired vitamin B12 or protein uptake? We will present the established Cubilin functions, discuss the developmental data and provide an overview of the emerging implications of Cubilin in the field of cardiovascular disease and cancer pathogenesis.
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Affiliation(s)
- Renata Kozyraki
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université de Paris, Paris, France.
| | - Pierre Verroust
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université de Paris, Paris, France
| | - Olivier Cases
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université de Paris, Paris, France
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Gu J, Yue H, Wang C, Zhang H, Hu W, Zhang Z. Vitamin D pathway gene variation rs3740165 is associated with serological uric acid levels in healthy Chinese women. Front Endocrinol (Lausanne) 2022; 13:1059964. [PMID: 36583005 PMCID: PMC9792855 DOI: 10.3389/fendo.2022.1059964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 11/25/2022] [Indexed: 12/15/2022] Open
Abstract
AIM To investigate the relationship between gene polymorphisms involved in the vitamin D metabolic pathway and serum uric acid (UA) levels in Chinese women. METHODS Fifteen key genes within the vitamin D metabolic pathway were screened using 96 single nucleotide polymorphisms in a group of 1,206 (37.96 ± 13.08 years) unrelated healthy Chinese women (aged 20-85 years). Blood and urine tests were performed at the same time. The Wilcoxon Mann-Whitney test was used to compare groups aged ≤50 years and >50 years. The mean serum UA values were computed within each group of homozygous referent, heterozygous, and homozygous variant genotypes for each single nucleotide polymorphism. RESULTS The exclusion process left 1,169 participants (38.16 ± 13.13 years) for analysis. One single nucleotide polymorphism in the CUBN gene (rs3740165) was identified as being significantly associated with serum UA levels in the group aged over 50 years. The wild type (C/C) population had higher serum UA levels in this group (P<0.001). In women aged over 50 years, allele C was associated with a higher risk of hyperuricemia than allele T (odds ratio 2.752, 95% confidence interval 1.458-5.192; P = 0.002). There was also a higher risk of hyperuricemia in genotype TC + CC compared with genotype TT (odds ratio 3.326, 95% confidence interval 1.513-7.313; P = 0.003) in women over 50 years of age. CONCLUSION The results suggest that the CUBN gene contributes to variability in serum UA levels in healthy Chinese Han women over 50 years of age.
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Affiliation(s)
- Jiemei Gu
- Shanghai Clinical Research Center of Bone Disease, Department of Osteoporosis and Bone Diseases, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hua Yue
- Shanghai Clinical Research Center of Bone Disease, Department of Osteoporosis and Bone Diseases, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chun Wang
- Shanghai Clinical Research Center of Bone Disease, Department of Osteoporosis and Bone Diseases, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hao Zhang
- Shanghai Clinical Research Center of Bone Disease, Department of Osteoporosis and Bone Diseases, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Weiwei Hu
- Shanghai Clinical Research Center of Bone Disease, Department of Osteoporosis and Bone Diseases, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhenlin Zhang
- Shanghai Clinical Research Center of Bone Disease, Department of Osteoporosis and Bone Diseases, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
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He X, Gu Y, Cao Y, Hu B, Fang H, Fei Y, Lv K, Liu X, Wang J, Lin C, Liu H, Zhang H, Li H, Li R, He H, Xu J. Impact of intratumoural CD73 expression on prognosis and therapeutic response in patients with gastric cancer. Eur J Cancer 2021; 157:114-123. [PMID: 34508993 DOI: 10.1016/j.ejca.2021.08.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 07/30/2021] [Accepted: 08/04/2021] [Indexed: 12/31/2022]
Abstract
AIM CD73 overexpression has been reported in several malignancies and is considered to be a novel immune checkpoint. However, the role and significance of CD73 in gastric cancer (GC) still remain obscure. We aim to investigate the role of CD73 expression in predicting prognosis, shaping immune contexture and guiding therapeutic strategy in GC. METHODS The study enrolled four independent cohorts with a total of 902 patients with GC. CD73 expression and immune contexture were examined by immunohistochemistry, single-sample gene set enrichment analysis and flow cytometry. Clinical outcomes of patient subgroups were evaluated using the Kaplan-Meier curves and Cox proportional hazard analysis. All statistical tests were two-sided. RESULTS CD73 was identified as an independent adverse prognostic factor for survival in GC. CD73high tumours showed a specific microenvironment with more CD8+ T cell infiltration, but these CD8+ T cells displayed a dysfunctional phenotype. Furthermore, the CD73 (NT5E) mRNA level was associated with the Cancer Genome Atlas molecular subtypes, and NT5E high tumours showed significant fibroblast growth factor receptor 2 activation and vascular endothelial growth factor and receptor enrichment. In addition, CD73high tumours indicated better chemotherapeutic responsiveness to fluorouracil yet a worse objective response rate to pembrolizumab in GC. CONCLUSIONS High CD73 expression indicated an immunoevasive contexture with CD8+ T cell dysfunction and represented an independent predictor for adverse clinical outcomes. As a potential immunotherapeutic target, CD73 could potentially be a novel biomarker for adjuvant chemotherapy, targeted therapies and immunotherapy. The crucial role of CD73 in the therapeutic landscape of GC needs further validation retrospectively and prospectively.
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Affiliation(s)
- Xudong He
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Yun Gu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Yifan Cao
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Baoying Hu
- Department of Immunology, School of Medicine, Nantong University, Nantong, China
| | - Hanji Fang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Yuchao Fei
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Kunpeng Lv
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Xin Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Jieti Wang
- Department of Gastric Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Chao Lin
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Hao Liu
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Heng Zhang
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - He Li
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Ruochen Li
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China.
| | - Hongyong He
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China.
| | - Jiejie Xu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China.
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Lacombe V, Chabrun F, Lacout C, Ghali A, Capitain O, Patsouris A, Lavigne C, Urbanski G. Persistent elevation of plasma vitamin B12 is strongly associated with solid cancer. Sci Rep 2021; 11:13361. [PMID: 34172805 PMCID: PMC8233305 DOI: 10.1038/s41598-021-92945-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 06/15/2021] [Indexed: 12/17/2022] Open
Abstract
Elevated plasma vitamin B12 has been associated with solid cancers, based on a single B12 measurement. We evaluated the incidence of solid cancers following B12 measurement in patients with persistent elevated B12, compared to patients without elevated B12 and to patients with non-persistent elevated B12. The study population included patients with at least two plasma B12 measurements without already known elevated-B12-related causes. Patients with elevated plasma B12 (≥ 1000 ng/L) at first measurement (n = 344) were matched for age and sex with patients having 2 normal B12 measurements (< 1000 ng/L) (NN group, n = 344). The patients with elevated plasma B12 at first measurement were split into 2 groups, according to the presence (EE group, n = 144) or the absence (EN group, n = 200) of persistent elevated plasma B12 at second measurement. We compared the cancer-free survival during 60 months between the groups after adjustment for the other elevated-B12-related causes in a survival competing risk model. Compared to the NN group, a persistent elevated plasma B12 ≥ 1000 ng/mL was strongly associated with the occurrence of solid cancer (HR 5.90 [95% CI 2.79-12.45], p < 0.001), contrary to non-persistent plasma B12 elevation (p = 0.29). These results could help to select patients in whom the screening for solid cancers would be of interest.
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Affiliation(s)
- Valentin Lacombe
- Department of Internal Medicine and Clinical Immunology, Angers University Hospital, Angers, France
| | - Floris Chabrun
- Department of Biochemistry and Genetics, Angers University Hospital, Angers, France
| | - Carole Lacout
- Department of Internal Medicine and Clinical Immunology, Angers University Hospital, Angers, France
| | - Alaa Ghali
- Department of Internal Medicine and Clinical Immunology, Angers University Hospital, Angers, France
| | | | | | - Christian Lavigne
- Department of Internal Medicine and Clinical Immunology, Angers University Hospital, Angers, France
| | - Geoffrey Urbanski
- Department of Internal Medicine and Clinical Immunology, Angers University Hospital, Angers, France.
- Department of Internal Medicine and Clinical Immunology, Angers University Hospital, 4 rue Larrey, 49000, Angers, France.
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Wu Y, Xu Y. Bioinformatics for The Prognostic Value and Function of Cubilin (CUBN) in Colorectal Cancer. Med Sci Monit 2020; 26:e922447. [PMID: 33235183 PMCID: PMC7702664 DOI: 10.12659/msm.922447] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Background Cubilin (CUBN) gene was reported to be a novel risk variant for colorectal cancer (CRC). Previous studies have shown that germline variants in known cancer driver genes are predictive of patient outcome, but no study has systematically analyzed CRC to identify CUBN that can predict patient outcome and function by using bioinformatics. Material/Methods The association in expression, clinicopathological parameters, and survival were analyzed by using Oncomine, UNCLA, and GEPIA, while CUBN alterations and related functional networks were identified using cBioPortal. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathways (KEGG) of CUBN in CRC were explored by using LinkOmics. Gene set enrichment analysis (GSEA) examined target networks of kinases, miRNAs, and transcription factors. Results We found that CUBN was overexpressed in CRC. Patients who were in advanced TNM stage tended to express higher CUBN mRNA levels, while those who received radiotherapy tended to express relatively lower CUBN mRNA levels. Higher expression of CUBN was found to be associated with shorter overall survival (OS) and disease-free survival (DFS). Moreover, functional networks analysis suggested that CUBN can regulate mismatch repair, terpenoid backbone biosynthesis, base excision repair, and proteasome via vitamin digestion and absorption pathway to influence CRC occurrence. Conclusions These findings suggested that CUBN could serve as a prognostic and therapeutic biomarker of CRC in the future.
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Affiliation(s)
- Yibin Wu
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China (mainland)
| | - Ye Xu
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China (mainland)
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High expression of TCN1 is a negative prognostic biomarker and can predict neoadjuvant chemosensitivity of colon cancer. Sci Rep 2020; 10:11951. [PMID: 32686693 PMCID: PMC7371683 DOI: 10.1038/s41598-020-68150-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 06/17/2020] [Indexed: 01/09/2023] Open
Abstract
Transcobalamin (TCN1) is a vitamin B12 (cobalamin)-binding protein that regulates cobalamin homeostasis. Recent studies and bioinformatic analyses have found that TCN1 is highly expressed in cancer tissues and is associated with tumour aggressiveness and poor prognosis. The present study aimed to detect TCN1 as a novel biomarker for prognosis and chemosensitivity of colon cancer. Next-generation sequencing showed that TCN1 was one of several upregulated mRNAs in colon cancer, which was verified by further bioinformatics analyses. Western blotting (n = 9) and quantitative real time polymerase chain reaction (qRT-PCR, n = 30) revealed that TCN1 was highly expressed in colon cancer tissues at both the protein and mRNA level. A total of 194 cases of colon cancer were examined by immunohistochemistry and revealed that TCN1 expression level was related to advanced stages (P < 0.005). Kaplan-Meier analysis verified that patients with lower TCN1 expression usually had longer overall survival (P = 0.008). In addition, TCN1 was highly expressed in pulmonary metastatic tumour tissues (n = 37, P = 0.025) and exhibited higher levels in right-sided colon cancer than in left-sided colon cancer (P = 0.029). TCN1 expression in specimens that had received neoadjuvant chemotherapy decreased compared with that in colonoscopy biopsy tissues (n = 42, P = 0.009). Further bioinformatics analyses verified that apoptosis pathways might have a role in high TCN1 expression. All the studies revealed that TCN1 expression in colon cancer was significantly associated with malignant biological behaviour. Therefore, TCN1 could be used as a novel biomarker for colon cancer aggressiveness and prognosis and might also be a potential biomarker for predicting neoadjuvant chemosensitivity.
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Liang B, Ding H, Huang L, Luo H, Zhu X. GWAS in cancer: progress and challenges. Mol Genet Genomics 2020; 295:537-561. [PMID: 32048005 DOI: 10.1007/s00438-020-01647-z] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 01/11/2020] [Indexed: 12/31/2022]
Abstract
The genome-wide association study (GWAS) is an effective method to detect single-nucleotide polymorphisms (SNPs) of multiple individual genes based on linkage disequilibrium (LD). GWAS examines genotypes and distinguishing gene characteristics that are exhibited in diseases. In the past few decades, more and more literature has reported the results of applying GWAS to study tumors. Although many pleiotropic loci associated with complex phenotypes have been identified by GWAS, the biological functions of many genetic variation loci remain unclear, and the genetic mechanisms of most complex phenotypes cannot be systematically explained. In this article, we will review the new findings of several tumor types, and categorize the new sites and mechanisms that have recently been discovered. We linked the mechanisms of action of various tumors and searched for links to related gene expression pathways. We found that susceptible sites can be divided into hub genes and peripheral genes; the two interact to link gene expression in a variety of diseases.
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Affiliation(s)
- Baiqiang Liang
- Guangdong Key Laboratory for Research and Development of Natural Drugs, Guangdong Medical University, Zhanjiang, 524023, China.,The Marine Biomedical Research Institute, Southern Marine Science and Engineering Guangdong Laboratory Zhanjiang, Guangdong Medical University, Zhanjiang, 524023, China.,Cancer Center, The Affiliated Hospital, Guangdong Medical University, Zhanjiang, 524023, China
| | - Hongrong Ding
- The Marine Biomedical Research Institute, Southern Marine Science and Engineering Guangdong Laboratory Zhanjiang, Guangdong Medical University, Zhanjiang, 524023, China.,Key Laboratory of Guangdong Provincial Medical Molecular Diagnosis, Dongguan, 523808, China
| | - Lianfang Huang
- Guangdong Key Laboratory for Research and Development of Natural Drugs, Guangdong Medical University, Zhanjiang, 524023, China.,The Marine Biomedical Research Institute, Southern Marine Science and Engineering Guangdong Laboratory Zhanjiang, Guangdong Medical University, Zhanjiang, 524023, China
| | - Haiqing Luo
- Cancer Center, The Affiliated Hospital, Guangdong Medical University, Zhanjiang, 524023, China.
| | - Xiao Zhu
- Guangdong Key Laboratory for Research and Development of Natural Drugs, Guangdong Medical University, Zhanjiang, 524023, China. .,The Marine Biomedical Research Institute, Southern Marine Science and Engineering Guangdong Laboratory Zhanjiang, Guangdong Medical University, Zhanjiang, 524023, China. .,Key Laboratory of Guangdong Provincial Medical Molecular Diagnosis, Dongguan, 523808, China.
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Kim K, Sun H. Incorporating genetic networks into case-control association studies with high-dimensional DNA methylation data. BMC Bioinformatics 2019; 20:510. [PMID: 31640538 PMCID: PMC6805595 DOI: 10.1186/s12859-019-3040-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 08/21/2019] [Indexed: 12/23/2022] Open
Abstract
Background In human genetic association studies with high-dimensional gene expression data, it has been well known that statistical selection methods utilizing prior biological network knowledge such as genetic pathways and signaling pathways can outperform other methods that ignore genetic network structures in terms of true positive selection. In recent epigenetic research on case-control association studies, relatively many statistical methods have been proposed to identify cancer-related CpG sites and their corresponding genes from high-dimensional DNA methylation array data. However, most of existing methods are not designed to utilize genetic network information although methylation levels between linked genes in the genetic networks tend to be highly correlated with each other. Results We propose new approach that combines data dimension reduction techniques with network-based regularization to identify outcome-related genes for analysis of high-dimensional DNA methylation data. In simulation studies, we demonstrated that the proposed approach overwhelms other statistical methods that do not utilize genetic network information in terms of true positive selection. We also applied it to the 450K DNA methylation array data of the four breast invasive carcinoma cancer subtypes from The Cancer Genome Atlas (TCGA) project. Conclusions The proposed variable selection approach can utilize prior biological network information for analysis of high-dimensional DNA methylation array data. It first captures gene level signals from multiple CpG sites using data a dimension reduction technique and then performs network-based regularization based on biological network graph information. It can select potentially cancer-related genes and genetic pathways that were missed by the existing methods. Electronic supplementary material The online version of this article (10.1186/s12859-019-3040-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kipoong Kim
- Department of Statistic, Pusan National University, Busan, 46241, Korea
| | - Hokeun Sun
- Department of Statistic, Pusan National University, Busan, 46241, Korea.
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Combinatorial Electrophoresis and Mass Spectrometry-Based Proteomics in Breast Milk for Breast Cancer Biomarker Discovery. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:451-467. [PMID: 31347064 DOI: 10.1007/978-3-030-15950-4_26] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Innovations in approaches for early detection and individual risk assessment of different cancers, including breast cancer (BC), are needed to reduce cancer morbidity and associated mortality. The assessment of potential cancer biomarkers in accessible bodily fluids provides a novel approach to identify the risk and/or onset of cancer. Biomarkers are biomolecules, such as proteins, that are indicative of an abnormality or a disease. Human milk is vastly underutilized biospecimen that offers the opportunity to investigate potential protein BC-biomarkers in young, reproductively active women. As a first step, we have examined the entire protein pattern in human milk samples from breastfeeding mothers with cancer, who were diagnosed either before or after milk donation, and from women without cancer, using mass spectrometry (MS)-based proteomics.
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Aslebagh R, Channaveerappa D, Arcaro KF, Darie CC. Proteomics analysis of human breast milk to assess breast cancer risk. Electrophoresis 2018; 39:653-665. [PMID: 29193311 DOI: 10.1002/elps.201700123] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 11/13/2017] [Accepted: 11/14/2017] [Indexed: 12/19/2022]
Abstract
Detection of breast cancer (BC) in young women is challenging because mammography, the most common tool for detecting BC, is not effective on the dense breast tissue characteristic of young women. In addition to the limited means for detecting their BC, young women face a transient increased risk of pregnancy-associated BC. As a consequence, reproductively active women could benefit significantly from a tool that provides them with accurate risk assessment and early detection of BC. One potential method for detection of BC is biochemical monitoring of proteins and other molecules in bodily fluids such as serum, nipple aspirate, ductal lavage, tear, urine, saliva and breast milk. Of all these fluids, only breast milk provides access to a large volume of breast tissue, in the form of exfoliated epithelial cells, and to the local breast environment, in the form of molecules in the milk. Thus, analysis of breast milk is a non-invasive method with significant potential for assessing BC risk. Here we analyzed human breast milk by mass spectrometry (MS)-based proteomics to build a biomarker signature for early detection of BC. Ten milk samples from eight women provided five paired-groups (cancer versus control) for analysis of dysregulatedproteins: two within woman comparisons (milk from a diseased breast versus a healthy breast of the same woman) and three across women comparisons (milk from a woman with cancer versus a woman without cancer). Despite a wide range in the time between milk donation and cancer diagnosis (cancer diagnosis occurred from 1 month before to 24 months after milk donation), the levels of some proteins differed significantly between cancer and control in several of the five comparison groups. These pilot data are supportive of the idea that molecular analysis of breast milk will identify proteins informative for early detection and accurate assessment of BC risk, and warrant further research. Data are available via ProteomeXchange with identifier PXD007066.
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Affiliation(s)
- Roshanak Aslebagh
- Biochemistry & Proteomics Group, Department of Chemistry & Biomolecular Science, Clarkson University, Potsdam, NY, USA
| | - Devika Channaveerappa
- Biochemistry & Proteomics Group, Department of Chemistry & Biomolecular Science, Clarkson University, Potsdam, NY, USA
| | - Kathleen F Arcaro
- Department of Veterinary & Animal Sciences, University of Massachusetts, Amherst, MA, USA
| | - Costel C Darie
- Biochemistry & Proteomics Group, Department of Chemistry & Biomolecular Science, Clarkson University, Potsdam, NY, USA
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Kozyraki R, Cases O. Cubilin, the Intrinsic Factor-Vitamin B12 Receptor in Development and Disease. Curr Med Chem 2018; 27:3123-3150. [PMID: 30295181 DOI: 10.2174/0929867325666181008143945] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 08/11/2018] [Accepted: 08/21/2018] [Indexed: 12/29/2022]
Abstract
Gp280/Intrinsic factor-vitamin B12 receptor/Cubilin (CUBN) is a large endocytic receptor serving multiple functions in vitamin B12 homeostasis, renal reabsorption of protein or toxic substances including albumin, vitamin D-binding protein or cadmium. Cubilin is a peripheral membrane protein consisting of 8 Epidermal Growth Factor (EGF)-like repeats and 27 CUB (defined as Complement C1r/C1s, Uegf, BMP1) domains. This structurally unique protein interacts with at least two molecular partners, Amnionless (AMN) and Lrp2/Megalin. AMN is involved in appropriate plasma membrane transport of Cubilin whereas Lrp2 is essential for efficient internalization of Cubilin and its ligands. Observations gleaned from animal models with Cubn deficiency or human diseases demonstrate the importance of this protein. In this review addressed to basic research and medical scientists, we summarize currently available data on Cubilin and its implication in renal and intestinal biology. We also discuss the role of Cubilin as a modulator of Fgf8 signaling during embryonic development and propose that the Cubilin-Fgf8 interaction may be relevant in human pathology, including in cancer progression, heart or neural tube defects. We finally provide experimental elements suggesting that some aspects of Cubilin physiology might be relevant in drug design.
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Affiliation(s)
- Renata Kozyraki
- INSERM UMRS 1138, Centre de Recherche des Cordeliers, Paris-Diderot University, Paris, France
| | - Olivier Cases
- INSERM UMRS 1138, Centre de Recherche des Cordeliers, Paris-Diderot University, Paris, France
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Surendran S, Adaikalakoteswari A, Saravanan P, Shatwaan IA, Lovegrove JA, Vimaleswaran KS. An update on vitamin B12-related gene polymorphisms and B12 status. GENES AND NUTRITION 2018; 13:2. [PMID: 29445423 PMCID: PMC5801754 DOI: 10.1186/s12263-018-0591-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 01/23/2018] [Indexed: 12/12/2022]
Abstract
Background Vitamin B12 is an essential micronutrient in humans needed for health maintenance. Deficiency of vitamin B12 has been linked to dietary, environmental and genetic factors. Evidence for the genetic basis of vitamin B12 status is poorly understood. However, advancements in genomic techniques have increased the knowledge-base of the genetics of vitamin B12 status. Based on the candidate gene and genome-wide association (GWA) studies, associations between genetic loci in several genes involved in vitamin B12 metabolism have been identified. Objective The objective of this literature review was to identify and discuss reports of associations between single-nucleotide polymorphisms (SNPs) in vitamin B12 pathway genes and their influence on the circulating levels of vitamin B12. Methods Relevant articles were obtained through a literature search on PubMed through to May 2017. An article was included if it examined an association of a SNP with serum or plasma vitamin B12 concentration. Beta coefficients and odds ratios were used to describe the strength of an association, and a P < 0.05 was considered as statistically significant. Two reviewers independently evaluated the eligibility for the inclusion criteria and extracted the data. Results From 23 studies which fulfilled the selection criteria, 16 studies identified SNPs that showed statistically significant associations with vitamin B12 concentrations. Fifty-nine vitamin B12-related gene polymorphisms associated with vitamin B12 status were identified in total, from the following populations: African American, Brazilian, Canadian, Chinese, Danish, English, European ancestry, Icelandic, Indian, Italian, Latino, Northern Irish, Portuguese and residents of the USA. Conclusion Overall, the data analyzed suggests that ethnic-specific associations are involved in the genetic determination of vitamin B12 concentrations. However, despite recent success in genetic studies, the majority of identified genes that could explain variation in vitamin B12 concentrations were from Caucasian populations. Further research utilizing larger sample sizes of non-Caucasian populations is necessary in order to better understand these ethnic-specific associations.
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Affiliation(s)
- S Surendran
- 1Hugh Sinclair Unit of Human Nutrition, Department of Food and Nutritional Sciences and Institute for Cardiovascular and Metabolic Research (ICMR), University of Reading, PO Box 226, Whiteknights, Reading, RG6 6AP UK
| | - A Adaikalakoteswari
- 2Warwick Medical School - Population Evidence and Technologies, University of Warwick, Coventry, CV4 7AL UK.,3UK Academic Department of Diabetes and Metabolism, George Eliot Hospital, Nuneaton, UK
| | - P Saravanan
- 2Warwick Medical School - Population Evidence and Technologies, University of Warwick, Coventry, CV4 7AL UK.,3UK Academic Department of Diabetes and Metabolism, George Eliot Hospital, Nuneaton, UK
| | - I A Shatwaan
- 1Hugh Sinclair Unit of Human Nutrition, Department of Food and Nutritional Sciences and Institute for Cardiovascular and Metabolic Research (ICMR), University of Reading, PO Box 226, Whiteknights, Reading, RG6 6AP UK
| | - J A Lovegrove
- 1Hugh Sinclair Unit of Human Nutrition, Department of Food and Nutritional Sciences and Institute for Cardiovascular and Metabolic Research (ICMR), University of Reading, PO Box 226, Whiteknights, Reading, RG6 6AP UK
| | - K S Vimaleswaran
- 1Hugh Sinclair Unit of Human Nutrition, Department of Food and Nutritional Sciences and Institute for Cardiovascular and Metabolic Research (ICMR), University of Reading, PO Box 226, Whiteknights, Reading, RG6 6AP UK
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