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Liu H, Shi H, Sun Y. Identification of a novel lymphangiogenesis signature associated with immune cell infiltration in colorectal cancer based on bioinformatics analysis. BMC Med Genomics 2024; 17:2. [PMID: 38167072 PMCID: PMC10763205 DOI: 10.1186/s12920-023-01781-8] [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: 08/07/2023] [Accepted: 12/16/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Lymphangiogenesis plays an important role in tumor progression and is significantly associated with tumor immune infiltration. However, the role and mechanisms of lymphangiogenesis in colorectal cancer (CRC) are still unknown. Thus, the objective is to identify the lymphangiogenesis-related genes associated with immune infiltration and investigation of their prognosis value. METHODS mRNA expression profiles and corresponding clinical information of CRC samples were obtained from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. The lymphangiogenesis-related genes (LymRGs) were collected from the Molecular Signatures database (MSigDB). Lymphangiogenesis score (LymScore) and immune cell infiltrating levels were quantified using ssGSEA. LymScore) and immune cell infiltrating levels-related hub genes were identified using weighted gene co-expression network analysis (WGCNA). Univariate Cox and LASSO regression analyses were performed to identify the prognostic gene signature and construct a risk model. Furthermore, a predictive nomogram was constructed based on the independent risk factor generated from a multivariate Cox model. RESULTS A total of 1076 LymScore and immune cell infiltrating levels-related hub genes from three key modules were identified by WGCNA. Lymscore is positively associated with natural killer cells as well as regulator T cells infiltrating. These modular genes were enriched in extracellular matrix and structure, collagen fibril organization, cell-substrate adhesion, etc. NUMBL, TSPAN11, PHF21A, PDGFRA, ZNF385A, and RIMKLB were eventually identified as the prognostic gene signature in CRC. And patients were divided into high-risk and low-risk groups based on the median risk score, the patients in the high-risk group indicated poor survival and were predisposed to metastasis and advanced stages. NUMBL and PHF21A were upregulated but PDGFRA was downregulated in tumor samples compared with normal samples in the Human Protein Atlas (HPA) database. CONCLUSION Our finding highlights the critical role of lymphangiogenesis in CRC progression and metastasis and provides a novel gene signature for CRC and novel therapeutic strategies for anti-lymphangiogenic therapies in CRC.
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Affiliation(s)
- Hong Liu
- Department of General Surgery, Wuxi Fifth People's Hospital Affiliated to Jiangnan University, Wuxi, Jiangsu, China
| | - Huiwen Shi
- Department of General Surgery, No.971 Hospital of PLA Navy, Qingdao, China
| | - Yinggang Sun
- Department of General Surgery, The 960th Hospital of Joint Logistics Support Force of Chinese People's Liberation Army, Jinan, China.
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Torres R, Hidalgo C. Subcellular localization and transcriptional regulation of brain ryanodine receptors. Functional implications. Cell Calcium 2023; 116:102821. [PMID: 37949035 DOI: 10.1016/j.ceca.2023.102821] [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: 09/01/2023] [Revised: 10/16/2023] [Accepted: 11/03/2023] [Indexed: 11/12/2023]
Abstract
Ryanodine receptors (RyR) are intracellular Ca2+ channels localized in the endoplasmic reticulum, where they act as critical mediators of Ca2+-induced Ca2+ calcium release (CICR). In the brain, mammals express in both neurons, and non-neuronal cells, a combination of the three RyR-isoforms (RyR1-3). Pharmacological approaches, which do not distinguish between isoforms, have indicated that RyR-isoforms contribute to brain function. However, isoform-specific manipulations have revealed that RyR-isoforms display different subcellular localizations and are differentially associated with neuronal function. These findings raise the need to understand RyR-isoform specific transcriptional regulation, as this knowledge will help to elucidate the causes of neuronal dysfunction for a growing list of brain disorders that show altered RyR channel expression and function.
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Affiliation(s)
- Rodrigo Torres
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Lago Panguipulli 1390, 5501842, Puerto Montt, Chile.
| | - Cecilia Hidalgo
- Department of Neurosciences. Biomedical Neuroscience Institute, Physiology and Biophysics Program, Institute of Biomedical Sciences, Center for Exercise, Metabolism and Cancer Studies, Faculty of Medicine, Universidad de Chile, Santiago, 8380000, Chile
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Joyce T, Jagasia S, Tasci E, Camphausen K, Krauze AV. An Overview of CD133 as a Functional Unit of Prognosis and Treatment Resistance in Glioblastoma. Curr Oncol 2023; 30:8278-8293. [PMID: 37754516 PMCID: PMC10528301 DOI: 10.3390/curroncol30090601] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 08/31/2023] [Accepted: 09/06/2023] [Indexed: 09/28/2023] Open
Abstract
Biomarkers for resistance in Glioblastoma multiforme (GBM) are lacking, and progress in the clinic has been slow to arrive. CD133 (prominin-1) is a membrane-bound glycoprotein on the surface of cancer stem cells (CSCs) that has been associated with poor prognosis, therapy resistance, and tumor recurrence in GBM. Due to its connection to CSCs, to which tumor resistance and recurrence have been partially attributed in GBM, there is a growing field of research revolving around the potential role of CD133 in each of these processes. However, despite encouraging results in vitro and in vivo, the biological interplay of CD133 with these components is still unclear, causing a lack of clinical application. In parallel, omic data from biospecimens that include CD133 are beginning to emerge, increasing the importance of understanding CD133 for the effective use of these highly dimensional data sets. Given the significant mechanistic overlap, prioritization of the most robust findings is necessary to optimize the transition of CD133 to clinical applications using patient-derived biospecimens. As a result, this review aims to compile and analyze the current research regarding CD133 as a functional unit in GBM, exploring its connections to prognosis, the tumor microenvironment, tumor resistance, and tumor recurrence.
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Affiliation(s)
| | | | | | | | - Andra Valentina Krauze
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, 9000 Rockville Pike, Building 10, CRC, Bethesda, MD 20892, USA; (T.J.); (S.J.); (E.T.); (K.C.)
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García-Cárdenas JM, Armendáriz-Castillo I, García-Cárdenas N, Pesantez-Coronel D, López-Cortés A, Indacochea A, Guerrero S. Data mining identifies novel RNA-binding proteins involved in colon and rectal carcinomas. Front Cell Dev Biol 2023; 11:1088057. [PMID: 37384253 PMCID: PMC10293682 DOI: 10.3389/fcell.2023.1088057] [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: 11/03/2022] [Accepted: 02/13/2023] [Indexed: 06/30/2023] Open
Abstract
Colorectal adenocarcinoma (COREAD) is the second most deadly cancer and third most frequently encountered malignancy worldwide. Despite efforts in molecular subtyping and subsequent personalized COREAD treatments, multidisciplinary evidence suggests separating COREAD into colon cancer (COAD) and rectal cancer (READ). This new perspective could improve diagnosis and treatment of both carcinomas. RNA-binding proteins (RBPs), as critical regulators of every hallmark of cancer, could fulfill the need to identify sensitive biomarkers for COAD and READ separately. To detect new RBPs involved in COAD and READ progression, here we used a multidata integration strategy to prioritize tumorigenic RBPs. We analyzed and integrated 1) RBPs genomic and transcriptomic alterations from 488 COAD and 155 READ patients, 2) ∼ 10,000 raw associations between RBPs and cancer genes, 3) ∼ 15,000 immunostainings, and 4) loss-of-function screens performed in 102 COREAD cell lines. Thus, we unraveled new putative roles of NOP56, RBM12, NAT10, FKBP1A, EMG1, and CSE1L in COAD and READ progression. Interestingly, FKBP1A and EMG1 have never been related with any of these carcinomas but presented tumorigenic features in other cancer types. Subsequent survival analyses highlighted the clinical relevance of FKBP1A, NOP56, and NAT10 mRNA expression to predict poor prognosis in COREAD and COAD patients. Further research should be performed to validate their clinical potential and to elucidate their molecular mechanisms underlying these malignancies.
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Affiliation(s)
- Jennyfer M. García-Cárdenas
- Laboratorio de Ciencia de Datos Biomédicos, Escuela de Medicina, Facultad de Ciencias Médicas de la Salud y de la Vida, Universidad Internacional del Ecuador, Quito, Ecuador
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), Madrid, Spain
| | - Isaac Armendáriz-Castillo
- Laboratorio de Ciencia de Datos Biomédicos, Escuela de Medicina, Facultad de Ciencias Médicas de la Salud y de la Vida, Universidad Internacional del Ecuador, Quito, Ecuador
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), Madrid, Spain
- Facultad de Ingenierías y Ciencias Aplicadas, Universidad Internacional SEK, Quito, Ecuador
| | | | - David Pesantez-Coronel
- Medical Oncology Department Hospital Clinic and Translational Genomics and Targeted Therapies in Solid Tumors, IDIBAPS, Barcelona, Spain
| | - Andrés López-Cortés
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), Madrid, Spain
- Cancer Research Group (CRG), Faculty of Medicine, Universidad de Las Américas, Quito, Ecuador
| | - Alberto Indacochea
- Medical Oncology Department Hospital Clinic and Translational Genomics and Targeted Therapies in Solid Tumors, IDIBAPS, Barcelona, Spain
| | - Santiago Guerrero
- Laboratorio de Ciencia de Datos Biomédicos, Escuela de Medicina, Facultad de Ciencias Médicas de la Salud y de la Vida, Universidad Internacional del Ecuador, Quito, Ecuador
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), Madrid, Spain
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Cao P, Wu Y, Sun D, Zhang W, Qiu J, Tang Z, Xue X, Qin L. IGF2BP2 promotes pancreatic carcinoma progression by enhancing the stability of B3GNT6 mRNA via m6A methylation. Cancer Med 2023; 12:4405-4420. [PMID: 35908253 PMCID: PMC9972174 DOI: 10.1002/cam4.5096] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 05/08/2022] [Accepted: 07/14/2022] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND Pancreatic carcinoma (PC) is a highly lethal cancer with an increasing mortality rate, its five-year survival rate is only approximately 4%. N6-methyladenosine (m6A) modification is the most common posttranscriptional modification of RNA, it could affect tumor formation by regulating m6A modifications in the mRNA of key oncogenes or tumor suppressor genes. However, its role in PC remains unclear. METHODS We combined bioinformatic analysis with in vitro and in vivo experiments to investigate the expression profile of methylation modulators and identify key m6A regulators in the progression of PC. Further study focused on exploring the target genes binding to the regulators through RIP and immunofluorescence staining experiment. RESULTS TCGA and Gene Expression Omnibus (GEO) analyses revealed an overall increasing trend in the expression of m6A regulators in PC, and consensus clustering analysis of m6A modification showed that the expression of regulators was negatively correlated with the survival rate. LASSO-Cox regression analysis revealed that IGF2BP2, METTL3, ALKBH5 and KIAA1429 were associated with hazard ratios (HR), but only IGF2BP2 was sufficiently appropriate for the m6A survival prognosis model. The IHC and WB results verified high protein expression of IGF2BP2 in PC, and IGF2BP2 knockdown inhibited the proliferation and migration of PC cells. We predicted and verified B3GNT6 was observably regulated by IGF2BP2 via RIP assays. In addition, IF staining confirmed the co-expression of IGF2BP2 and B3GNT6. The tumor-promoting effect of IGF2BP2 and its co-expression with B3GNT6 were verified in an animal model. CONCLUSIONS Elevated m6A levels promote PC progression. IGF2BP2 is a credible marker and modulates B3GNT6 mRNA stability, indicating that IGF2BP2 is a potential prognostic marker and therapeutic target in PC progression.
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Affiliation(s)
- Pei Cao
- Department of General SurgeryThe First Affiliated Hospital of Soochow UniversitySuzhouJiangsuChina
| | - Yufan Wu
- Department of General SurgeryThe First Affiliated Hospital of Soochow UniversitySuzhouJiangsuChina
| | - Ding Sun
- Department of General SurgeryThe First Affiliated Hospital of Soochow UniversitySuzhouJiangsuChina
| | - Weigang Zhang
- Department of General SurgeryThe First Affiliated Hospital of Soochow UniversitySuzhouJiangsuChina
| | - Junyi Qiu
- Department of General SurgeryThe First Affiliated Hospital of Soochow UniversitySuzhouJiangsuChina
| | - Zuxiong Tang
- Department of General SurgeryThe First Affiliated Hospital of Soochow UniversitySuzhouJiangsuChina
| | - Xiaofeng Xue
- Department of General SurgeryThe First Affiliated Hospital of Soochow UniversitySuzhouJiangsuChina
| | - Lei Qin
- Department of General SurgeryThe First Affiliated Hospital of Soochow UniversitySuzhouJiangsuChina
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m 6A-modified circFNDC3B inhibits colorectal cancer stemness and metastasis via RNF41-dependent ASB6 degradation. Cell Death Dis 2022; 13:1008. [PMID: 36446779 PMCID: PMC9709059 DOI: 10.1038/s41419-022-05451-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 11/14/2022] [Accepted: 11/16/2022] [Indexed: 11/30/2022]
Abstract
Colorectal cancer (CRC) is the third most frequently diagnosed cancer with unfavorable clinical outcomes worldwide. circFNDC3B plays as a tumor suppressor in CRC, however, the mechanism of circFNDC3B in CRC remains ambiguous. The stem-like properties of CRC cells were detected by the evaluation of stemness markers, sphere formation assay and flow cytometry. qRT-PCR, FISH, IHC, and western blotting assessed the expression and localization of circFNDC3B, RNF41, ASB6, and stemness markers in CRC. The metastatic capabilities of CRC cells were examined by wound healing and Transwell assays, as well as in vivo liver metastasis model. Bioinformatics analysis, RNA immunoprecipitation (RIP), RNA pull-down assay and co-IP were used to detect the associations among circFNDC3B, FXR2, RNF41, and ASB6. Downregulated circFNDC3B was associated with unfavorite survival in CRC patients, and circFNDC3B overexpression suppressed CRC stemness and metastasis. Mechanistically, studies revealed that YTHDC1 facilitated cytoplasmic translocation of m6A-modified circFNDC3B, and circFNDC3B enhanced RNF41 mRNA stability and expression via binding to FXR2. circFNDC3B promoted ASB6 degradation through RNF41-mediated ubiquitination. Functional studies showed that silencing of RNF41 counteracted circFNDC3B-suppressed CRC stemness and metastasis, and ASB6 overexpression reversed circFNDC3B- or RNF41-mediated regulation of CRC stemness and metastasis. Elevated ASB6 was positively correlated with unfavorite survival in CRC patients. In vivo experiments further showed that circFNDC3B or RNF41 overexpression repressed tumor growth, stemness and liver metastasis via modulating ASB6. Taken together, m6A-modified circFNDC3B inhibited CRC stemness and metastasis via RNF41-dependent ASB6 degradation. These findings provide novel insights and important clues for targeted therapeutic strategies of CRC.
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Wang Z, Huang C, Wu J, Zhang H, Shao Y, Fu Z. Analysis of the Prognostic Significance and Immune Infiltration of the Amino Acid Metabolism-Related Genes in Colon Adenocarcinoma. Front Genet 2022; 13:951461. [PMID: 36035152 PMCID: PMC9399353 DOI: 10.3389/fgene.2022.951461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 06/20/2022] [Indexed: 11/19/2022] Open
Abstract
Amino acid metabolization is verified to be a part in the progression of cancer. However, genes related to the amino acid metabolism have not been identified in colon adenocarcinoma (COAD). A systematic prognostic model of COAD becomes a pressing need. Among genes related to the amino acid metabolism, RIMKLB, ASPG, TH, MTAP, AZIN2, PSMB2, HDC, ACMSD, and PSMA8 were identified to construct a risk model. Kaplan–Meier (K–M) analyses demonstrated that the high-risk group achieved a poor prognosis. Area under the respective ROC (AUC) values indicated the robustness of the model. To highlight its clinical value, multivariate Cox was used to obtain the optimal variables to construct a nomogram. A higher tumor mutation burden was observed in the high-risk group. However, the low-risk group had a stronger immune infiltration. Seven molecular subtypes were found by consensus cluster. Twenty-two hub genes were identified related to the ESTIMATE score using WGCNA. In brief, our research constructed a stable prognostic model related to the amino acid metabolism in COAD, revealing its connection to the immune microenvironment. The model guided the outcome of COAD and the direction of immunotherapy.
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Affiliation(s)
- Zhenling Wang
- The First College of Clinical Medicine, Nanjing Medical University, Nanjing, China
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Changzhi Huang
- The First College of Clinical Medicine, Nanjing Medical University, Nanjing, China
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jingyu Wu
- The First College of Clinical Medicine, Nanjing Medical University, Nanjing, China
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Hongqiang Zhang
- The First College of Clinical Medicine, Nanjing Medical University, Nanjing, China
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yu Shao
- The First College of Clinical Medicine, Nanjing Medical University, Nanjing, China
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Zan Fu
- The First College of Clinical Medicine, Nanjing Medical University, Nanjing, China
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- *Correspondence: Zan Fu,
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