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Jiang C, Zhang S, Jiang L, Chen Z, Chen H, Huang J, Tang J, Luo X, Yang G, Liu J, Chi H. Precision unveiled: Synergistic genomic landscapes in breast cancer-Integrating single-cell analysis and decoding drug toxicity for elite prognostication and tailored therapeutics. ENVIRONMENTAL TOXICOLOGY 2024; 39:3448-3472. [PMID: 38450906 DOI: 10.1002/tox.24205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 02/19/2024] [Accepted: 02/25/2024] [Indexed: 03/08/2024]
Abstract
BACKGROUND Globally, breast cancer, with diverse subtypes and prognoses, necessitates tailored therapies for enhanced survival rates. A key focus is glutamine metabolism, governed by select genes. This study explored genes associated with T cells and linked them to glutamine metabolism to construct a prognostic staging index for breast cancer patients for more precise medical treatment. METHODS Two frameworks, T-cell related genes (TRG) and glutamine metabolism (GM), stratified breast cancer patients. TRG analysis identified key genes via hdWGCNA and machine learning. T-cell communication and spatial transcriptomics emphasized TRG's clinical value. GM was defined using Cox analyses and the Lasso algorithm. Scores categorized patients as TRG_high+GM_high (HH), TRG_high+GM_low (HL), TRG_low+GM_high (LH), or TRG_low+GM_low (LL). Similarities between HL and LH birthed a "Mixed" class and the TRG_GM classifier. This classifier illuminated gene variations, immune profiles, mutations, and drug responses. RESULTS Utilizing a composite of two distinct criteria, we devised a typification index termed TRG_GM classifier, which exhibited robust prognostic potential for breast cancer patients. Our analysis elucidated distinct immunological attributes across the classifiers. Moreover, by scrutinizing the genetic variations across groups, we illuminated their unique genetic profiles. Insights into drug sensitivity further underscored avenues for tailored therapeutic interventions. CONCLUSION Utilizing TRG and GM, a robust TRG_GM classifier was developed, integrating clinical indicators to create an accurate predictive diagnostic map. Analysis of enrichment disparities, immune responses, and mutation patterns across different subtypes yields crucial subtype-specific characteristics essential for prognostic assessment, clinical decision-making, and personalized therapies. Further exploration is warranted into multiple fusions between metrics to uncover prognostic presentations across various dimensions.
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Affiliation(s)
- Chenglu Jiang
- Department of Clinical Medicine, Southwest Medical University, Luzhou, China
| | - Shengke Zhang
- Department of Clinical Medicine, Southwest Medical University, Luzhou, China
| | - Lai Jiang
- Department of Clinical Medicine, Southwest Medical University, Luzhou, China
| | - Zipei Chen
- Department of Clinical Medicine, Southwest Medical University, Luzhou, China
| | - Haiqing Chen
- Department of Clinical Medicine, Southwest Medical University, Luzhou, China
| | - Jinbang Huang
- Department of Clinical Medicine, Southwest Medical University, Luzhou, China
| | - Jingyi Tang
- Department of Clinical Medicine, Southwest Medical University, Luzhou, China
| | - Xiufang Luo
- Geriatric department, Dazhou Central Hospital, Dazhou, China
| | - Guanhu Yang
- Department of Specialty Medicine, Ohio University, Athens, Ohio, USA
| | - Jie Liu
- Department of General Surgery, Dazhou Central Hospital, Dazhou, China
| | - Hao Chi
- Department of Clinical Medicine, Southwest Medical University, Luzhou, China
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Hallén T, Johannsson G, Thorsell A, Olsson DS, Örndal C, Engvall A, Jacobson F, Widgren A, Bergquist J, Skoglund T. Proteomic Profiles Associated With Postsurgical Progression in Nonfunctioning Pituitary Adenomas. J Clin Endocrinol Metab 2024; 109:1485-1493. [PMID: 38157275 PMCID: PMC11099478 DOI: 10.1210/clinem/dgad767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/16/2023] [Accepted: 12/28/2023] [Indexed: 01/03/2024]
Abstract
CONTEXT There is a lack of reliable biomarkers capable of predicting postoperative tumor progression of nonfunctioning pituitary adenomas (NFPAs). OBJECTIVE To discover proteomic profiles associated with postoperative tumor progression in patients with NFPAs. This was a case-controlled exploratory study at a tertiary university hospital. Tissue samples were obtained from 46 patients with residual tumor following surgery for NFPAs of gonadotroph lineage. Two patient groups were compared: patients requiring reintervention due to residual tumor progression (cases; reintervention group, n = 29) and patients with a residual tumor showing no progression for a minimum of 5 years (controls; radiologically stable group, n = 17). Differentially expressed proteins (DEPs) between patient groups were measured. RESULTS Global quantitative proteomic analysis identified 4074 proteins, of which 550 were differentially expressed between the 2 groups (fold change >80%, false discovery rate-adjusted P ≤ .05). Principal component analysis showed good separation between the 2 groups. Functional enrichment analysis of the DEPs indicated processes involving translation, ROBO-receptor signaling, energy metabolism, mRNA metabolism, and RNA splicing. Several upregulated proteins in the reintervention group, including SNRPD1, SRSF10, SWAP-70, and PSMB1, are associated with tumor progression in other cancer types. CONCLUSION This is the first exploratory study analyzing proteomic profiles as markers of postoperative tumor progression in NFPAs. The findings clearly showed different profiles between tumors with indolent postoperative behavior and those with postoperative tumor progression. Both enriched pathways involving DEPs and specific upregulated proteins have previously been associated with tumor aggressiveness. These results suggest the value of proteomic profiling for predicting tumor progression in patients with NFPAs.
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Affiliation(s)
- Tobias Hallén
- Department of Neurosurgery, Sahlgrenska University Hospital, 412 65 Gothenburg, Sweden
- Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Gudmundur Johannsson
- Department of Endocrinology, Sahlgrenska University Hospital, 413 46 Gothenburg, Sweden
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Annika Thorsell
- Proteomics Core Facility at Sahlgrenska Academy, Gothenburg University, 413 90 Gothenburg, Sweden
| | - Daniel S Olsson
- Department of Endocrinology, Sahlgrenska University Hospital, 413 46 Gothenburg, Sweden
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden
- Late-stage Clinical Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, 431 83 Gothenburg, Sweden
| | - Charlotte Örndal
- Department of Pathology, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Angelica Engvall
- Department of Neuroradiology, Sahlgrenska University Hospital, 413 46 Gothenburg, Sweden
| | - Frida Jacobson
- Proteomics Core Facility at Sahlgrenska Academy, Gothenburg University, 413 90 Gothenburg, Sweden
| | - Anna Widgren
- Department of Chemistry–BMC, Analytical Chemistry and Neurochemistry, Uppsala University, 75124 Uppsala, Sweden
| | - Jonas Bergquist
- Department of Chemistry–BMC, Analytical Chemistry and Neurochemistry, Uppsala University, 75124 Uppsala, Sweden
| | - Thomas Skoglund
- Department of Neurosurgery, Sahlgrenska University Hospital, 412 65 Gothenburg, Sweden
- Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden
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Ali W, Xiao W, Hoang H, Cali V, Kajdacsy-Balla A. Carcinogenesis and Prognostic Utility of Arginine Methylation-Related Genes in Hepatocellular Cancer. Curr Issues Mol Biol 2023; 45:9422-9430. [PMID: 38132437 PMCID: PMC10742294 DOI: 10.3390/cimb45120591] [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: 09/04/2023] [Revised: 10/16/2023] [Accepted: 10/17/2023] [Indexed: 12/23/2023] Open
Abstract
Protein arginine methylation is among the most important post-translational modifications and has been studied in cancers such as those of the lung and breast. However, comparatively less has been investigated regarding hepatocellular carcinoma, with an annual incidence of almost one million cases. Through using in silico methods, this study examined arginine methylation-related gene expression and methylation levels, and alongside network and enrichment analysis attempted to find how said genes can drive tumorigenesis and offer possible therapeutic targets. We found a robust relationship among the selected methylation genes, with ⅞ showing prognostic value regarding overall survival, and a medley of non-arginine methylation pathways also being highlighted through the aforementioned analysis. This study furthers our knowledge of the methylation and expression patterns of arginine histone methylation-related genes, offering jumping points for further wet-lab studies.
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Affiliation(s)
- Waleed Ali
- Albert Einstein College of Medicine, The Bronx, NY 10461, USA; (W.A.); (W.X.); (H.H.); (V.C.)
| | - Weirui Xiao
- Albert Einstein College of Medicine, The Bronx, NY 10461, USA; (W.A.); (W.X.); (H.H.); (V.C.)
| | - Henry Hoang
- Albert Einstein College of Medicine, The Bronx, NY 10461, USA; (W.A.); (W.X.); (H.H.); (V.C.)
| | - Vincent Cali
- Albert Einstein College of Medicine, The Bronx, NY 10461, USA; (W.A.); (W.X.); (H.H.); (V.C.)
| | - Andre Kajdacsy-Balla
- Department of Pathology, College of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
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Li Y, Chen Z, Peng J, Yuan C, Yan S, Yang N, Li P, Kong B. The splicing factor SNRPB promotes ovarian cancer progression through regulating aberrant exon skipping of POLA1 and BRCA2. Oncogene 2023:10.1038/s41388-023-02763-x. [PMID: 37391593 DOI: 10.1038/s41388-023-02763-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 06/08/2023] [Accepted: 06/22/2023] [Indexed: 07/02/2023]
Abstract
Splicing factors play a crucial role in the initiation and development of various human cancers. SNRPB, a core spliceosome component, regulates pre-mRNA alternative splicing. However, its function and underlying mechanism in ovarian cancer remain unclear. This study identified SNRPB as a critical driver of ovarian cancer through TCGA and CPTAC database analysis. SNRPB was highly upregulated in fresh frozen ovarian cancer tissues compared with normal fallopian tubes. Immunohistochemistry revealed that SNRPB expression was increased in formalin-fixed, paraffin-embedded ovarian cancer sections and was positively correlated with a poor prognosis for ovarian cancer. Functionally, SNRPB knockdown suppressed ovarian cancer cell proliferation and invasion, and overexpression exerted opposite effects. SNRPB expression increased after cisplatin treatment, and silencing SNRPB sensitized ovarian cancer cells to cisplatin. KEGG pathway analysis revealed that the differentially expressed genes (DEGs) were mainly enriched in DNA replication and homologous recombination, and almost all DEGs related to DNA replication and homologous recombination were downregulated after SNRPB knockdown according to RNA-seq. Exon 3 skipping of the DEGs DNA polymerase alpha 1 (POLA1) and BRCA2 was induced by SNRPB silencing. Exon 3 skipping of POLA1 yielded premature termination codons and led to nonsense-mediated RNA decay (NMD); exon 3 skipping of BRCA2 led to loss of the PALB2 binding domain, which is necessary for homologous recombination, and increased ovarian cancer cell cisplatin sensitivity. POLA1 or BRCA2 knockdown partially impaired the increased malignancy of SNRPB-overexpressing ovarian cancer cells. Moreover, miR-654-5p was found to reduce SNRPB mRNA expression by directly binding to the SNRPB 3'-UTR. Overall, SNRPB was identified as an important oncogenic driver that promotes ovarian cancer progression by repressing exon 3 skipping of POLA1 and BRCA2. Thus, SNRPB is a potential treatment target and prognostic marker for ovarian cancer.
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Affiliation(s)
- Yingwei Li
- Department of Obstetrics and Gynecology, Qilu Hospital, Shandong University, 107 Wenhua Xi Road, Ji'nan 250012, Shandong Province, China.
- Medical Integration and Practice Center, Cheeloo College of Medicine, Shandong University, Ji'nan 250012, Shandong Province, China.
- Gynecology Oncology Key Laboratory, Qilu Hospital, Shandong University, Ji'nan 250012, Shandong Province, China.
| | - Zhongshao Chen
- Department of Obstetrics and Gynecology, Qilu Hospital, Shandong University, 107 Wenhua Xi Road, Ji'nan 250012, Shandong Province, China
- Gynecology Oncology Key Laboratory, Qilu Hospital, Shandong University, Ji'nan 250012, Shandong Province, China
| | - Jiali Peng
- Department of Obstetrics and Gynecology, Qilu Hospital, Shandong University, 107 Wenhua Xi Road, Ji'nan 250012, Shandong Province, China
- Gynecology Oncology Key Laboratory, Qilu Hospital, Shandong University, Ji'nan 250012, Shandong Province, China
| | - Cunzhong Yuan
- Department of Obstetrics and Gynecology, Qilu Hospital, Shandong University, 107 Wenhua Xi Road, Ji'nan 250012, Shandong Province, China
- Gynecology Oncology Key Laboratory, Qilu Hospital, Shandong University, Ji'nan 250012, Shandong Province, China
| | - Shi Yan
- Department of Obstetrics and Gynecology, Qilu Hospital, Shandong University, 107 Wenhua Xi Road, Ji'nan 250012, Shandong Province, China
- Gynecology Oncology Key Laboratory, Qilu Hospital, Shandong University, Ji'nan 250012, Shandong Province, China
| | - Ning Yang
- Department of Obstetrics and Gynecology, Qilu Hospital, Shandong University, 107 Wenhua Xi Road, Ji'nan 250012, Shandong Province, China
- Gynecology Oncology Key Laboratory, Qilu Hospital, Shandong University, Ji'nan 250012, Shandong Province, China
| | - Peng Li
- Department of Obstetrics and Gynecology, Qilu Hospital, Shandong University, 107 Wenhua Xi Road, Ji'nan 250012, Shandong Province, China
- Gynecology Oncology Key Laboratory, Qilu Hospital, Shandong University, Ji'nan 250012, Shandong Province, China
| | - Beihua Kong
- Department of Obstetrics and Gynecology, Qilu Hospital, Shandong University, 107 Wenhua Xi Road, Ji'nan 250012, Shandong Province, China.
- Gynecology Oncology Key Laboratory, Qilu Hospital, Shandong University, Ji'nan 250012, Shandong Province, China.
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Wang H, Chen M, Yang C, Hu H, Jiang Y, Yang F, Lv L. SNRPD1 inhibition suppresses the proliferation of hepatocellular carcinoma and promotes autophagy through the PI3K/AKT/mTOR/4EBP1 pathway. Arch Biochem Biophys 2023; 743:109661. [PMID: 37268273 DOI: 10.1016/j.abb.2023.109661] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/12/2023] [Accepted: 05/30/2023] [Indexed: 06/04/2023]
Abstract
BACKGROUND Small nuclear ribonucleoprotein Sm D1 (SNRPD1) has been reported as an oncogene in some solid cancers. Our previous study suggested that SNRPD1 has diagnostic and prognostic value in hepatocellular carcinoma (HCC), but its role in tumor growth and biological behavior remains unknown. In this study, we aimed to unravel the role and mechanism of SNRPD1 in HCC. METHODS We investigated the SNRPD1 mRNA level in adjacent normal liver tissues and HCC tissues with different tumor stages in the UALCAN database. The associations between SNRPD1 mRNA expression and HCC prognosis were investigated in TCGA database. Then, 52 pairs of frozen HCC tissues and corresponding adjacent normal liver tissues were collected to perform qPCR and immunohistochemistry assay. Next, we carried out a series of experiments in vitro and in vivo to investigate the effects of SNRPD1 expression on cell invasion, migration, proliferation, autophagy, and the PI3K/AKT/mTOR pathway. RESULTS The bioinformatics analysis and qPCR in our patient cohort demonstrated that the SNRPD1 mRNA level in HCC tissues was higher than in adjacent normal tissues. In addition, the immunohistochemistry assay exhibited an increased SNRPD1 protein level with the tumor stage increase. Survival analysis suggested that higher expression of SNRPD1 was significantly associated with unfavorable prognosis of patients with HCC. The functional experiments in vitro indicated that SNRPD1 knockdown suppressed the cellular proliferation, migration, and invasion capacities. Furthermore, SNRPD1 inhibition induced cellular apoptosis and arrested the HCC cells at the G0/G1 phase of the cell cycle. Mechanistic analyses demonstrated that SNRPD1 knockdown induced the increase of autophagic vacuoles and the expression of autophagy-related genes (ATG5, ATG7, and ATG12) and blocked the PI3K/AKT/mTOR/4EBP1 pathway in vitro. Moreover, SNRPD1 inhibition suppressed tumor growth and expression of the Ki67 protein in vivo. CONCLUSIONS SNRPD1 may serve as an oncogene in HCC and promote tumor proliferation via inhibiting autophagy induced through the PI3K/Akt/mTOR/4EBP1 pathway.
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Affiliation(s)
- Huaxiang Wang
- Department of Hepatobiliary and Pancreatic Surgery, Taihe Hospital, Affiliated Hospital of Hubei University of Medicine, Shiyan, Hubei, 442000, China; The Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, Fujian, 350025, China; Department of Hepatobiliary Surgery, 900 Hospital of the Joint Logistic Team, Fuzhou, Fujian, 350025, China.
| | - Minyong Chen
- Department of Hepatobiliary and Pancreatic Surgery, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, 350014, Fuzhou, Fujian, 350025, China
| | - Chengkai Yang
- Department of Hepatobiliary and Pancreatic Surgery, Taihe Hospital, Affiliated Hospital of Hubei University of Medicine, Shiyan, Hubei, 442000, China; The Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, Fujian, 350025, China
| | - Huanzhang Hu
- Department of Hepatobiliary and Pancreatic Surgery, Taihe Hospital, Affiliated Hospital of Hubei University of Medicine, Shiyan, Hubei, 442000, China; The Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, Fujian, 350025, China
| | - Yi Jiang
- Department of Hepatobiliary and Pancreatic Surgery, Taihe Hospital, Affiliated Hospital of Hubei University of Medicine, Shiyan, Hubei, 442000, China; The Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, Fujian, 350025, China
| | - Fang Yang
- Department of Hepatobiliary and Pancreatic Surgery, Taihe Hospital, Affiliated Hospital of Hubei University of Medicine, Shiyan, Hubei, 442000, China; The Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, Fujian, 350025, China
| | - Lizhi Lv
- Department of Hepatobiliary and Pancreatic Surgery, Taihe Hospital, Affiliated Hospital of Hubei University of Medicine, Shiyan, Hubei, 442000, China; The Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, Fujian, 350025, China.
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6
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Zhang Y, Weh KM, Howard CL, Riethoven JJ, Clarke JL, Lagisetty KH, Lin J, Reddy RM, Chang AC, Beer DG, Kresty LA. Characterizing isoform switching events in esophageal adenocarcinoma. MOLECULAR THERAPY - NUCLEIC ACIDS 2022; 29:749-768. [PMID: 36090744 PMCID: PMC9437810 DOI: 10.1016/j.omtn.2022.08.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 08/14/2022] [Indexed: 12/14/2022]
Abstract
Isoform switching events with predicted functional consequences are common in many cancers, but characterization of switching events in esophageal adenocarcinoma (EAC) is lacking. Next-generation sequencing was used to detect levels of RNA transcripts and identify specific isoforms in treatment-naïve esophageal tissues ranging from premalignant Barrett’s esophagus (BE), BE with low- or high-grade dysplasia (BE.LGD, BE.HGD), and EAC. Samples were stratified by histopathology and TP53 mutation status, identifying significant isoform switching events with predicted functional consequences. Comparing BE.LGD with BE.HGD, a histopathology linked to cancer progression, isoform switching events were identified in 75 genes including KRAS, RNF128, and WRAP53. Stratification based on TP53 status increased the number of significant isoform switches to 135, suggesting switching events affect cellular functions based on TP53 mutation and tissue histopathology. Analysis of isoforms agnostic, exclusive, and shared with mutant TP53 revealed unique signatures including demethylation, lipid and retinoic acid metabolism, and glucuronidation, respectively. Nearly half of isoform switching events were identified without significant gene-level expression changes. Importantly, two TP53-interacting isoforms, RNF128 and WRAP53, were significantly linked to patient survival. Thus, analysis of isoform switching events may provide new insight for the identification of prognostic markers and inform new potential therapeutic targets for EAC.
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Affiliation(s)
- Yun Zhang
- Department of Surgery, Thoracic Surgery Section, University of Michigan, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Katherine M. Weh
- Department of Surgery, Thoracic Surgery Section, University of Michigan, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Connor L. Howard
- Department of Surgery, Thoracic Surgery Section, University of Michigan, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jean-Jack Riethoven
- Nebraska Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
- Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Jennifer L. Clarke
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Kiran H. Lagisetty
- Department of Surgery, Thoracic Surgery Section, University of Michigan, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jules Lin
- Department of Surgery, Thoracic Surgery Section, University of Michigan, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Rishindra M. Reddy
- Department of Surgery, Thoracic Surgery Section, University of Michigan, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Andrew C. Chang
- Department of Surgery, Thoracic Surgery Section, University of Michigan, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - David G. Beer
- Department of Surgery, Thoracic Surgery Section, University of Michigan, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Laura A. Kresty
- Department of Surgery, Thoracic Surgery Section, University of Michigan, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
- Corresponding author Laura A. Kresty, PhD, Department of Surgery, Thoracic Surgery Section, University of Michigan, Ann Arbor, MI 48109, USA.
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Qin S, Liu G, Jin H, Chen X, He J, Xiao J, Qin Y, Mao Y, Zhao L. The comprehensive expression and functional analysis of m6A modification "readers" in hepatocellular carcinoma. Aging (Albany NY) 2022; 14:6269-6298. [PMID: 35963644 PMCID: PMC9417225 DOI: 10.18632/aging.204217] [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: 04/01/2022] [Accepted: 07/21/2022] [Indexed: 11/25/2022]
Abstract
N6-methyladenosine (m6A) modification regulators are essential for the diagnosis and treatment of various cancers. However, the comprehensive analysis about roles of m6A "readers" in hepatocellular carcinoma (HCC) remains unclear. UALCAN, GEPIA2, HPA, Kaplan Meier plotter, cBioPortal, STRING WebGestalt, Metascape and TIMER 2.0 database and Cytoscape software were used to comprehensively analyze the bioinformatic data. We found that m6A "readers" were upregulated at the mRNA level and protein level in HCC patients. Highly expressed YTHDF1, IGF2BP3 and NKAP were positively correlated with advanced HCC stage and had a poor prognosis in OS and PFS. The gene alterations of m6A "readers" happened frequently, and YTHDF3 had the highest mutation rate. The function of m6A "readers" on HCC may be closely correlated with splicing related proteins (including HNRNP family, SNRP family, and SR family), metabolic process, protein binding and RNA splicing related signaling pathways. Moreover, although the correlation of YTHDF3 and CD8+ T cell infiltration, and the correlation of IGF2BP3 and infiltration of mast cells and CAF are negative, most m6A "readers" had a positive correlation with immune cells (including CD8+ T cell, CD4+ T cell, Tregs, B cell, neutrophil, monocyte, macrophage, myeloid dendritic cell, nature killer cell, mast cell, and CAF). Macrophages, CD4+ T cell, Treg, B cell, monocyte, and myeloid dendritic cell had a positively strong correlation (Rho>0.4) with most m6A "readers" (such as YTHDC1, YTHDC2, YTHDF1, IGF2BP3, HNRNPA2B1 and HNRNPC). In conclusion, by comprehensive analysis of m6A "readers", we found that they were involved in the prognosis of HCC, and m6A "readers" might regulate the development and progression of HCC by participating in some metabolism-related and RNA splicing-related signaling pathways as well as immune cell infiltration.
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Affiliation(s)
- Sha Qin
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Department of Pathology, School of Basic Medical Science, Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Gaoming Liu
- Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Haoer Jin
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Department of Pathology, School of Basic Medical Science, Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Xue Chen
- Early Clinical Trial Center, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Jiang He
- Center for Molecular Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Juxiong Xiao
- Department of Radiology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yan Qin
- Department of Radiology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yitao Mao
- Department of Radiology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Luqing Zhao
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Department of Pathology, School of Basic Medical Science, Xiangya School of Medicine, Central South University, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
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8
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Fang K, Liang G, Zhuang Z, Fang Y, Dong Y, Liang C, Chen X, Guo X. Screening the hub genes and analyzing the mechanisms in discharged COVID-19 patients retesting positive through bioinformatics analysis. J Clin Lab Anal 2022; 36:e24495. [PMID: 35657140 PMCID: PMC9279949 DOI: 10.1002/jcla.24495] [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] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND After encountering COVID-19 patients who test positive again after discharge, our study analyzed the pathogenesis to further assess the risk and possibility of virus reactivation. METHODS A separate microarray was acquired from the Gene Expression Omnibus (GEO), and its samples were divided into two groups: a "convalescent-RTP" group consisting of convalescent and "retesting positive" (RTP) patients (group CR) and a "healthy-RTP" group consisting of healthy control and RTP patients (group HR). The enrichment analysis was performed with R software, obtaining the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). Subsequently, the protein-protein interaction (PPI) networks of each group were established, and the hub genes were discovered using the cytoHubba plugin. RESULTS In this study, 6622 differentially expressed genes were identified in the group CR, among which RAB11B-AS1, DISP1, MICAL3, PSMG1, and DOCK4 were up-regulated genes, and ANAPC1, IGLV1-40, SORT1, PLPPR2, and ATP1A1-AS1 were down-regulated. 7335 genes were screened in the group HR, including the top 5 up-regulated genes ALKBH6, AMBRA1, MIR1249, TRAV18, and LRRC69, and the top 5 down-regulated genes FAM241B, AC018529.3, AL031963.3, AC006946.1, and FAM149B1. The GO and KEGG analysis of the two groups revealed a significant enrichment in immune response and apoptosis. In the PPI network constructed, group CR and group HR identified 10 genes, respectively, and TP53BP1, SNRPD1, and SNRPD2 were selected as hub genes. CONCLUSIONS Using the messenger ribonucleic acid (mRNA) expression data from GSE166253, we found TP53BP1, SNRPD1, and SNRPD2 as hub genes in RTP patients, which is vital to the management and prognostic prediction of RTP patients.
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Affiliation(s)
- Ke‐Ying Fang
- Department of Clinical Laboratory MedicineThe Third Affiliated Hospital of Guangzhou Hospital of Guangzhou Medical UniversityGuangzhouChina
- Department of Clinical MedicineThe Third Clinical School of Guangzhou Medical UniversityGuangzhouChina
| | - Gui‐Ning Liang
- Department of Clinical Laboratory MedicineThe Third Affiliated Hospital of Guangzhou Hospital of Guangzhou Medical UniversityGuangzhouChina
- Department of Clinical MedicineNan Shan School of Guangzhou Medical UniversityGuangzhouChina
| | - Zhuo‐Qing Zhuang
- Department of Clinical Laboratory MedicineThe Third Affiliated Hospital of Guangzhou Hospital of Guangzhou Medical UniversityGuangzhouChina
- Department of Clinical MedicineThe Third Clinical School of Guangzhou Medical UniversityGuangzhouChina
| | - Yong‐Xin Fang
- Department of Clinical Laboratory MedicineThe Third Affiliated Hospital of Guangzhou Hospital of Guangzhou Medical UniversityGuangzhouChina
- Department of Clinical MedicineThe Third Clinical School of Guangzhou Medical UniversityGuangzhouChina
| | - Yu‐Qian Dong
- Department of Clinical Laboratory MedicineThe Third Affiliated Hospital of Guangzhou Hospital of Guangzhou Medical UniversityGuangzhouChina
- Department of PeriodonticsThe Stomatologe Medical School of Guangzhou Medical UniversityGuangzhouChina
| | - Chuang‐Jia Liang
- Department of Clinical Laboratory MedicineThe Third Affiliated Hospital of Guangzhou Hospital of Guangzhou Medical UniversityGuangzhouChina
- Department of Clinical MedicineThe Third Clinical School of Guangzhou Medical UniversityGuangzhouChina
| | - Xin‐Yan Chen
- Department of Clinical Laboratory MedicineThe Third Affiliated Hospital of Guangzhou Hospital of Guangzhou Medical UniversityGuangzhouChina
- Department of Clinical MedicineThe Third Clinical School of Guangzhou Medical UniversityGuangzhouChina
| | - Xu‐Guang Guo
- Department of Clinical Laboratory MedicineThe Third Affiliated Hospital of Guangzhou Hospital of Guangzhou Medical UniversityGuangzhouChina
- Department of Clinical MedicineThe Third Clinical School of Guangzhou Medical UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Major Obstetric DiseasesThe Third Affiliated GuangzhouGuangzhouChina
- Key Laboratory of Reproduction and Genetics of Guangdong Higher Education InstitutesThe Third Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
- Guangzhou Key Laboratory for Clinical Rapid Diagnosis and Early Warning of Infectious Diseases, KingMed School of Laboratory MedicineGuangzhou Medical UniversityGuangzhouChina
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9
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Li FP, Liu GH, Zhang XQ, Kong WJ, Mei J, Wang M, Dai YH. Overexpressed SNRPB/D1/D3/E/F/G correlate with poor survival and immune infiltration in hepatocellular carcinoma. Am J Transl Res 2022; 14:4207-4228. [PMID: 35836882 PMCID: PMC9274562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Prior reports have indicated that the abnormal expression of small nuclear ribonucleoproteins (snRNPs) genes is related to malignant tumors. However, in hepatocellular carcinoma (HCC), the precise role of snRNPs is not well understood. Therefore, the purpose of this study was to evaluate the prognostic roles of SNRPB/D1/D2/D3/E/F/G and their correlation to immune infiltration in HCC. METHODS The study was carried out via the following databases, software, and experimental validation: ONCOMINE, GEPIA2, UALCAN, The Cancer Genome Atlas, Gene Expression Omnibus, ArrayExpress, Kaplan-Meier plotter, cBioPortal, STRING, DAVID 6.8, TIMER, Cytoscape software, and immunohistochemistry experiments. RESULTS Overexpressed SNRPB/D1/D2/D3/E/F/G proteins were found in HCC tissues. The transcription levels of 7 snRNPs genes were related to the TP53 mutation and tumor grades. SNRPB/D1/D2/D3/F/G expression was significantly correlated with cancer staging, whereas SNRPE was not. Moreover, Kaplan-Meier survival analysis showed that upregulation of SNRPB/D1/D2/E/G was relevant to worse OS in HCC patients, especially in patients with alcohol consumption and those without viral hepatitis. Multivariate Cox regression analysis indicated that expression of SNRPB/D1/D3/E/F/G were independent prognostic factors for unfavorable OS in HCC. In addition, a high mutation rate of snRNPs genes (44%) was also found in HCC. The mRNA expression levels of snRNPs were meaningfully and positively related to six types of infiltrating immune cells (B cells, CD4+ T cells, CD8+ T cells, neutrophil, macrophage, and dendritic cells). Also, SNRPB/D1/G genes were significantly associated with molecular markers of various immune cells in HCC. CONCLUSIONS SNRPB/D1/D3/E/F/G are potential prognostic biomarkers for a short OS in HCC, and SNRPB/D1/G were novel immune therapy targets in HCC patients.
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Affiliation(s)
- Fu-Ping Li
- Department of Clinical Medicine, Shaanxi University of Chinese MedicineXianyang 712046, Shaanxi, China
| | - Gao-Hua Liu
- Department of Oncology, Fujian Medical University Union HospitalFuzhou 350001, Fujian, China
| | - Xue-Qin Zhang
- Jincheng Institute of Sichuan UniversityChengdu 610000, Sichuan, China
| | - Wei-Jie Kong
- Department of Clinical Medicine, Shaanxi University of Chinese MedicineXianyang 712046, Shaanxi, China
| | - Jian Mei
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Fujian Medical UniversityFuzhou 350005, China
| | - Mao Wang
- Department of Surgical Oncology Medicine, Second Affiliated Hospital of Shaanxi University of Chinese MedicineXianyang 712000, Shaanxi, China
| | - Yin-Hai Dai
- Department of Clinical Medicine, Shaanxi University of Chinese MedicineXianyang 712046, Shaanxi, China
- Department of Surgical Oncology Medicine, Second Affiliated Hospital of Shaanxi University of Chinese MedicineXianyang 712000, Shaanxi, China
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10
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Liu G, Li F, Chen M, Luo Y, Dai Y, Hou P. SNRPD1/E/F/G Serve as Potential Prognostic Biomarkers in Lung Adenocarcinoma. Front Genet 2022; 13:813285. [PMID: 35356432 PMCID: PMC8959887 DOI: 10.3389/fgene.2022.813285] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 02/14/2022] [Indexed: 12/30/2022] Open
Abstract
Objectives: Sm proteins (SNRPB/D1/D2/D3/E/F/G), involved in pre-mRNA splicing, were previously reported in the tumorigenesis of several cancers. However, their specific role in lung adenocarcinoma (LUAD) remains obscure. Our study aims to feature abnormal expressions and mutations of genes for Sm proteins and assess their potential as therapeutic targets via integrated bioinformatics analysis. Methods: In this research, we explored the expression pattern and prognostic worth of genes for Sm proteins in LUAD across TCGA, GEO, UALCAN, Oncomine, Metascape, David 6.8, and Kaplan-Meier Plotter, and confirmed its independent prognostic value via univariate and multivariate cox regression analysis. Meanwhile, their expression patterns were validated by RT-qPCR. Gene mutations and co-expression of genes for Sm proteins were analyzed by the cBioPortal database. The PPI network for Sm proteins in LUAD was visualized by the STRING and Cytoscape. The correlations between genes for Sm proteins and immune infiltration were analyzed by using the “GSVA” R package. Results: Sm proteins genes were found upregulated expression in both LUAD tissues and LUAD cell lines. Moreover, highly expressed mRNA levels for Sm proteins were strongly associated with short survival time in LUAD. Genes for Sm proteins were positively connected with the infiltration of Th2 cells, but negatively connected with the infiltration of mast cells, Th1 cells, and NK cells. Importantly, Cox regression analysis showed that high SNRPD1/E/F/G expression were independent risk factors for the overall survival of LUAD. Conclusion: Our study showed that SNRPD1/E/F/G could independently predict the prognostic outcome of LUAD and was correlated with immune infiltration. Also, this report laid the foundation for additional exploration on the potential treatment target’s role of SNRPD1/E/F/G in LUAD.
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Affiliation(s)
- Gaohua Liu
- Department of Oncology Medicine, Fujian Medical University Union Hospital, Fuzhou, China
| | - Fuping Li
- Department of Clinical Medicine, Shaanxi University of Chinese Medicine, Xianyang, China
| | - Meichun Chen
- Department of Hematology, Fujian Medical University Union Hospital, Fuzhou, China
| | - Yang Luo
- Department of Oncology Medicine, Fujian Medical University Union Hospital, Fuzhou, China
| | - Yinhai Dai
- Department of Surgical Oncology Medicine, Second Affiliated Hospital of Shaanxi University of Chinese Medicine, Xianyang, China
- *Correspondence: Yinhai Dai, ; Peifeng Hou,
| | - Peifeng Hou
- Department of Oncology Medicine, Fujian Medical University Union Hospital, Fuzhou, China
- Fujian Medical University Stem Cell Research Institute, Fuzhou, China
- Fujian Key Laboratory of Translational Cancer Medicine, Fuzhou, China
- *Correspondence: Yinhai Dai, ; Peifeng Hou,
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11
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Wang H, Xu F, Lu L, Yang F, Huang X, Lv L, Hu H, Jiang Y. The diagnostic and prognostic significance of small nuclear ribonucleoprotein Sm D1 aberrantly high expression in hepatocellular carcinoma. J Cancer 2022; 13:184-201. [PMID: 34976182 PMCID: PMC8692702 DOI: 10.7150/jca.65225] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 11/09/2021] [Indexed: 12/29/2022] Open
Abstract
Small nuclear ribonucleoprotein Sm D1 (SNRPD1), one of the crucial genes encoding core spliceosome components, was abnormally highly expressed in multiple types of tumors. In this study, we investigated the diagnostic and prognostic significance of SNRPD1 in hepatocellular carcinoma (HCC). The investigation of datasets from GEO and TCGA databases revealed that SNRPD1 expression in HCC was significantly higher than adjacent normal liver tissues, which was validated by immunohistochemistry (IHC). Both GO, KEGG analysis showed that the SNRPD1 co-expressed genes mainly enriched in Cell division, Nuclear import, mRNA splicing via spliceosome, Ribosome, Cell cycle, etc. Survival analysis from the GSE14520 dataset and 154 HCC cohorts exhibited a significant association of high SNRPD1 expression with poor overall survival and recurrence-free survival. ROC analysis showed that the abnormally high SNRPD1 mRNA expression has diagnostic significance in distinguishing between HCC and normal liver tissue (AUC = 0.819). Gene set enrichment analysis (GSEA) demonstrated that the high expression of SNRPD1 might regulate HCC tumorigenesis and progression by affecting the cell cycle, mismatch repair, DNA replication, and RNA degradation, etc. The luciferase report assay revealed that SNRPD1 was the direct target gene of miR-100 manifested by decreased SNRPD1 expression and luciferase activity in the HCC cells upon miR-100 overexpression. Finally, SNRPD1 may as an oncogene affecting the progression of HCC through regulates the mTOR pathway and autophagy.
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Affiliation(s)
- Huaxiang Wang
- The Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, Fujian 350025, PR China
| | - Fengfeng Xu
- The Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, Fujian 350025, PR China
- Department of Hepatobiliary Surgery, 900 Hospital of the Joint Logistic Team, Fuzhou, Fujian 350025, PR China
| | - Lingling Lu
- The Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, Fujian 350025, PR China
| | - Fang Yang
- The Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, Fujian 350025, PR China
- Department of Hepatobiliary Surgery, 900 Hospital of the Joint Logistic Team, Fuzhou, Fujian 350025, PR China
| | - Xinghua Huang
- The Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, Fujian 350025, PR China
- Department of Hepatobiliary Surgery, 900 Hospital of the Joint Logistic Team, Fuzhou, Fujian 350025, PR China
| | - Lizhi Lv
- The Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, Fujian 350025, PR China
- Department of Hepatobiliary Surgery, 900 Hospital of the Joint Logistic Team, Fuzhou, Fujian 350025, PR China
| | - Huanzhang Hu
- The Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, Fujian 350025, PR China
- Department of Hepatobiliary Surgery, 900 Hospital of the Joint Logistic Team, Fuzhou, Fujian 350025, PR China
| | - Yi Jiang
- The Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, Fujian 350025, PR China
- Department of Hepatobiliary Surgery, 900 Hospital of the Joint Logistic Team, Fuzhou, Fujian 350025, PR China
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