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Liu G, He Y, Yin Z, Feng Z. An anoikis-related gene signature predicts prognosis, drug sensitivity, and immune microenvironment in cholangiocarcinoma. Heliyon 2024; 10:e32337. [PMID: 38947446 PMCID: PMC11214491 DOI: 10.1016/j.heliyon.2024.e32337] [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: 11/30/2023] [Revised: 05/31/2024] [Accepted: 06/02/2024] [Indexed: 07/02/2024] Open
Abstract
Background Cholangiocarcinoma is a malignant invasive biliary tract carcinoma with a poor prognosis. Anoikis-related genes are prognostic features of a variety of cancers. However, the value of prognostication and therapeutic effect of anoikis-related genes in cholangiocarcinoma have not been reported. The aim of this research was developing an ARGs signature associated with cholangiocarcinoma patients. Methods We introduced transcriptome data to discover genes that were differentially expressed in cholangiocarcinoma. Subsequently, WGCNA was utilized to screen critical module genes in reference to anoikis. The univariate Cox, Lasso regression and Kaplan-Meier survival were executed to build a prognostic signature. We further performed gene functional enrichment, immune microenvironment and immunotherapy analysis between two risk subgroups. Finally, the pRRophetic algorithm was applied to compare the half inhibitory concentration value of several drugs. Results A grand total of 1844 genes with differential expression related to the cholangiocarcinoma patients were identified. Furthermore, we obtained 2678 key module genes related to anoikis. Then, a prognostic signature was developed using the 6 prognostic genes (FXYD2, PCBD1, C1RL, GMNN, LAMA4 and HACL1). Independent prognostic analysis showed that risk score and alcohol could function as separate prognostic variables. We found cetain distinction in the immune microenvironment between the two risk subgroups. Moreover, immunotherapy evaluation showed that the anoikis-related gene signature could be applied as a therapy predictor. Finally, Chemotherapeutic drug sensitivity results showed that the low-risk group responded better to bosutinib, gefitinib, gemcitabine, and paclitaxel, while the high-risk group responded better to axitinib, cisplatin, and imatinib. Conclusion The prognostic signature comprised of FXYD2, PCBD1, C1RL, GMNN, LAMA4 and HACL1 based on anoikis-related genes was established, which provided theoretical basis and reference value for the research and treatment of cholangiocarcinoma.
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Affiliation(s)
- Guochao Liu
- Department of Minimally Invasive and Biliary Surgery, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Yujian He
- Department of Gastroenterology, The Second Hospital of Hebei Medical University, Hebei Key Laboratory of Gastroenterology, Hebei Institute of Gastroenterology, Shijiazhuang, China
| | - Zhaoqiang Yin
- Department of Minimally Invasive and Biliary Surgery, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Zhijie Feng
- Department of Gastroenterology, The Second Hospital of Hebei Medical University, Hebei Key Laboratory of Gastroenterology, Hebei Institute of Gastroenterology, Shijiazhuang, China
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Yang J, Shen L, Yang J, Qu Y, Gong C, Zhou F, Liu Y, Luo M, Zhao L. Complement and coagulation cascades are associated with prognosis and the immune microenvironment of lower-grade glioma. Transl Cancer Res 2024; 13:112-136. [PMID: 38410234 PMCID: PMC10894340 DOI: 10.21037/tcr-23-906] [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: 05/26/2023] [Accepted: 11/29/2023] [Indexed: 02/28/2024]
Abstract
Background Abnormal coagulation is a common feature of glioma. There is a strong correlation between coagulation and the complement system, named complement and coagulation cascades (CCC). However, the role of CCC genes in lower-grade glioma (LGG) remains unclear. This study aimed to investigate the role of CCC genes in LGG. Methods In total, 5,628 differential expressed genes were identified between 498 LGG tissues from The Cancer Genome Atlas (TCGA) and 207 normal brain tissues from Genotype-Tissue Expression Project (GTEx). Among them, 20 overlapped CCC genes were identified as differentially expressed CCC genes. Then, comprehensive bioinformatics analysis was used to investigate the role of CCC genes in LGG; 271 LGG tissues from the Chinese Glioma Genome Atlas (CGGA) were used as the validation dataset. Cell Counting Kit-8 (CCK8) proliferation assay, colony formation assay, and wound healing assay were conducted to explore the anti-glioma effect of the sensitive drugs we predicted. Results We constructed a risk signature consisting of six CCC genes, including F2R, SERPINA1, TFPI, C1QC, C2, and C3AR1. The CCC gene-based risk signature could accurately predict the prognosis of patients with LGG. In addition, we found that the JAK-STAT, NOD-like receptor, Notch, PI3K-Akt, and Rap1 signaling pathways might be activated and had crosstalk with CCC in the high-risk group. Our findings analyses demonstrated that samples in high- and low-risk groups had different immune landscapes. Moreover, patients in the high-risk group might have greater resistance to immunotherapy. We validated the accuracy of the risk signature in predicting immunotherapy response in two public immunotherapy cohorts, GSE135222 and GSE78220. By means of oncoPredict, MG-132, BMS-536924, PLX-4720, and AZD6482 were identified as potential sensitive drugs for high-risk patients, of which MG-132 was particularly recommended for high-risk patients. We performed in vitro experiments to explore the anti-glioma effect of MG-132, and the results demonstrated MG-132 could inhibit the proliferation and migration of glioma cells. Conclusions Our findings show that CCC genes are associated with the prognosis and immune infiltration of LGG and provide possible immunotherapeutic and novel chemotherapeutic strategies for patients with LGG based on the risk signature.
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Affiliation(s)
- Jianmei Yang
- Department of Gastroenterology, Hubei Provincial Hospital of Integrated Chinese & Western Medicine, Wuhan, China
| | - Lei Shen
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jingyi Yang
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yinzong Qu
- Department of Gastroenterology, Hubei Provincial Hospital of Integrated Chinese & Western Medicine, Wuhan, China
| | - Chengxian Gong
- Department of Gastroenterology, Hubei Provincial Hospital of Integrated Chinese & Western Medicine, Wuhan, China
| | - Fang Zhou
- Department of Gastroenterology, Hubei Provincial Hospital of Integrated Chinese & Western Medicine, Wuhan, China
| | - Yuhan Liu
- Department of Gastroenterology, Hubei Provincial Hospital of Integrated Chinese & Western Medicine, Wuhan, China
| | - Ming Luo
- Department of Neurosurgery, Wuhan No. 1 Hospital, Wuhan, China
| | - Li Zhao
- Department of Gastroenterology, Hubei Provincial Hospital of Integrated Chinese & Western Medicine, Wuhan, China
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Yoon HG, Cheong JH, Ryu JI, Won YD, Min KW, Han MH. The genes significantly associated with an improved prognosis and long-term survival of glioblastoma. PLoS One 2023; 18:e0295061. [PMID: 38019838 PMCID: PMC10686432 DOI: 10.1371/journal.pone.0295061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 11/14/2023] [Indexed: 12/01/2023] Open
Abstract
BACKGROUND AND PURPOSE Glioblastoma multiforme (GBM) is the most devastating brain tumor with less than 5% of patients surviving 5 years following diagnosis. Many studies have focused on the genetics of GBM with the aim of improving the prognosis of GBM patients. We investigated specific genes whose expressions are significantly related to both the length of the overall survival and the progression-free survival in patients with GBM. METHODS We obtained data for 12,042 gene mRNA expressions in 525 GBM tissues from the Cancer Genome Atlas (TCGA) database. Among those genes, we identified independent genes significantly associated with the prognosis of GBM. Receiver operating characteristic (ROC) curve analysis was performed to determine the genes significant for predicting the long-term survival of patients with GBM. Bioinformatics analysis was also performed for the significant genes. RESULTS We identified 33 independent genes whose expressions were significantly associated with the prognosis of 525 patients with GBM. Among them, the expressions of five genes were independently associated with an improved prognosis of GBM, and the expressions of 28 genes were independently related to a poorer prognosis of GBM. The expressions of the ADAM22, ATP5C1, RAC3, SHANK1, AEBP1, C1RL, CHL1, CHST2, EFEMP2, and PGCP genes were either positively or negatively related to the long-term survival of GBM patients. CONCLUSIONS Using a large-scale and open database, we found genes significantly associated with both the prognosis and long-term survival of patients with GBM. We believe that our findings may contribute to improving the understanding of the mechanisms underlying GBM.
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Affiliation(s)
- Hong Gyu Yoon
- Department of Neurosurgery, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jin Hwan Cheong
- Department of Neurosurgery, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri, Gyeonggi-do, Republic of Korea
| | - Je Il Ryu
- Department of Neurosurgery, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri, Gyeonggi-do, Republic of Korea
| | - Yu Deok Won
- Department of Neurosurgery, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri, Gyeonggi-do, Republic of Korea
| | - Kyueng-Whan Min
- Department of Pathology Uijeongbu Eulji Medical Center, Eulji University School of Medicine, Uijeongbu, Gyeonggi-do, Republic of Korea
| | - Myung-Hoon Han
- Department of Neurosurgery, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri, Gyeonggi-do, Republic of Korea
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Atashi M, Reyes CDG, Sandilya V, Purba W, Ahmadi P, Hakim MA, Kobeissy F, Plazzi G, Moresco M, Lanuzza B, Ferri R, Mechref Y. LC-MS/MS Quantitation of HILIC-Enriched N-glycopeptides Derived from Low-Abundance Serum Glycoproteins in Patients with Narcolepsy Type 1. Biomolecules 2023; 13:1589. [PMID: 38002271 PMCID: PMC10669497 DOI: 10.3390/biom13111589] [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: 09/06/2023] [Revised: 10/18/2023] [Accepted: 10/20/2023] [Indexed: 11/26/2023] Open
Abstract
Glycoproteomic analysis is always challenging because of low abundance and complex site-specific heterogeneity. Glycoproteins are involved in various biological processes such as cell signaling, adhesion, and cell-cell communication and may serve as potential biomarkers when analyzing different diseases. Here, we investigate glycoproteins in narcolepsy type 1 (NT1) disease, a form of narcolepsy characterized by cataplexy-the sudden onset of muscle paralysis that is typically triggered by intense emotions. In this study, 27 human blood serum samples were analyzed, 16 from NT1 patients and 11 from healthy individuals serving as controls. We quantified hydrophilic interaction liquid chromatography (HILIC)-enriched glycopeptides from low-abundance serum samples of controls and NT1 patients via LC-MS/MS. Twenty-eight unique N-glycopeptides showed significant changes between the two studied groups. The sialylated N-glycopeptide structures LPTQNITFQTESSVAEQEAEFQSPK HexNAc6, Hex3, Neu5Ac2 (derived from the ITIH4 protein) and the structure IVLDPSGSMNIYLVLDGSDSIGASNFTGAK HexNAc5, Hex4, Fuc1 (derived from the CFB protein), with p values of 0.008 and 0.01, respectively, were elevated in NT1 samples compared with controls. In addition, the N-glycopeptide protein sources Ceruloplasmin, Complement factor B, and ITH4 were observed to play an important role in the complement activation and acute-phase response signaling pathways. This may explain the possible association between the biomarkers and pathophysiological effects.
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Affiliation(s)
- Mojgan Atashi
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA; (M.A.); (C.D.G.R.); (V.S.); (W.P.); (P.A.); (M.A.H.)
| | - Cristian D. Gutierrez Reyes
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA; (M.A.); (C.D.G.R.); (V.S.); (W.P.); (P.A.); (M.A.H.)
| | - Vishal Sandilya
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA; (M.A.); (C.D.G.R.); (V.S.); (W.P.); (P.A.); (M.A.H.)
| | - Waziha Purba
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA; (M.A.); (C.D.G.R.); (V.S.); (W.P.); (P.A.); (M.A.H.)
| | - Parisa Ahmadi
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA; (M.A.); (C.D.G.R.); (V.S.); (W.P.); (P.A.); (M.A.H.)
| | - Md. Abdul Hakim
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA; (M.A.); (C.D.G.R.); (V.S.); (W.P.); (P.A.); (M.A.H.)
| | - Firas Kobeissy
- Department of biochemistry and molecular genetics, Faculty of Biochemistry and Molecular Genetics, American University of Beirut, Beirut 11072020, Lebanon;
- Department of Neurobiology, Center for Neurotrauma, Multiomics & Biomarkers (CNMB), Neuroscience Institute, Morehouse School of Medicine, Atlanta, GE 30310, USA
| | - Giuseppe Plazzi
- IRCCS, Instituto delle Scienze Neurologiche di Bologna, 40124 Bologna, Italy; (G.P.); (M.M.)
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Monica Moresco
- IRCCS, Instituto delle Scienze Neurologiche di Bologna, 40124 Bologna, Italy; (G.P.); (M.M.)
| | - Bartolo Lanuzza
- Sleep Research Center, Department of Neurology IC, Oasi Research Institute-IRCCS, 94018 Tronia, Italy; (B.L.); (R.F.)
| | - Raffaele Ferri
- Sleep Research Center, Department of Neurology IC, Oasi Research Institute-IRCCS, 94018 Tronia, Italy; (B.L.); (R.F.)
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA; (M.A.); (C.D.G.R.); (V.S.); (W.P.); (P.A.); (M.A.H.)
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Sanni A, Goli M, Zhao J, Wang J, Barsa C, El Hayek S, Talih F, Lanuzza B, Kobeissy F, Plazzi G, Moresco M, Mondello S, Ferri R, Mechref Y. LC-MS/MS-Based Proteomics Approach for the Identification of Candidate Serum Biomarkers in Patients with Narcolepsy Type 1. Biomolecules 2023; 13:420. [PMID: 36979356 PMCID: PMC10046664 DOI: 10.3390/biom13030420] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/13/2023] [Accepted: 02/17/2023] [Indexed: 02/25/2023] Open
Abstract
Narcolepsy type 1 (NT1) is the most common type of narcolepsy known to be caused by the loss of specific neurons responsible for producing peptide neurotransmitters (orexins/hypocretins), resulting in a sleep-wake cycle disorder. It is characterized by its association with cataplexy and abnormalities in rapid eye movement. To date, no cure has been established for this life-threatening condition. Misdiagnosis of NT1 is also quite common, although it is not exceedingly rare. Therefore, successfully identifying candidate serum biomarkers for NT1 would be a head start for accurate diagnosis and development of therapeutics for this disorder. This study aims to identify such potential serum biomarkers. A depletion protocol was employed for 27 human serum samples (16 NT1 and 11 healthy controls), followed by applying LC-MS/MS bottom-up proteomics analysis, then LC-PRM-MS for validation. The comparison of the proteome profiles of the low-abundant proteins in the samples was then investigated based on age, sex, sample groups, and the presence of the Human Leukocyte Antigen (HLA) DQB1*0602 allele. The results were tracked to gene expression studies as well as system biology to identify key proteins and understand their relationship in the pathogenesis of NT1. Our results revealed 36 proteins significantly and differentially expressed. Among the impaired pathways and bioprocesses, the complement activation pathway is impaired by six of the differentially expressed proteins (DEPs). They are coded by the genes C2, CFB, C5, C1R, C1S, and MASP1, while 11 DEPs are involved in Acute Phase Response Signaling (APRS), which are coded by the genes FN1, AMBP, APOH, CFB, CP, ITIH2, C5, C2, F2, C1, and ITIH4. The combined AUCs of the downregulated and upregulated DEPs are 0.95 and 0.76, respectively. Overall, this study reveals potential serum-protein biomarkers of NT1 and explains the possible correlation between the biomarkers and pathophysiological effects, as well as important biochemical pathways involved in NT1.
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Affiliation(s)
- Akeem Sanni
- Chemistry and Biochemistry Department, Texas Tech University, Lubbock, TX 79409, USA
| | - Mona Goli
- Chemistry and Biochemistry Department, Texas Tech University, Lubbock, TX 79409, USA
| | - Jingfu Zhao
- Chemistry and Biochemistry Department, Texas Tech University, Lubbock, TX 79409, USA
| | - Junyao Wang
- Chemistry and Biochemistry Department, Texas Tech University, Lubbock, TX 79409, USA
| | - Chloe Barsa
- Faculty of Biochemistry and Molecular Genetics, American University of Beirut, Beirut 1107 2020, Lebanon
| | - Samer El Hayek
- Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL 33124, USA
| | - Farid Talih
- Department of Psychiatry, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon
| | - Bartolo Lanuzza
- Sleep Research Centre, Department of Neurology IC, Oasi Research Institute-IRCCS, 94018 Troina, Italy
| | - Firas Kobeissy
- Faculty of Biochemistry and Molecular Genetics, American University of Beirut, Beirut 1107 2020, Lebanon
- Multiomics & Biomarkers, Department of Neurobiology, Center for Neurotrauma, Morehouse School of Medicine (MSM), Atlanta, GA 30310, USA
| | - Giuseppe Plazzi
- IRCCS, Instituto delle Scienze Neurologiche di Bologna, 40139 Bologna, Italy
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Monica Moresco
- IRCCS, Instituto delle Scienze Neurologiche di Bologna, 40139 Bologna, Italy
| | - Stefania Mondello
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, 98122 Messina, Italy
| | - Raffaele Ferri
- Sleep Research Centre, Department of Neurology IC, Oasi Research Institute-IRCCS, 94018 Troina, Italy
| | - Yehia Mechref
- Chemistry and Biochemistry Department, Texas Tech University, Lubbock, TX 79409, USA
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Fan S, Wu N, Chang S, Chen L, Sun X. The immune regulation of BCL3 in glioblastoma with mutated IDH1. Aging (Albany NY) 2022; 14:3856-3873. [PMID: 35488886 PMCID: PMC9134951 DOI: 10.18632/aging.204048] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 01/25/2022] [Indexed: 11/25/2022]
Abstract
Background: Glioblastoma in the brain is the most malignant solid tumor with a poor prognosis. Screening critical targets and exploring underlying mechanisms will be a benefit for diagnoses and treatment. IDH1 mutation (R132) was used to distinguish glioblastoma grade and predict prognosis as a significant marker. However, the manner of IDH1 mutation regulating glioblastoma development was still unclear. Methods: To study the function of IDH1 mutation, multi-type sequencing data (transcriptome, methylation and copy number variation) from the GEO and TCGA database were analyzed using bioinformatics techniques. The biological functions of IDH1 mutation (R132) would be comprehensively evaluated from the regulatory networks, tumor immune microenvironment and clinical relevance. Then the analysis result would be validated by experimental techniques. Results: Compared with adjacent tissues, IDH1 was up-regulated in glioblastoma, which also positively correlated with the malignant degree and a poor prognosis. To further study the mechanism of mutated IDH1 (R132) function, 5 correlated genes (FABP5, C1RL, MIR155HG, CSTA and BCL3) were identified by different expression gene screening, enrichment analysis and network construction successively. Among them, the BCL3 was a transcription factor that may induce IDH1expression. Through calculating the correlation coefficient, it was found that in IDH1mut glioblastoma, the dendritic cell infiltration was reduced which may result in a better prognosis. In addition, the level of IDH1, FABP5, C1RL, MIR155HG, CSTA and BCL3 might also influence lymphocytes infiltration (eg. CD4+ T cell) and chemokine expression (CXCL family). Conclusions: IDH1 may participate in pathological mechanisms of glioblastoma via expression alteration or gene mutation. Furthermore, IDH1 mutation might improve prognosis via suppressing the expression of FABP5, C1RL, MIR155HG, CSTA and BCL3. Meanwhile, it was identified that BCL3 might perform similar immunomodulatory functions with IDH1 as an upstream transcript factor.
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Affiliation(s)
- Shibing Fan
- Department of Neurosurgery, Chongqing Medical University, Chongqing, China.,Chongqing University Three Gorges Hospital, Wanzhou, Chongqing, China
| | - Na Wu
- Department of Neurosurgery, Chongqing Medical University, Chongqing, China.,Chongqing University Three Gorges Hospital, Wanzhou, Chongqing, China
| | - Shichuan Chang
- Chongqing University Three Gorges Hospital, Wanzhou, Chongqing, China
| | - Long Chen
- Chongqing University, Shapingba, Chongqing, China
| | - Xiaochuan Sun
- Department of Neurosurgery, Chongqing Medical University, Chongqing, China
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