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Calì F, Vinci M, Treccarichi S, Papa C, Gloria A, Musumeci A, Federico C, Vitello GA, Nicotera AG, Di Rosa G, Vetri L, Saccone S, Elia M. PLEKHG1: New Potential Candidate Gene for Periventricular White Matter Abnormalities. Genes (Basel) 2024; 15:1096. [PMID: 39202455 PMCID: PMC11353482 DOI: 10.3390/genes15081096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2024] [Revised: 08/16/2024] [Accepted: 08/19/2024] [Indexed: 09/03/2024] Open
Abstract
Hypoxic-ischemic brain damage presents a significant neurological challenge, often manifesting during the perinatal period. Specifically, periventricular leukomalacia (PVL) is emerging as a notable contributor to cerebral palsy and intellectual disabilities. It compromises cerebral microcirculation, resulting in insufficient oxygen or blood flow to the periventricular region of the brain. As widely documented, these pathological conditions can be caused by several factors encompassing preterm birth (4-5% of the total cases), as well single cotwin abortion and genetic variants such as those associated with GTPase pathways. Whole exome sequencing (WES) analysis identified a de novo causative variant within the pleckstrin homology domain-containing family G member 1 (PLEKHG1) gene in a patient presenting with PVL. The PLEKHG1 gene is ubiquitously expressed, showing high expression patterns in brain tissues. PLEKHG1 is part of a family of Rho guanine nucleotide exchange factors, and the protein is essential for cell division control protein 42 (CDC42) activation in the GTPase pathway. CDC42 is a key small GTPase of the Rho-subfamily, regulating various cellular functions such as cell morphology, migration, endocytosis, and cell cycle progression. The molecular mechanism involving PLEKHG1 and CDC42 has an intriguing role in the reorientation of cells in the vascular endothelium, thus suggesting that disruption responses to mechanical stress in endothelial cells may be involved in the formation of white matter lesions. Significantly, CDC42 association with white matter abnormalities is underscored by its MIM phenotype number. In contrast, although PLEKHG1 has been recently associated with patients showing white matter hyperintensities, it currently lacks a MIM phenotype number. Additionally, in silico analyses classified the identified variant as pathogenic. Although the patient was born prematurely and subsequently to dichorionic gestation, during which its cotwin died, we suggest that the variant described can strongly contribute to PVL. The aim of the current study is to establish a plausible association between the PLEKHG1 gene and PVL.
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Affiliation(s)
- Francesco Calì
- Oasi Research Institute—IRCCS, 94018 Troina, Italy; (F.C.); (M.V.); (S.T.); (C.P.); (A.G.); (A.M.); (G.A.V.); (L.V.); (M.E.)
| | - Mirella Vinci
- Oasi Research Institute—IRCCS, 94018 Troina, Italy; (F.C.); (M.V.); (S.T.); (C.P.); (A.G.); (A.M.); (G.A.V.); (L.V.); (M.E.)
| | - Simone Treccarichi
- Oasi Research Institute—IRCCS, 94018 Troina, Italy; (F.C.); (M.V.); (S.T.); (C.P.); (A.G.); (A.M.); (G.A.V.); (L.V.); (M.E.)
| | - Carla Papa
- Oasi Research Institute—IRCCS, 94018 Troina, Italy; (F.C.); (M.V.); (S.T.); (C.P.); (A.G.); (A.M.); (G.A.V.); (L.V.); (M.E.)
| | - Angelo Gloria
- Oasi Research Institute—IRCCS, 94018 Troina, Italy; (F.C.); (M.V.); (S.T.); (C.P.); (A.G.); (A.M.); (G.A.V.); (L.V.); (M.E.)
| | - Antonino Musumeci
- Oasi Research Institute—IRCCS, 94018 Troina, Italy; (F.C.); (M.V.); (S.T.); (C.P.); (A.G.); (A.M.); (G.A.V.); (L.V.); (M.E.)
| | - Concetta Federico
- Department Biological, Geological and Environmental Sciences, University of Catania, Via Androne 81, 95124 Catania, Italy;
| | - Girolamo Aurelio Vitello
- Oasi Research Institute—IRCCS, 94018 Troina, Italy; (F.C.); (M.V.); (S.T.); (C.P.); (A.G.); (A.M.); (G.A.V.); (L.V.); (M.E.)
| | - Antonio Gennaro Nicotera
- Unit of Child Neurology and Psychiatry, Department of Human Pathology of the Adult and Developmental Age, “Gaetano Barresi” University of Messina, 98124 Messina, Italy; (A.G.N.); (G.D.R.)
| | - Gabriella Di Rosa
- Unit of Child Neurology and Psychiatry, Department of Human Pathology of the Adult and Developmental Age, “Gaetano Barresi” University of Messina, 98124 Messina, Italy; (A.G.N.); (G.D.R.)
| | - Luigi Vetri
- Oasi Research Institute—IRCCS, 94018 Troina, Italy; (F.C.); (M.V.); (S.T.); (C.P.); (A.G.); (A.M.); (G.A.V.); (L.V.); (M.E.)
| | - Salvatore Saccone
- Department Biological, Geological and Environmental Sciences, University of Catania, Via Androne 81, 95124 Catania, Italy;
| | - Maurizio Elia
- Oasi Research Institute—IRCCS, 94018 Troina, Italy; (F.C.); (M.V.); (S.T.); (C.P.); (A.G.); (A.M.); (G.A.V.); (L.V.); (M.E.)
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Zhao S, Li J, Zhang H, Qi L, Du Y, Kogiso M, Braun FK, Xiao S, Huang Y, Li J, Teo WY, Lindsay H, Baxter P, Su JMF, Adesina A, Laczik M, Genevini P, Veillard AC, Schvartzman S, Berguet G, Ding SR, Du L, Stephan C, Yang J, Davies PJA, Lu X, Chintagumpala M, Parsons DW, Perlaky L, Xia YF, Man TK, Huang Y, Sun D, Li XN. Epigenetic Alterations of Repeated Relapses in Patient-matched Childhood Ependymomas. Nat Commun 2022; 13:6689. [PMID: 36335125 PMCID: PMC9637194 DOI: 10.1038/s41467-022-34514-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 10/27/2022] [Indexed: 11/07/2022] Open
Abstract
Recurrence is frequent in pediatric ependymoma (EPN). Our longitudinal integrated analysis of 30 patient-matched repeated relapses (3.67 ± 1.76 times) over 13 years (5.8 ± 3.8) reveals stable molecular subtypes (RELA and PFA) and convergent DNA methylation reprogramming during serial relapses accompanied by increased orthotopic patient derived xenograft (PDX) (13/27) formation in the late recurrences. A set of differentially methylated CpGs (DMCs) and DNA methylation regions (DMRs) are found to persist in primary and relapse tumors (potential driver DMCs) and are acquired exclusively in the relapses (potential booster DMCs). Integrating with RNAseq reveals differentially expressed genes regulated by potential driver DMRs (CACNA1H, SLC12A7, RARA in RELA and HSPB8, GMPR, ITGB4 in PFA) and potential booster DMRs (PLEKHG1 in RELA and NOTCH, EPHA2, SUFU, FOXJ1 in PFA tumors). DMCs predicators of relapse are also identified in the primary tumors. This study provides a high-resolution epigenetic roadmap of serial EPN relapses and 13 orthotopic PDX models to facilitate biological and preclinical studies.
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Affiliation(s)
- Sibo Zhao
- grid.39382.330000 0001 2160 926XPre-clinical Neuro-oncology Research Program, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX 77030 USA ,grid.39382.330000 0001 2160 926XTexas Children’s Cancer Center, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX 77030 USA ,grid.413584.f0000 0004 0383 5679Jane and John Justin Neurosciences Center, Cook Children’s Medical Center, Fort Worth, TX 76104 USA ,grid.413584.f0000 0004 0383 5679Hematology and Oncology Center, Cook Children’s Medical Center, Fort Worth, TX 76104 USA
| | - Jia Li
- grid.264756.40000 0004 4687 2082Center for Epigenetics & Disease Prevention, Texas A&M University, Houston, TX 77030 USA ,grid.264756.40000 0004 4687 2082Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030 USA ,grid.470124.4State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University; and Guangzhou Laboratory, Bioland, 510120 Guangzhou, Guangdong P. R. China
| | - Huiyuan Zhang
- grid.39382.330000 0001 2160 926XPre-clinical Neuro-oncology Research Program, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX 77030 USA ,grid.39382.330000 0001 2160 926XTexas Children’s Cancer Center, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX 77030 USA
| | - Lin Qi
- grid.39382.330000 0001 2160 926XPre-clinical Neuro-oncology Research Program, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX 77030 USA ,grid.39382.330000 0001 2160 926XTexas Children’s Cancer Center, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX 77030 USA ,grid.16753.360000 0001 2299 3507Program of Precision Medicine PDOX Modeling of Pediatric Tumors, Division of Hematology-Oncology, Neuro-Oncology & Stem Cell transplantation, Ann & Robert H. Lurie Children’s Hospital of Chicago; Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Yuchen Du
- grid.39382.330000 0001 2160 926XPre-clinical Neuro-oncology Research Program, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX 77030 USA ,grid.39382.330000 0001 2160 926XTexas Children’s Cancer Center, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX 77030 USA ,grid.16753.360000 0001 2299 3507Program of Precision Medicine PDOX Modeling of Pediatric Tumors, Division of Hematology-Oncology, Neuro-Oncology & Stem Cell transplantation, Ann & Robert H. Lurie Children’s Hospital of Chicago; Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Mari Kogiso
- grid.39382.330000 0001 2160 926XPre-clinical Neuro-oncology Research Program, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX 77030 USA ,grid.39382.330000 0001 2160 926XTexas Children’s Cancer Center, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX 77030 USA
| | - Frank K. Braun
- grid.39382.330000 0001 2160 926XPre-clinical Neuro-oncology Research Program, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX 77030 USA ,grid.39382.330000 0001 2160 926XTexas Children’s Cancer Center, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX 77030 USA
| | - Sophie Xiao
- grid.16753.360000 0001 2299 3507Program of Precision Medicine PDOX Modeling of Pediatric Tumors, Division of Hematology-Oncology, Neuro-Oncology & Stem Cell transplantation, Ann & Robert H. Lurie Children’s Hospital of Chicago; Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Yulun Huang
- grid.39382.330000 0001 2160 926XPre-clinical Neuro-oncology Research Program, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX 77030 USA ,grid.39382.330000 0001 2160 926XTexas Children’s Cancer Center, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX 77030 USA ,grid.263761.70000 0001 0198 0694Department of Neurosurgery and Brain and Nerve Research Laboratory, the First Affiliated Hospital, and Department of Neurosurgery, Dushu Lake Hospital, Suzhou Medical College, Soochow University, 215007 Suzhou, P. R. China
| | - Jianfang Li
- grid.264756.40000 0004 4687 2082Center for Epigenetics & Disease Prevention, Texas A&M University, Houston, TX 77030 USA
| | - Wan-Yee Teo
- grid.410724.40000 0004 0620 9745Humphrey Oei Institute of Cancer Research, National Cancer Center Singapore, Singapore, 169610 Singapore ,grid.428397.30000 0004 0385 0924Cancer and Stem Cell Biology Program, Duke-NUS Medical School Singapore, Singapore, Singapore ,grid.414963.d0000 0000 8958 3388KK Women’s & Children’s Hospital Singapore, Singapore, Singapore ,grid.418812.60000 0004 0620 9243Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore
| | - Holly Lindsay
- grid.39382.330000 0001 2160 926XPre-clinical Neuro-oncology Research Program, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX 77030 USA ,grid.39382.330000 0001 2160 926XTexas Children’s Cancer Center, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX 77030 USA
| | - Patricia Baxter
- grid.39382.330000 0001 2160 926XTexas Children’s Cancer Center, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX 77030 USA
| | - Jack M. F. Su
- grid.39382.330000 0001 2160 926XTexas Children’s Cancer Center, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX 77030 USA
| | - Adekunle Adesina
- grid.39382.330000 0001 2160 926XDepartment of Pathology, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX 77030 USA
| | - Miklós Laczik
- grid.424287.f0000 0004 0555 845XEpigenetic Services, Diagenode, Liège Belgium
| | - Paola Genevini
- grid.424287.f0000 0004 0555 845XEpigenetic Services, Diagenode, Liège Belgium
| | | | - Sol Schvartzman
- grid.424287.f0000 0004 0555 845XEpigenetic Services, Diagenode, Liège Belgium
| | - Geoffrey Berguet
- grid.424287.f0000 0004 0555 845XEpigenetic Services, Diagenode, Liège Belgium
| | - Shi-Rong Ding
- grid.488530.20000 0004 1803 6191State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine; Department of Radiation, Sun Yat-sen University Cancer Center, 510060 Guangzhou, Guangdong P. R. China
| | - Liping Du
- grid.16753.360000 0001 2299 3507Clinical Cytogenetic Laboratory, Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Clifford Stephan
- grid.264756.40000 0004 4687 2082Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030 USA
| | - Jianhua Yang
- grid.39382.330000 0001 2160 926XTexas Children’s Cancer Center, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX 77030 USA
| | - Peter J. A. Davies
- grid.264756.40000 0004 4687 2082Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030 USA
| | - Xinyan Lu
- grid.16753.360000 0001 2299 3507Clinical Cytogenetic Laboratory, Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Murali Chintagumpala
- grid.39382.330000 0001 2160 926XTexas Children’s Cancer Center, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX 77030 USA
| | - Donald William Parsons
- grid.39382.330000 0001 2160 926XTexas Children’s Cancer Center, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX 77030 USA
| | - Laszlo Perlaky
- grid.39382.330000 0001 2160 926XTexas Children’s Cancer Center, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX 77030 USA
| | - Yun-Fei Xia
- grid.488530.20000 0004 1803 6191State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine; Department of Radiation, Sun Yat-sen University Cancer Center, 510060 Guangzhou, Guangdong P. R. China
| | - Tsz-Kwong Man
- grid.39382.330000 0001 2160 926XTexas Children’s Cancer Center, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX 77030 USA
| | - Yun Huang
- grid.264756.40000 0004 4687 2082Center for Epigenetics & Disease Prevention, Texas A&M University, Houston, TX 77030 USA
| | - Deqiang Sun
- grid.264756.40000 0004 4687 2082Center for Epigenetics & Disease Prevention, Texas A&M University, Houston, TX 77030 USA
| | - Xiao-Nan Li
- grid.39382.330000 0001 2160 926XPre-clinical Neuro-oncology Research Program, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX 77030 USA ,grid.39382.330000 0001 2160 926XTexas Children’s Cancer Center, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX 77030 USA ,grid.16753.360000 0001 2299 3507Program of Precision Medicine PDOX Modeling of Pediatric Tumors, Division of Hematology-Oncology, Neuro-Oncology & Stem Cell transplantation, Ann & Robert H. Lurie Children’s Hospital of Chicago; Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
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Zhou XD, Qu YW, Wang L, Jia FH, Chen P, Wang YP, Liu HF. Identification of potential hub genes of gastric cancer. Medicine (Baltimore) 2022; 101:e30741. [PMID: 36254003 PMCID: PMC9575828 DOI: 10.1097/md.0000000000030741] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Gastric cancer (GC) is a malignant tumor originated from gastric mucosa epithelium. It is the third leading cause of cancer mortality in China. The early symptoms are not obvious. When it is discovered, it has developed to the advanced stage, and the prognosis is poor. In order to screen for potential genes for GC development, this study obtained GSE118916 and GSE109476 from the gene expression omnibus (GEO) database for bioinformatics analysis. METHODS First, GEO2R was used to identify differentially expressed genes (DEG) and the functional annotation of DEGs was performed by gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. The Search Tool for the Retrieval of Interacting Genes (STRING) tool was used to construct protein-protein interaction (PPI) network and the most important modules and hub genes were mined. Real time quantitative polymerase chain reaction assay was performed to verify the expression level of hub genes. RESULTS A total of 139 DEGs were identified. The functional changes of DEGs are mainly concentrated in the cytoskeleton, extracellular matrix and collagen synthesis. Eleven genes were identified as core genes. Bioinformatics analysis shows that the core genes are mainly enriched in many processes related to cell adhesion and collagen. CONCLUSION In summary, the DEGs and hub genes found in this study may be potential diagnostic and therapeutic targets.
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Affiliation(s)
- Xu-Dong Zhou
- The Clinical College of the General Hospital of Chinese People's Armed Police Forces, Anhui Medical University, Hefei, P.R. China
| | - Ya-Wei Qu
- Department of Gastroenterology, Third Medical Center of PLA General Hospital, Beijing, P.R. China
| | - Li Wang
- Department of Gastroenterology, Huamei Hospital of China National University of Science and Technology, Ningbo, P.R. China
| | - Fu-Hua Jia
- Department of Gastroenterology, Huamei Hospital of China National University of Science and Technology, Ningbo, P.R. China
| | - Peng Chen
- Department of Ultrasound, Graduate School of Jinzhou Medical University, Jinzhou, P.R. China
| | - Yin-Pu Wang
- Department of Gastroenterology, Baoji Hospital Affiliated to Xi’an Jiaotong University, Baoji, P.R. China
| | - Hai-Feng Liu
- The Clinical College of the General Hospital of Chinese People's Armed Police Forces, Anhui Medical University, Hefei, P.R. China
- *Correspondence: Hai-Feng Liu, The Clinical College of the General Hospital of Chinese People's Armed Police Forces, Anhui Medical University, Hefei 230032, P.R. China (e-mail: )
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Kaczor-Urbanowicz KE, Saad M, Grogan TR, Li F, Heo YJ, Elashoff D, Bresalier RS, Wong DTW, Kim Y. Performance of Salivary Extracellular RNA Biomarker Panels for Gastric Cancer Differs between Distinct Populations. Cancers (Basel) 2022; 14:3632. [PMID: 35892889 PMCID: PMC9331389 DOI: 10.3390/cancers14153632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/27/2022] [Accepted: 07/19/2022] [Indexed: 11/16/2022] Open
Abstract
Gastric cancer (GC) has the fifth highest incidence among cancers and is the fourth leading cause of cancer-related death GC has predominantly a higher number of cases in certain ethnic groups such as the Korean population. GC found at an early stage is more treatable and has a higher survival rate as compared with GC found at a late stage. However, a diagnosis of GC is often delayed due to the lack of early symptoms and available screening programs in United States. Extracellular RNA (exRNA) is an emerging paradigm; exRNAs have the potential to serve as biomarkers in panels aimed at early detection of cancer. We previously reported the successful use of a panel of salivary exRNA for detecting GC in a high-prevalence Korean cohort, and that genetic changes reflected cancer-associated salivary exRNA changes. The current study is a case-control study of salivary exRNA biomarkers for detecting GC in an ethnically distinct U.S. cohort. A model constructed for the U.S. cohort combined demographic characteristics and salivary miRNA and mRNA biomarkers for GC and yielded an area under the receiver operating characteristic (ROC) curve (AUC) of 0.78. However, the constituents of this model differed from that constructed for the Korean cohort, thus, emphasizing the importance of population-specific biomarker development and validation.
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Affiliation(s)
- Karolina Elżbieta Kaczor-Urbanowicz
- Center for Oral and Head/Neck Oncology Research, School of Dentistry, University of California at Los Angeles, Los Angeles, CA 90095, USA; (K.E.K.-U.); (M.S.); (F.L.); (Y.J.H.)
- UCLA Institute for Quantitative and Computational Biosciences, University of California at Los Angeles, Los Angeles, CA 90095, USA
- UCLA Section of Orthodontics, University of California at Los Angeles, Los Angeles, CA 90095, USA
- Section of Biosystems and Function, School of Dentistry, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Mustafa Saad
- Center for Oral and Head/Neck Oncology Research, School of Dentistry, University of California at Los Angeles, Los Angeles, CA 90095, USA; (K.E.K.-U.); (M.S.); (F.L.); (Y.J.H.)
| | - Tristan R. Grogan
- Department of Medicine Statistics Core, David Geffen School of Medicine at the University of California at Los Angeles, Los Angeles, CA 90024, USA; (T.R.G.); (D.E.)
| | - Feng Li
- Center for Oral and Head/Neck Oncology Research, School of Dentistry, University of California at Los Angeles, Los Angeles, CA 90095, USA; (K.E.K.-U.); (M.S.); (F.L.); (Y.J.H.)
- Section of Biosystems and Function, School of Dentistry, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - You Jeong Heo
- Center for Oral and Head/Neck Oncology Research, School of Dentistry, University of California at Los Angeles, Los Angeles, CA 90095, USA; (K.E.K.-U.); (M.S.); (F.L.); (Y.J.H.)
| | - David Elashoff
- Department of Medicine Statistics Core, David Geffen School of Medicine at the University of California at Los Angeles, Los Angeles, CA 90024, USA; (T.R.G.); (D.E.)
| | - Robert S. Bresalier
- Department of Gastroenterology, Hepatology and Nutrition, Division of Internal Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - David T. W. Wong
- Center for Oral and Head/Neck Oncology Research, School of Dentistry, University of California at Los Angeles, Los Angeles, CA 90095, USA; (K.E.K.-U.); (M.S.); (F.L.); (Y.J.H.)
- Section of Biosystems and Function, School of Dentistry, University of California at Los Angeles, Los Angeles, CA 90095, USA
- UCLA’s Jonsson Comprehensive Cancer Center, Los Angeles, CA 90024, USA
| | - Yong Kim
- Center for Oral and Head/Neck Oncology Research, School of Dentistry, University of California at Los Angeles, Los Angeles, CA 90095, USA; (K.E.K.-U.); (M.S.); (F.L.); (Y.J.H.)
- Section of Biosystems and Function, School of Dentistry, University of California at Los Angeles, Los Angeles, CA 90095, USA
- Department of Gastroenterology, Hepatology and Nutrition, Division of Internal Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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Chen L, Ge C, Feng X, Fu H, Wang S, Zhu J, Linghu E, Zheng X. Identification of Combinations of Plasma lncRNAs and mRNAs as Potential Biomarkers for Precursor Lesions and Early Gastric Cancer. JOURNAL OF ONCOLOGY 2022; 2022:1458320. [PMID: 35186077 PMCID: PMC8856804 DOI: 10.1155/2022/1458320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/14/2022] [Accepted: 01/19/2022] [Indexed: 12/18/2022]
Abstract
Patients with gastric cancer (GC) are usually first diagnosed at an advanced stage due to the absence of obvious symptoms at an early GC (EGC) stage. Therefore, it is necessary to identify an effective screening method to detect precursor lesions of GC (PLGC) and EGC to increase the 5-year survival rate of patients. Cell-free RNA, as a biomarker, has shown potential in early diagnosis, personalised treatment, and prognosis of cancer. In this study, six RNAs (CEBPA-AS1, INHBA-AS1, AK001058, UCA1, PPBP, and RGS18) were analysed via real-time quantitative polymerase chain reaction (RT-qPCR) using the plasma of patients with EGC and PLGC to identify diagnostic biomarkers. The receiver operating characteristic (ROC) curve analysis was used to evaluate the diagnostic accuracy. Among the six RNAs, four lncRNAs (CEBPA-AS1, INHBA-AS1, AK001058, and UCA1) were upregulated and two mRNAs (PPBP and RGS18) were downregulated in the plasma of patients with PLGC and EGC. According to the findings of the ROC analysis, the four-RNA combination of INHBA-AS1, AK001058, UCA1, and RGS18 had the highest area under the curve (AUC) value for determining risk of GC in patients with PLGC and the six-RNA combination including CEBPA-AS1, INHBA-AS1, AK001058, UCA1, PPBP, and RGS18 had the highest AUC value for determining the risk of GC in patients with EGC. The results suggest the potential usefulness of noninvasive biomarkers for the molecular diagnosis of GC at earlier stages.
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Affiliation(s)
- Lu Chen
- 1Department of Experimental Hematology and Biochemistry, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Changhui Ge
- 1Department of Experimental Hematology and Biochemistry, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Xiuxue Feng
- 2Division of Gastroenterology, The First Medical Center of Chinese PLA General Hospital, Beijing 1000853, China
| | - Hanjiang Fu
- 1Department of Experimental Hematology and Biochemistry, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Shasha Wang
- 2Division of Gastroenterology, The First Medical Center of Chinese PLA General Hospital, Beijing 1000853, China
| | - Jie Zhu
- 1Department of Experimental Hematology and Biochemistry, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Enqiang Linghu
- 2Division of Gastroenterology, The First Medical Center of Chinese PLA General Hospital, Beijing 1000853, China
| | - Xiaofei Zheng
- 1Department of Experimental Hematology and Biochemistry, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing 100850, China
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Wu SC, Chi SY, Rau CS, Kuo PJ, Huang LH, Wu YC, Wu CJ, Lin HP, Hsieh CH. Identification of circulating biomarkers for differentiating patients with papillary thyroid cancers from benign thyroid tumors. J Endocrinol Invest 2021; 44:2375-2386. [PMID: 33646556 DOI: 10.1007/s40618-021-01543-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 02/25/2021] [Indexed: 11/26/2022]
Abstract
BACKGROUND This study aimed to identify the potential circulating biomarkers of protein, mRNAs, and long non-coding RNAs (lncRNAs) to differentiate the papillary thyroid cancers from benign thyroid tumors. METHODS The study population of 100 patients was classified into identification (10 patients with papillary thyroid cancers and 10 patients with benign thyroid tumors) and validation groups (45 patients with papillary thyroid cancers and 35 patients with benign thyroid tumors). The Sengenics Immunome Protein Array-combined data mining approach using the Open Targets Platform was used to identify the putative protein biomarkers, and their expression validated using the enzyme-linked immunosorbent assay. Next-generation sequencing by Illumina HiSeq was used for the detection of dysregulated mRNAs and lncRNAs. The website Timer v2.0 helped identify the putative mRNA biomarkers, which were significantly over-expressed in papillary thyroid cancers than in adjacent normal thyroid tissue. The mRNA and lncRNA biomarker expression was validated by a real-time polymerase chain reaction. RESULTS Although putative protein and mRNA biomarkers have been identified, their serum expression could not be confirmed in the validation cohorts. In addition, seven lncRNAs (TCONS_00516490, TCONS_00336559, TCONS_00311568, TCONS_00321917, TCONS_00336522, TCONS_00282483, and TCONS_00494326) were identified and validated as significantly downregulated in patients with papillary thyroid cancers compared to those with benign thyroid tumors. These seven lncRNAs showed moderate accuracy based on the area under the curve (AUC = 0.736) of receiver operating characteristic in predicting the occurrence of papillary thyroid cancers. CONCLUSIONS We identified seven downregulated circulating lncRNAs with the potential for predicting the occurrence of papillary thyroid cancers.
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Affiliation(s)
- S-C Wu
- Department of Anesthesiology, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung City, Taiwan
| | - S-Y Chi
- Department of General Surgery, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung City, Taiwan
| | - C-S Rau
- Department of Neurosurgery, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung City, Taiwan
| | - P-J Kuo
- Department of Plastic Surgery, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, No.123, Ta-Pei Road, Niao-Song District, Kaohsiung City 833, Taiwan
| | - L-H Huang
- Department of Plastic Surgery, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, No.123, Ta-Pei Road, Niao-Song District, Kaohsiung City 833, Taiwan
| | - Y-C Wu
- Department of Plastic Surgery, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, No.123, Ta-Pei Road, Niao-Song District, Kaohsiung City 833, Taiwan
| | - C-J Wu
- Department of Plastic Surgery, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, No.123, Ta-Pei Road, Niao-Song District, Kaohsiung City 833, Taiwan
| | - H-P Lin
- Department of Plastic Surgery, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, No.123, Ta-Pei Road, Niao-Song District, Kaohsiung City 833, Taiwan
| | - C-H Hsieh
- Department of Plastic Surgery, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, No.123, Ta-Pei Road, Niao-Song District, Kaohsiung City 833, Taiwan.
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Liu L, Pang H, He Q, Pan B, Sun X, Shan J, Wu L, Wu K, Yao X, Guo Y. A novel strategy to identify candidate diagnostic and prognostic biomarkers for gastric cancer. Cancer Cell Int 2021; 21:335. [PMID: 34215253 PMCID: PMC8254335 DOI: 10.1186/s12935-021-02007-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 06/03/2021] [Indexed: 02/08/2023] Open
Abstract
Background Gastric cancer (GC) is one of the most common cancer worldwide. It is essential to identify non-invasive diagnostic and prognostic biomarkers of GC. The aim of the present study was to screen candidate biomarkers associated with the pathogenesis and prognosis of GC by a novel strategy. Methods The expression level of gene higher in cancer than in adjacent non-cancer tissue was defined as “positive”, and the top 5% genes with “positive rate” were filtered out as candidate diagnostic biomarkers in three Gene Expression Omnibus (GEO) datasets. Further, a prognostic risk model was constructed by multivariate Cox regression analysis in GEO dataset and validated in The Cancer Genome Atlas (TCGA). The expression level of candidate biomarkers was determined in serum and serum-derived exosomes of GC patients. Moreover, the effect of biomarkers in exosomes on migration of GC cells was analyzed by transwell assay. Results Ten candidate biomarkers (AGT, SERPINH1, WNT2, LIPG, PLAU, COL1A1, MMP7, MXRA5, CXCL1 and COL11A1) were identified with efficient diagnostic value in GC. A prognostic gene signature consisted of AGT, SERPINH1 and MMP7 was constructed and showed a good performance in predicting overall survivals in TCGA. Consistently, serum levels of the three biomarkers also showed high sensitivity and specificity in distinguishing GC patients from controls. In addition, the expression level of the three biomarkers were associated with malignant degree and decreased after surgery in GC patients. Moreover, the expression level of AGT and MMP7 in exosomes correlated positively with serum level. The exosomes derived from serum of GC patients can promote migration of SGC‐7901 cells. After neutralized the expression level of three proteins in exosomes with antibodies, the migration of GC cells was obviously suppressed. Conclusions Our findings provided a novel strategy to identify diagnostic biomarkers based on public datasets, and suggested that the three-gene signature was a candidate diagnostic and prognostic biomarker for patients with GC.
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Affiliation(s)
- Lei Liu
- Medical Research Center, The Third People's Hospital of Chengdu, The Affiliated Hospital of Southwest Jiaotong University, 82 Qinglong Road, Chengdu, 610031, Sichuan, China.
| | - Honglin Pang
- College of Medicine, Southwest Jiaotong University, Chengdu, 610036, Sichuan, China
| | - Qiao He
- Department of Clinical Laboratory, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610031, Sichuan, China
| | - Biran Pan
- Assisted Reproductive Center, The Maternal and Child Health Hospital of Qinzhou, Qinzhou, 535000, Sichuan, China
| | - Xiaobin Sun
- Department of Gastroenterology, The Third People's Hospital of Chengdu, The Affiliated Hospital of Southwest Jiaotong University, Chengdu, 610031, Sichuan, China
| | - Jing Shan
- Department of Gastroenterology, The Third People's Hospital of Chengdu, The Affiliated Hospital of Southwest Jiaotong University, Chengdu, 610031, Sichuan, China
| | - Liping Wu
- Department of Gastroenterology, The Third People's Hospital of Chengdu, The Affiliated Hospital of Southwest Jiaotong University, Chengdu, 610031, Sichuan, China
| | - Kaiwen Wu
- College of Medicine, Southwest Jiaotong University, Chengdu, 610036, Sichuan, China
| | - Xue Yao
- College of Medicine, Southwest Jiaotong University, Chengdu, 610036, Sichuan, China
| | - Yuanbiao Guo
- Medical Research Center, The Third People's Hospital of Chengdu, The Affiliated Hospital of Southwest Jiaotong University, 82 Qinglong Road, Chengdu, 610031, Sichuan, China.
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Leja M, Linē A. Early detection of gastric cancer beyond endoscopy - new methods. Best Pract Res Clin Gastroenterol 2021; 50-51:101731. [PMID: 33975677 DOI: 10.1016/j.bpg.2021.101731] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 02/08/2021] [Indexed: 01/31/2023]
Abstract
Early detection of gastric cancer is remaining a challenge. This review summarizes current knowledge on non-invasive methods that could be used for the purpose. The role of traditional cancer markers such as CEA, CA 72-4, CA 19-9, CA 15-3, and CA 12-5 lies mainly in therapy monitoring than early detection. Most extensive studied biomarkers (pepsinogens, ABC method) are aiming at the detection of precancerous lesions with modest sensitivity for cancer. Tests based on the detection of cancer-specific methylation patterns (PanSeer), circulating proteins and mutations in circulating tumour DNA (CancerSEEK), as well as miRNA panels have demonstrated promising results bringing those closer to practice. More extensive research is required before tests based on the detection of circulating tumour cells, extracellular vesicles and cell-free RNA could reach the practice. Detection of volatile organic compounds in the human breath is a promising development; sensor technologies for this purpose could be very attractive in screening settings.
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Affiliation(s)
- Mārcis Leja
- Institute of Clinical and Preventive Medicine, University of Latvia, 1 Gailezera iela iela, LV1079, Riga, Latvia.
| | - Aija Linē
- Latvian Biomedical Research and Study Centre, Latvia.
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Wang J, Pan W. The Biological Role of the Collagen Alpha-3 (VI) Chain and Its Cleaved C5 Domain Fragment Endotrophin in Cancer. Onco Targets Ther 2020; 13:5779-5793. [PMID: 32606789 PMCID: PMC7319802 DOI: 10.2147/ott.s256654] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 05/26/2020] [Indexed: 12/13/2022] Open
Abstract
The collagen alpha-3 (VI) chain encoded by the gene COL6A3 is one of the 3 subunits of collagen VI which is a microfibrillar component of the extracellular matrix and is essential for the stable assembly process of collagen VI. The collagen alpha-3 (VI) chain and the cleaved C5 domain fragment, called endotrophin, are highly expressed in a variety of cancers and play a crucial role in cancer progression. The biological functions of endotrophin in tumors can be driven by adipocytes. Studies have demonstrated that endotrophin can directly affect the malignancy of cancer cells through TGF-β-dependent mechanisms, inducing epithelial–mesenchymal transition and fibrosis of the tumor microenvironment. In addition, endotrophin can also recruit macrophages and endothelial cells through chemotaxis to regulate the tumor microenvironment and ultimately promote tumor inflammation and angiogenesis. Furthermore, COL6A3 and endotrophin serve as novel diagnostic and prognostic biomarkers in cancer and contribute to clinical therapeutic applications in the future. In summary, in this review, we discuss the importance of the collagen alpha-3 (VI) chain and endotrophin in cancer progression, the future clinical applications of endotrophin and the remaining challenges in this field.
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Affiliation(s)
- Jingya Wang
- Department of Gastroenterology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, People's Republic of China
| | - Wensheng Pan
- Department of Gastroenterology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, People's Republic of China
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SERPINH1 regulates EMT and gastric cancer metastasis via the Wnt/β-catenin signaling pathway. Aging (Albany NY) 2020; 12:3574-3593. [PMID: 32091407 PMCID: PMC7066881 DOI: 10.18632/aging.102831] [Citation(s) in RCA: 124] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 01/22/2020] [Indexed: 12/12/2022]
Abstract
In this study, we investigated the role of SERPINH1 in gastric cancer (GC) progression. GC patient tissues show significantly higher SERPINH1 mRNA and protein levels than normal gastric mucosal tissues. GC patients with high SERPINH1 expression are associated with lymph node metastasis and poor prognosis. SERPINH1 mRNA levels negatively correlate with E-cadherin mRNA levels and positively correlate with levels of N-cadherin, MMP2, and MMP9 mRNA levels. This suggests SERPINH1 regulates epithelial to mesenchymal transition (EMT). SERPINH1 expression was significantly higher in the HGC-27, AGS, MGC-803, and SGC-7901 GC cell lines than in the GES-1 normal gastric mucosal cell line. In SERPINH1-silenced SGC-7901 cells, survival, colony formation, migration and invasion were all reduced, whereas they were all enhanced in SERPINH1-overexpressing MGC-803 cells. Levels of WNT/β-catenin signaling pathway proteins, including β-catenin, Wnt2, GSK-3β, p-GSK-3β, NF-κB P65, Snail1, Slug and TWIST, were all reduced in SERPINH1-silenced SGC-7901 cells, and increased in the SERPINH1-overexpressing MGC-803 cells. Inhibition of SERPINH1 protein using Co1003 significantly decreased survival, invasion, and migration of GC cells. SERPINH1 thus appears to regulate EMT and GC progression via the Wnt/β-catenin pathway, making SERPINH1 a potential prognostic biomarker and therapeutic target in GC patients.
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Wang YR, Meng LB, Su F, Qiu Y, Shi JH, Xu X, Luo QF. Insights regarding novel biomarkers and the pathogenesis of primary colorectal carcinoma based on bioinformatic analysis. Comput Biol Chem 2020; 85:107229. [PMID: 32058945 DOI: 10.1016/j.compbiolchem.2020.107229] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 01/29/2020] [Accepted: 02/02/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND Biomarkers are important in the study of tumor processes for early detection and precise treatment. The biomarkers that have been previously detected are not useful for clinical application for primary colorectal carcinoma (PCRC). The aim of this study was to explore clinically valuable biomarkers of PCRC based on integrated bioinformatic analysis. MATERIAL AND METHODS Gene expression data were acquired from the GSE41258 dataset, and the differentially expressed genes were determined between PCRC and normal colorectal samples. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses were implemented via Gene Set Enrichment Analysis. A protein-protein interaction (PPI) network was constructed. The significant modules and hub genes were screened and identified in the PPI network. RESULTS A total of 202 DEGs were identified, including 58 upregulated and 144 downregulated genes in PCRC samples compared to those in normal colorectal samples. Enrichment analysis demonstrated that the gene sets enriched in PCRC were significantly related to bicarbonate transport, regulation of sodium ion transport, potassium ion homeostasis, regulation of telomere maintenance, and other processes. A total of 10 hub genes was identified by cytoHubba: PYY, CXCL3, CXCL11, CXCL8, CXCL12, CCL20, MMP3, P2RY14, NPY1R, and CXCL1. CONCLUSION The hub genes, such as NPY1R, P2RY14, and CXCL12, and the electrolyte disequilibrium resulting from the differential expression of genes, especially bicarbonate imbalance, may provide novel insights and evidence for the future diagnosis and targeted therapy of PCRC.
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Affiliation(s)
- Yi-Ran Wang
- Department of Gastroenterology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China.
| | - Ling-Bing Meng
- Department of Neurology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China.
| | - Fei Su
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China.
| | - Yong Qiu
- Department of Anesthesia, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China.
| | - Ji-Hua Shi
- Department of Gastroenterology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China.
| | - Xue Xu
- Department of Gastroenterology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China.
| | - Qing-Feng Luo
- Department of Gastroenterology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China.
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