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Bai Z, Yan C, Nie Y, Zeng Q, Xu L, Wang S, Chang D. Glucose metabolism-based signature predicts prognosis and immunotherapy strategies for colon adenocarcinoma. J Gene Med 2024; 26:e3620. [PMID: 37973153 DOI: 10.1002/jgm.3620] [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: 08/30/2023] [Revised: 09/25/2023] [Accepted: 10/09/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND The global prevalence and metastasis rates of colon adenocarcinoma (COAD) are high, and therapeutic success is limited. Although previous research has primarily explored changes in gene phenotypes, the incidence rate of COAD remains unchanged. Metabolic reprogramming is a crucial aspect of cancer research and therapy. The present study aims to develop cluster and polygenic risk prediction models for COAD based on glucose metabolism pathways to assess the survival status of patients and potentially identify novel immunotherapy strategies and related therapeutic targets. METHODS COAD-specific data (including clinicopathological information and gene expression profiles) were sourced from The Cancer Genome Atlas (TCGA) and two Gene Expression Omnibus (GEO) datasets (GSE33113 and GSE39582). Gene sets related to glucose metabolism were obtained from the MSigDB database. The Gene Set Variation Analysis (GSVA) method was utilized to calculate pathway scores for glucose metabolism. The hclust function in R, part of the Pheatmap package, was used to establish a clustering system. The mutation characteristics of identified clusters were assessed via MOVICS software, and differentially expressed genes (DEGs) were filtered using limma software. Signature analysis was performed using the least absolute shrinkage and selection operator (LASSO) method. Survival curves, survival receiver operating characteristic (ROC) curves and multivariate Cox regression were analyzed to assess the efficacy and accuracy of the signature for prognostic prediction. The pRRophetic program was employed to predict drug sensitivity, with data sourced from the Genomics of Drug Sensitivity in Cancer (GDSC) database. RESULTS Four COAD subgroups (i.e., C1, C2, C3 and C4) were identified based on glucose metabolism, with the C4 group having higher survival rates. These four clusters were bifurcated into a new Clust2 system (C1 + C2 + C3 and C4). In total, 2175 DEGs were obtained (C1 + C2 + C3 vs. C4), from which 139 prognosis-related genes were identified. ROC curves predicting 1-, 3- and 5-year survival based on a signature containing nine genes showed an area under the curve greater than 0.7. Meanwhile, the study also found this feature to be an important predictor of prognosis in COAD and accordingly assessed the risk score, with higher risk scores being associated with a worse prognosis. The high-risk and low-risk groups responded differently to immunotherapy and chemotherapeutic agents, and there were differences in functional enrichment pathways. CONCLUSIONS This unique signature based on glucose metabolism may potentially provide a basis for predicting patient prognosis, biological characteristics and more effective immunotherapy strategies for COAD.
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Affiliation(s)
- Zilong Bai
- Department of Surgical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shanxi, China
| | - Chunyu Yan
- Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shanxi, China
| | - Yuanhua Nie
- Department of Surgical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shanxi, China
| | - Qingnuo Zeng
- Department of Surgical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shanxi, China
| | - Longwen Xu
- Department of Surgical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shanxi, China
| | - Shilong Wang
- Department of Surgical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shanxi, China
| | - Dongmin Chang
- Department of Surgical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shanxi, China
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Tallgren A, Kager L, O’Grady G, Tuominen H, Körkkö J, Kuismin O, Feucht M, Wilson C, Behunova J, England E, Kurki MI, Palotie A, Hallman M, Kaarteenaho R, Laccone F, Boztug K, Hinttala R, Uusimaa J. Novel patients with NHLRC2 variants expand the phenotypic spectrum of FINCA disease. Front Neurosci 2023; 17:1123327. [PMID: 37179546 PMCID: PMC10173879 DOI: 10.3389/fnins.2023.1123327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 02/08/2023] [Indexed: 05/15/2023] Open
Abstract
Purpose FINCA disease (Fibrosis, Neurodegeneration and Cerebral Angiomatosis, OMIM 618278) is an infantile-onset neurodevelopmental and multiorgan disease. Since our initial report in 2018, additional patients have been described. FINCA is the first human disease caused by recessive variants in the highly conserved NHLRC2 gene. Our previous studies have shown that Nhlrc2-null mouse embryos die during gastrulation, indicating the essential role of the protein in embryonic development. Defect in NHLRC2 leads to cerebral neurodegeneration and severe pulmonary, hepatic and cardiac fibrosis. Despite having a structure suggestive of an enzymatic role and the clinical importance of NHLRC2 in multiple organs, the specific physiological role of the protein is unknown. Methods The clinical histories of five novel FINCA patients diagnosed with whole exome sequencing were reviewed. Segregation analysis of the biallelic, potentially pathogenic NHLRC2 variants was performed using Sanger sequencing. Studies on neuropathology and NHLRC2 expression in different brain regions were performed on autopsy samples of three previously described deceased FINCA patients. Results One patient was homozygous for the pathogenic variant c.442G > T, while the other four were compound heterozygous for this variant and two other pathogenic NHLRC2 gene variants. All five patients presented with multiorgan dysfunction with neurodevelopmental delay, recurrent infections and macrocytic anemia as key features. Interstitial lung disease was pronounced in infancy but often stabilized. Autopsy samples revealed widespread, albeit at a lower intensity than the control, NHLRC2 expression in the brain. Conclusion This report expands on the characteristic clinical features of FINCA disease. Presentation is typically in infancy, and although patients can live to late adulthood, the key clinical and histopathological features are fibrosis, infection susceptibility/immunodeficiency/intellectual disability, neurodevelopmental disorder/neurodegeneration and chronic anemia/cerebral angiomatosis (hence the acronym FINCA) that enable an early diagnosis confirmed by genetic investigations.
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Affiliation(s)
- Antti Tallgren
- Research Unit of Clinical Medicine and Medical Research Center, Oulu University Hospital, University of Oulu, Oulu, Finland
| | - Leo Kager
- St. Anna Children’s Hospital, Vienna, Austria
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
- St. Anna Children’s Cancer Research Institute (CCRI), Vienna, Austria
| | - Gina O’Grady
- Paediatric Neuroservices, Starship Children’s Health, Te Whatu Ora Health New Zealand, Auckland, New Zealand
| | - Hannu Tuominen
- Department of Pathology, Oulu University Hospital, University of Oulu, Oulu, Finland
| | - Jarmo Körkkö
- Center for Intellectual Disability Care, Oulu University Hospital, Oulu, Finland
| | - Outi Kuismin
- Research Unit of Clinical Medicine and Medical Research Center, Oulu University Hospital, University of Oulu, Oulu, Finland
- Department of Clinical Genetics, Oulu University Hospital, Oulu, Finland
| | - Martha Feucht
- Department of Paediatrics, Center for Rare and Complex Epilepsies, Medical University of Vienna, Vienna, Austria
| | - Callum Wilson
- National Metabolic Service, Auckland City Hospital, Auckland, New Zealand
| | - Jana Behunova
- Department of Medical Genetics, Medical University of Vienna, Vienna, Austria
| | - Eleina England
- Mendelian Genomics, Programme in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Mitja I. Kurki
- Programme in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, United States
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, United States
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Aarno Palotie
- Programme in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, United States
- Psychiatric and Neurodevelopmental Genetics Unit, Department of Psychiatry, Massachusetts General Hospital, Boston, MA, United States
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, United States
- Department of Neurology, Massachusetts General Hospital, Boston, MA, United States
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Mikko Hallman
- Research Unit of Clinical Medicine and Medical Research Center, Oulu University Hospital, University of Oulu, Oulu, Finland
- Clinic for Children and Adolescents, Oulu University Hospital, Oulu, Finland
| | - Riitta Kaarteenaho
- Research Unit of Internal Medicine, University of Oulu, Oulu, Finland
- Center of Internal Medicine and Respiratory Medicine and Medical Research Center Oulu, Oulu University Hospital, Oulu, Finland
| | - Franco Laccone
- Department of Medical Genetics, Medical University of Vienna, Vienna, Austria
| | - Kaan Boztug
- St. Anna Children’s Hospital, Vienna, Austria
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
- St. Anna Children’s Cancer Research Institute (CCRI), Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Reetta Hinttala
- Research Unit of Clinical Medicine and Medical Research Center, Oulu University Hospital, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Johanna Uusimaa
- Research Unit of Clinical Medicine and Medical Research Center, Oulu University Hospital, University of Oulu, Oulu, Finland
- Clinic for Children and Adolescents, Oulu University Hospital, Oulu, Finland
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Li X, Kang K, Shen L, Shen L, Zhou Y. Integrative Analysis of the Predictive Value of Perilipin Family on Clinical Significance, Prognosis and Immunotherapy of Glioma. Biomedicines 2023; 11:biomedicines11041009. [PMID: 37189627 DOI: 10.3390/biomedicines11041009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/06/2023] [Accepted: 03/07/2023] [Indexed: 03/29/2023] Open
Abstract
Gliomas are common tumors of the central nervous system. The PLINs family is widely involved in the regulation of lipid metabolism and has been associated with the development and invasive metastasis of various malignancies. However, the biological role of the PLINs family in gliomas is still unclear. TIMER and UALCAN were used to assess PLINs mRNA expression in gliomas. “Survminer” and “Survival” were used to evaluate the connection between PLINs expression and glioma patients’ survival. cBioPortal was applied to assess PLINs’ genetic alterations in glioblastoma multiforme (GBM) and low-grade glioma (LGG). The correlation of PLINs expression with tumor immune cells was analyzed by TIMER. The expressions of PLIN1, PLIN4, and PLIN5 were decreased in GBM compared to normal tissues. However, PLIN2 and PLIN3 were significantly increased in GBM. Prognostic analysis showed that LGG patients with high PLIN1 expression had better overall survival (OS), and high expression of PLIN2/3/4/5 was associated with unfavorable OS. We further determined that the expression of PLINs members in gliomas was strongly related to tumor immune cells and immune checkpoint-associated genes. PLINS may be potential biomarkers for regulating the tumor microenvironment and predicting the efficacy of immunotherapy. In addition, we determined that PLIN1 may affect glioma patients’ therapeutic sensitivity to temozolomide. Our results demonstrated the biological significance and clinical values of PLINs in gliomas and provide a basis for future in-depth exploration of the specific mechanisms of each member of PLINs in gliomas.
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Feng J, Tang X, Song L, Zhou Z, Jiang Y, Huang Y. A telomerase regulation-related lncRNA signature predicts prognosis and immunotherapy response for gastric cancer. J Cancer Res Clin Oncol 2023; 149:135-146. [PMID: 36333566 DOI: 10.1007/s00432-022-04456-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 10/27/2022] [Indexed: 11/07/2022]
Abstract
BACKGROUND Telomeres are involved in the development and progression of gastric cancer (GC). However, the association of telomerase regulation-related lncRNAs with prognosis and immunotherapy responsiveness in gastric cancer is unclear. METHODS This study systematically evaluated the relationship between lncRNAs co-expressed with 67 telomerase regulatory genes and gastric cancer prognosis. The risk scores of the samples were calculated based on telomerase regulation-related lncRNAs with prognostic value, and the samples were classified into high-/low-risk groups. The prognostic value of risk groups was then evaluated, a GC prognostic prediction model based on risk groups and clinical characteristics was established, and the prediction accuracy of the model was clarified by receiving operating characteristic (ROC) curves and calibration curves. Finally, the value of risk grouping in GC immunotherapy sensitivity was predicted by comparing MSI status and tumor mutation load between the high- and low-risk groups. RESULTS We identified 13 lncRNAs with prognostic value co-expressed with telomerase regulatory genes and observed that the prognosis of the low-risk group was significantly better than that of the high-risk group. Meanwhile, a GC overall survival (OS) prediction model based on risk grouping and clinical characteristics was developed, and ROC curves and calibration curves confirmed the good predictive ability of the model. In addition, the low-risk group exhibited a higher tumor mutation load and MSI-H, suggesting a possible benefit of immunotherapy. CONCLUSION We found that telomerase regulation-related lncRNAs have prognostic value in GC patients and contribute to the exploration of more effective immunotherapeutic strategies.
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Affiliation(s)
- Jinggao Feng
- Department of Gastrointestinal and Anorectal Surgery, The Central Hospital of Yongzhou, No. 151, Xiaoshui West Road, Lingling District, Yongzhou, 425100, Hunan Province, China.
| | - Xiayu Tang
- Department of Gastrointestinal and Anorectal Surgery, The Central Hospital of Yongzhou, No. 151, Xiaoshui West Road, Lingling District, Yongzhou, 425100, Hunan Province, China
| | - Liusong Song
- Department of Gastrointestinal and Anorectal Surgery, The Central Hospital of Yongzhou, No. 151, Xiaoshui West Road, Lingling District, Yongzhou, 425100, Hunan Province, China
| | - Zhipeng Zhou
- Department of Gastrointestinal and Anorectal Surgery, The Central Hospital of Yongzhou, No. 151, Xiaoshui West Road, Lingling District, Yongzhou, 425100, Hunan Province, China
| | - Yuan Jiang
- Department of Gastrointestinal and Anorectal Surgery, The Central Hospital of Yongzhou, No. 151, Xiaoshui West Road, Lingling District, Yongzhou, 425100, Hunan Province, China
| | - Yao Huang
- Department of Gastrointestinal and Anorectal Surgery, The Central Hospital of Yongzhou, No. 151, Xiaoshui West Road, Lingling District, Yongzhou, 425100, Hunan Province, China
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Kreus M, Lehtonen S, Hinttala R, Salonen J, Porvari K, Kaarteenaho R. NHLRC2 expression is increased in idiopathic pulmonary fibrosis. Respir Res 2022; 23:206. [PMID: 35964085 PMCID: PMC9375339 DOI: 10.1186/s12931-022-02129-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 07/29/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Variants of NHL repeat-containing protein 2 (NHLRC2) have been associated with severe fibrotic interstitial lung disease in early childhood and NHLRC2 has been listed as a differentially expressed gene between rapidly and slowly progressing idiopathic pulmonary fibrosis (IPF) patients. However, its cell type-specific localization in human lung tissue is unknown. The aim of this study was to evaluate NHLRC2 mRNA and protein expression in different cell types of lung tissue samples and to investigate the effect of transforming growth factor (TGF)-β1 exposure on NHLRC2 expression in vitro. METHODS The NHLRC2 expression in lung tissue samples was studied by immunohistochemistry (50 IPF, 10 controls) and mRNA in situ hybridization (8 IPF, 3 controls). The immunohistochemical NHLRC2 expression was quantified with image analysis software and associated with the clinical and smoking data of the patients. NHLRC2 expression levels in primary stromal and small airway epithelial cell lines after exposure to TGF-β1 was measured by quantitative reverse transcription polymerase chain reaction and Western blot analysis. RESULTS NHLRC2 expression was detected especially in bronchiolar epithelial cells, type II pneumocytes and macrophages in normal lung. In the lungs of IPF patients, NHLRC2 was mainly expressed in hyperplastic alveolar epithelial cells lining fibroblast foci and honeycombs. NHLRC2 expression assessed by image analysis was higher in IPF compared to controls (p < 0.001). Ever-smokers had more prominent NHLRC2 staining than non-smokers (p = 0.037) among IPF patients. TGF-β1 exposure did not influence NHLRC2 levels in lung cell lines. CONCLUSIONS NHLRC2 expression was higher in IPF compared to controls being widely expressed in type II pneumocytes, macrophages, bronchiolar epithelium, and hyperplastic alveolar epithelium. Additionally, its expression was not regulated by the exposure to TGF-β1 in vitro. Further studies are needed to clarify the role of NHLRC2 in IPF.
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Affiliation(s)
- Mervi Kreus
- Research Unit of Internal Medicine, University of Oulu, Oulu, Finland. .,Center of Internal Medicine and Respiratory Medicine and Medical Research Center Oulu, Oulu University Hospital, Oulu, Finland.
| | - Siri Lehtonen
- Department of Obstetrics and Gynecology and Medical Research Center Oulu, Oulu University Hospital, Oulu, Finland.,Medical Research Center Oulu and PEDEGO Research Unit, University of Oulu and Oulu University Hospital, Oulu, Finland
| | - Reetta Hinttala
- Medical Research Center Oulu and PEDEGO Research Unit, University of Oulu and Oulu University Hospital, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Johanna Salonen
- Research Unit of Internal Medicine, University of Oulu, Oulu, Finland.,Center of Internal Medicine and Respiratory Medicine and Medical Research Center Oulu, Oulu University Hospital, Oulu, Finland
| | - Katja Porvari
- Research Unit of Internal Medicine, University of Oulu, Oulu, Finland.,Center of Internal Medicine and Respiratory Medicine and Medical Research Center Oulu, Oulu University Hospital, Oulu, Finland.,Department of Forensic Medicine, University of Oulu, Oulu, Finland
| | - Riitta Kaarteenaho
- Research Unit of Internal Medicine, University of Oulu, Oulu, Finland.,Center of Internal Medicine and Respiratory Medicine and Medical Research Center Oulu, Oulu University Hospital, Oulu, Finland
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Nooreldeen R, Bach H. Current and Future Development in Lung Cancer Diagnosis. Int J Mol Sci 2021; 22:8661. [PMID: 34445366 PMCID: PMC8395394 DOI: 10.3390/ijms22168661] [Citation(s) in RCA: 276] [Impact Index Per Article: 92.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/05/2021] [Accepted: 08/10/2021] [Indexed: 12/16/2022] Open
Abstract
Lung cancer is the leading cause of cancer-related deaths in North America and other developed countries. One of the reasons lung cancer is at the top of the list is that it is often not diagnosed until the cancer is at an advanced stage. Thus, the earliest diagnosis of lung cancer is crucial, especially in screening high-risk populations, such as smokers, exposure to fumes, oil fields, toxic occupational places, etc. Based on the current knowledge, it looks that there is an urgent need to identify novel biomarkers. The current diagnosis of lung cancer includes different types of imaging complemented with pathological assessment of biopsies, but these techniques can still not detect early lung cancer developments. In this review, we described the advantages and disadvantages of current methods used in diagnosing lung cancer, and we provide an analysis of the potential use of body fluids as carriers of biomarkers as predictors of cancer development and progression.
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Affiliation(s)
| | - Horacio Bach
- Division of Infectious Diseases, Faculty of Medicine, The University of British Columbia, Vancouver, BC V6H 3Z6, Canada;
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Mass Sanchez PB, Krizanac M, Weiskirchen R, Asimakopoulos A. Understanding the Role of Perilipin 5 in Non-Alcoholic Fatty Liver Disease and Its Role in Hepatocellular Carcinoma: A Review of Novel Insights. Int J Mol Sci 2021; 22:5284. [PMID: 34067931 PMCID: PMC8156377 DOI: 10.3390/ijms22105284] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 05/07/2021] [Accepted: 05/16/2021] [Indexed: 12/24/2022] Open
Abstract
Consumption of high-calorie foods, such as diets rich in fats, is an important factor leading to the development of steatohepatitis. Several studies have suggested how lipid accumulation creates a lipotoxic microenvironment for cells, leading cells to deregulate their transcriptional and translational activity. This deregulation induces the development of liver diseases such as non-alcoholic fatty liver disease (NAFLD) and subsequently also the appearance of hepatocellular carcinoma (HCC) which is one of the deadliest types of cancers worldwide. Understanding its pathology and studying new biomarkers with better specificity in predicting disease prognosis can help in the personalized treatment of the disease. In this setting, understanding the link between NAFLD and HCC progression, the differentiation of each stage in between as well as the mechanisms underlying this process, are vital for development of new treatments and in exploring new therapeutic targets. Perilipins are a family of five closely related proteins expressed on the surface of lipid droplets (LD) in several tissues acting in several pathways involved in lipid metabolism. Recent studies have shown that Plin5 depletion acts protectively in the pathogenesis of liver injury underpinning the importance of pathways associated with PLIN5. PLIN5 expression is involved in pro-inflammatory cytokine regulation and mitochondrial damage, as well as endoplasmic reticulum (ER) stress, making it critical target of the NAFLD-HCC studies. The aim of this review is to dissect the recent findings and functions of PLIN5 in lipid metabolism, metabolic disorders, and NAFLD as well as the progression of NAFLD to HCC.
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Affiliation(s)
| | | | - Ralf Weiskirchen
- Institute of Molecular Pathobiochemistry, Experimental Gene Therapy and Clinical Chemistry (IFMPEGKC), RWTH University Hospital Aachen, D-52074 Aachen, Germany; (P.B.M.S.); (M.K.)
| | - Anastasia Asimakopoulos
- Institute of Molecular Pathobiochemistry, Experimental Gene Therapy and Clinical Chemistry (IFMPEGKC), RWTH University Hospital Aachen, D-52074 Aachen, Germany; (P.B.M.S.); (M.K.)
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Zhang X, Su L, Sun K. Expression status and prognostic value of the perilipin family of genes in breast cancer. Am J Transl Res 2021; 13:4450-4463. [PMID: 34150026 PMCID: PMC8205812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 03/10/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND The Perilipin (PLIN) family of genes were previously shown to be involved in the formation and degradation of Lipid Droplets (LDs). In addition, they may play important roles in the development and progression of breast cancer. However, the prognostic value of PLIN family members in breast cancer patients remains unclear. METHODS Mutations and copy number alterations of PLIN family genes in breast cancer were examined using the cBioportal for Cancer Genomics. In addition, the expression patterns of PLIN family genes were explored using the UCSC Xena online tool. Finally, the Kaplan-Meier Plotter was used to investigate the prognostic value of PLIN family genes in breast cancer. RESULTS The findings revealed a low frequency of genetic alterations and amplification was the most frequent change in the PLIN family genes. Additionally, there was an increase in the expression of Perilipin 3 (PLIN3) in breast cancer tissues compared to normal breast tissues. However, expression of the other genes in the PLIN family was significantly lower in breast cancer tissues compared to normal breast tissues. Moreover, there was an increase in the expression levels of Perilipin 1 (PLIN1), PLIN3, Perilipin 4 (PLIN4) and Perilipin 5 (PLIN5) in the luminal A and luminal B subgroups. On the other hand, the expression of Perilipin 2 (PLIN2) was elevated in the human epidermal growth factor receptor 2 (HER2) positive and basal-like subgroups. Furthermore, Kaplan-Meier Plotter analysis demonstrated that high expression of PLIN1 might predict a longer Overall Survival (OS) in patients with breast cancer while overexpression of PLIN2 indicated poor OS of breast cancer patients. CONCLUSION The findings from this study indicated that genes in the PLIN family were aberrantly expressed in breast cancer and may serve as novel therapeutic targets as well as prognostic biomarkers for the disease.
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Affiliation(s)
- Xuede Zhang
- Department of Hematology and Oncology, Beilun District People’s HospitalNingbo, Zhejiang, China
| | - Lei Su
- Department of Oncology, Zhangqiu District People’s HospitalJinan, Shandong, China
| | - Kai Sun
- Department of Oncology, Liuzhou People’s HospitalLiuzhou 545001, Guangxi Zhuang Autonomous Region, China
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Merid SK, Bustamante M, Standl M, Sunyer J, Heinrich J, Lemonnier N, Aguilar D, Antó JM, Bousquet J, Santa-Marina L, Lertxundi A, Bergström A, Kull I, Wheelock ÅM, Koppelman GH, Melén E, Gruzieva O. Integration of gene expression and DNA methylation identifies epigenetically controlled modules related to PM 2.5 exposure. ENVIRONMENT INTERNATIONAL 2021; 146:106248. [PMID: 33212358 DOI: 10.1016/j.envint.2020.106248] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 09/24/2020] [Accepted: 10/25/2020] [Indexed: 05/28/2023]
Abstract
Air pollution has been associated with adverse health effects across the life-course. Although underlying mechanisms are unclear, several studies suggested pollutant-induced changes in transcriptomic profiles. In this meta-analysis of transcriptome-wide association studies of 656 children and adolescents from three European cohorts participating in the MeDALL Consortium, we found two differentially expressed transcript clusters (FDR p < 0.05) associated with exposure to particulate matter < 2.5 µm in diameter (PM2.5) at birth, one of them mapping to the MIR1296 gene. Further, by integrating gene expression with DNA methylation using Functional Epigenetic Modules algorithms, we identified 9 and 6 modules in relation to PM2.5 exposure at birth and at current address, respectively (including NR1I2, MAPK6, TAF8 and SCARA3). In conclusion, PM2.5 exposure at birth was linked to differential gene expression in children and adolescents. Importantly, we identified several significant interactome hotspots of gene modules of relevance for complex diseases in relation to PM2.5 exposure.
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Affiliation(s)
- Simon Kebede Merid
- Department of Clinical Sciences and Education, Karolinska Institutet, Södersjukhuset, Stockholm, Sweden
| | - Mariona Bustamante
- ISGlobal, Institute for Global Health, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Marie Standl
- Institute of Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Jordi Sunyer
- ISGlobal, Institute for Global Health, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Madrid, Spain; IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Joachim Heinrich
- Institute and Clinic for Occupational, Social and Environmental Medicine, University Hospital, LMU Munich, Ziemssenstraße 1, 80336 Munich, Germany; Allergy and Lung Health Unit, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
| | - Nathanaël Lemonnier
- Institute for Advanced Biosciences, UGA-INSERM U1209-CNRS UMR5309, Allée des Alpes, France
| | - Daniel Aguilar
- Biomedical Research Networking Center in Hepatic and Digestive Diseases (CIBEREHD), Instituto de Salud Carlos III, Barcelona, Spain
| | - Josep Maria Antó
- ISGlobal, Institute for Global Health, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Madrid, Spain; IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Jean Bousquet
- Charité, Universitätsmedizin Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Comprehensive Allergy Center, Department of Dermatology and Allergy, Berlin, Germany; University Hospital, Montpellier, France; MACVIA-France, Montpellier, France
| | - Loreto Santa-Marina
- Health Research Institute-BIODONOSTIA, Basque Country, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Spain; Health Department of Basque Government, Sub-directorate of Public Health of Gipuzkoa, 20013 San Sebastian, Spain
| | - Aitana Lertxundi
- Health Research Institute-BIODONOSTIA, Basque Country, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Spain; Preventive Medicine and Public Health Department, University of Basque Country (UPV/EHU), Spain
| | - Anna Bergström
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden; Centre for Occupational and Environmental Medicine, Region Stockholm, Sweden
| | - Inger Kull
- Department of Clinical Sciences and Education, Karolinska Institutet, Södersjukhuset, Stockholm, Sweden; Sachs Children's Hospital, Stockholm, Sweden
| | - Åsa M Wheelock
- Respiratory Medicine Unit, Department of Medicine and Center for Molecular Medicine, Karolinska Institutet, Solna, Stockholm, Sweden
| | - Gerard H Koppelman
- University of Groningen, University Medical Center Groningen, Beatrix Children's Hospital, Department of Pediatric Pulmonology and Pediatric Allergology, Groningen, the Netherlands; University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, the Netherlands
| | - Erik Melén
- Department of Clinical Sciences and Education, Karolinska Institutet, Södersjukhuset, Stockholm, Sweden; Sachs Children's Hospital, Stockholm, Sweden
| | - Olena Gruzieva
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden; Centre for Occupational and Environmental Medicine, Region Stockholm, Sweden.
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10
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Zhang Y, Zhou H, Zhang M, Xing L, Yang C, Xia B, Lou G. Integrated analysis of a competing endogenous RNA network reveals an 11-lncRNA prognostic signature in ovarian cancer. Aging (Albany NY) 2020; 12:25153-25171. [PMID: 33223503 PMCID: PMC7803494 DOI: 10.18632/aging.104116] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 09/09/2020] [Indexed: 01/22/2023]
Abstract
Long noncoding RNA (lncRNA) can function as a competing endogenous RNA (ceRNA) involved in tumor initiation and progression. However, the prognostic roles of lncRNAs in the integrated analysis of the ceRNA network in ovarian cancer (OVC) are still lacking. This study aimed to identify lncRNAs associated with the prognosis of OVC. Differential expression analysis and WGCNA were used to screen OVC-specific RNAs. A lncRNA-miRNA-mRNA regulatory network consisting of 201 lncRNAs, 85 miRNA and 146 mRNAs was constructed, and functional enrichment and protein-protein network analyses were performed. Then, the OVC-specific RNAs were submitted to Cox regression analysis. Twelve differentially expressed lncRNAs and mRNAs were identified as significantly associated with OS of OVC patients. Meanwhile, 11 lncRNAs (including C4A-AS1, LINC02408, LINC00488) were established as prognostic risk formulas. The low-risk group had better OS and DFS than the high-risk group (P <0.01). Univariate and multivariate Cox regression analyses revealed the 11-lncRNA risk score as an independent prognostic factor. A prognostic nomogram was developed based on independent prognostic factors. Our data provide evidence that the 11-lncRNA signature could serve as an independent prognostic indicator. This study also suggests that these 11 lncRNAs potentially participate in the progression of OVC.
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Affiliation(s)
- Yongjian Zhang
- Department of Gynecology Oncology, Harbin Medical University Cancer Hospital, Harbin 150081, Heilongjiang Province, China
| | - Hu Zhou
- Department of Gynecology Oncology, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, Hefei 230001, Anhui Province, China
| | - Meiyin Zhang
- Department of Gynecology Oncology, Harbin Medical University Cancer Hospital, Harbin 150081, Heilongjiang Province, China
| | - Linan Xing
- Department of Gynecology Oncology, Harbin Medical University Cancer Hospital, Harbin 150081, Heilongjiang Province, China
| | - Chang Yang
- Department of Gynecology Oncology, Harbin Medical University Cancer Hospital, Harbin 150081, Heilongjiang Province, China
| | - Bairong Xia
- Department of Gynecology Oncology, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, Hefei 230001, Anhui Province, China
| | - Ge Lou
- Department of Gynecology Oncology, Harbin Medical University Cancer Hospital, Harbin 150081, Heilongjiang Province, China
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11
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Ye J, Liu H, Xu ZL, Zheng L, Liu RY. Identification of a multidimensional transcriptome prognostic signature for lung adenocarcinoma. J Clin Lab Anal 2019; 33:e22990. [PMID: 31402485 PMCID: PMC6868416 DOI: 10.1002/jcla.22990] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 07/05/2019] [Accepted: 07/06/2019] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Lung adenocarcinoma (LUAD) is one of the leading contributors to cancer-related deaths worldwide. The objective of the current study is to identify a multidimensional transcriptome prognostic signature by combining protein-coding gene (PCG) with long non-coding RNA (lncRNA) for patients with LUAD. METHODS We obtained LUAD PCG and lncRNA expression profile data from three datasets in the Gene Expression Omnibus database and conducted survival analyzes for these individuals. RESULTS We established a predictive model comprising the three PCGs (NHLRC2, PLIN5, GNAI3), and one lncRNA (AC087521.1). This model segregated patients with LUAD into low- and high-risk groups based on significant differences in survival in the training dataset (GSE31210, n = 226, log-rank test P < .001). Risk stratification of the model was subsequently validated in other two test datasets (GSE37745, n = 106, log-rank test P < .001; GSE30219, n = 85, log-rank test P = .006). Time-dependent receiver operating characteristic (timeROC) curve analysis demonstrated that the model correlated strongly with disease progression and outperformed pathological stage in terms of prognostic ability. Cox proportional hazards regression analysis revealed that the signature could serve as an independent predictor of clinical outcomes in patients with LUAD. CONCLUSIONS We describe a novel multidimensional transcriptome signature that can predict survival probabilities in patients with LUAD.
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Affiliation(s)
- Jing Ye
- First Affiliated Hospital, Anhui Medical University, Hefei, China.,Second Affiliated Hospital, Anhui Medical University, Hefei, China
| | - Hui Liu
- Second Affiliated Hospital, Anhui Medical University, Hefei, China
| | - Zhi-Li Xu
- Second Affiliated Hospital, Anhui Medical University, Hefei, China
| | - Ling Zheng
- Second Affiliated Hospital, Anhui Medical University, Hefei, China
| | - Rong-Yu Liu
- First Affiliated Hospital, Anhui Medical University, Hefei, China
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