1
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Cheng X, Yang F, Li Y, Cao Y, Zhang M, JI J, Bai Y, Li Q, Yu Q, Gao D. The crosstalk role of CDKN2A between tumor progression and cuproptosis resistance in colorectal cancer. Aging (Albany NY) 2024; 16:10512-10538. [PMID: 38888512 PMCID: PMC11236303 DOI: 10.18632/aging.205945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 04/15/2024] [Indexed: 06/20/2024]
Abstract
BACKGROUND Cuproptosis is a type of cell death characterized by excessive copper-lipid reactions in the tricarboxylic acid cycle, resulting in protein toxicity stress and cell death. Although known as a cuproptosis inhibitor through CRISPR-Cas9 screening, the role of cyclin-dependent kinase inhibitor 2A (CDKN2A) in cuproptosis resistance and its connection to tumor development remains unclear. METHODS In this study, we combined single-cell sequencing, spatial transcriptomics, pathological image analysis, TCGA multi-omics analysis and in vitro experimental validation to comprehensively investigate CDKN2A distribution, expression, epigenetic modification, regulation and genomic features in colorectal cancer cells. We further explored the associations between CDKN2A and cellular pathway, immune infiltration and spatial signal communication. RESULTS Our findings showed an increasing trend in cuproptosis in the trajectory of tumor progression, accompanied by an upward trend of CDKN2A. CDKN2A underwent transcriptional activation by MEF2D and via the SNHG7/miR-133b axis, upregulating glycolysis, copper metabolism and copper ion efflux. CDKN2A likely drives epithelial-mesenchymal transition (EMT) and progression by activating Wnt signaling. CDKN2A is associated with high genomic instability and sensitivity to radiation and chemotherapy. Tumor regions expressing CDKN2A exhibit distinctive SPP1+ tumor-associated macrophage (TAM) infiltration and MMP7 enrichment, along with unique signaling crosstalk with adjacent areas. CONCLUSIONS CDKN2A mediates cuproptosis resistance through regulating glycolysis and copper homeostasis, accompanied by a malignant phenotype and pro-tumor niche. Radiation and chemotherapy are expected to potentially serve as therapeutic approaches for cuproptosis-resistant colorectal cancer with high CDKN2A expression.
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Affiliation(s)
- Xifu Cheng
- Department of Gastroenterology and Hepatology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
- Department of Pathogen Biology and Immunology, School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
- School of Ophthalmology and Optometry, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
| | - Famin Yang
- Department of Pathogen Biology and Immunology, School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
| | - Yuanheng Li
- Queen Mary School, Jiangxi Medical College, Nanchang University, Nanchang 330031, China
- Department of Gastroenterology and Hepatology, Shenzhen Hospital of Southern Medical University, Shenzhen 518000, China
| | - Yuke Cao
- School of Ophthalmology and Optometry, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
| | - Meng Zhang
- Department of Pathogen Biology and Immunology, School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
| | - Jiameng JI
- Department of Pathogen Biology and Immunology, School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
| | - Yuxiao Bai
- Department of Pathogen Biology and Immunology, School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
| | - Qing Li
- Department of Oncology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
| | - Qiongfang Yu
- Department of Gastroenterology and Hepatology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
| | - Dian Gao
- Department of Pathogen Biology and Immunology, School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
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Silva-Rodríguez P, Bande M, Pardo M, Domínguez F, Loidi L, Blanco-Teijeiro MJ. Bilateral Uveal Melanoma: An Insight into Genetic Predisposition in Four New Unrelated Patients and Review of Published Cases. J Clin Med 2024; 13:3035. [PMID: 38892746 PMCID: PMC11172988 DOI: 10.3390/jcm13113035] [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: 04/15/2024] [Revised: 05/12/2024] [Accepted: 05/17/2024] [Indexed: 06/21/2024] Open
Abstract
Background: Primary bilateral uveal melanoma (BUM) is an exceptionally rare form of uveal melanoma (UM). This study aimed to explore the potential existence of a genetic predisposition towards the development of BUM. Methods: We employed an exome sequencing approach on germline DNA from four unrelated patients diagnosed with BUM, seeking pathogenic or likely pathogenic variants indicative of a genetic predisposition to UM. Results: None of the patients exhibited pathogenic variants in the BAP1 gene. However, loss-of-function (LoF) variants in the TERF2IP and BAX genes were identified in two of the BUM patients. For patients BUM1 and BUM2, no pathogenic/likely pathogenic variants of significant clinical relevance to BUM were found to warrant inclusion in this report. Conclusions: Our findings suggest the presence of yet-to-be-discovered genes that may contribute to UM predisposition, as evidenced by the absence of pathogenic variants in known UM predisposition genes among the four BUM patients studied. The TERF2IP and BAX genes emerge as noteworthy candidates for further investigation regarding their role in genetic predisposition to UM. Specifically, the potential role of UM as a candidate cancer within the spectrum of cancers linked to pathogenic variants in the TERF2IP gene and other genes associated with the shelterin complex warrants further examination. Additional functional studies are necessary to support or challenge this hypothesis.
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Affiliation(s)
- Paula Silva-Rodríguez
- Fundación Pública Galega de Medicina Xenómica (FPGMX), 15706 Santiago de Compostela, Spain; (P.S.-R.); (L.L.)
- Grupo de Oftalmología Traslacional, Área Oncología, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), 15706 Santiago de Compostela, Spain;
| | - Manuel Bande
- Grupo de Oftalmología Traslacional, Área Oncología, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), 15706 Santiago de Compostela, Spain;
- Department of Ophthalmology, Clinical University Hospital of Santiago de Compostela, 15706 Santiago de Compostela, Spain
| | - María Pardo
- Grupo Obesidómica, Área de Endocrinología, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), 15706 Santiago de Compostela, Spain;
| | - Fernando Domínguez
- Department of Physiology and Centro de Investigaciones en Medicina Molecular y Enfermedades Crónicas (CiMUS), University of Santiago de Compostela, 15782 Santiago de Compostela, Spain;
| | - Lourdes Loidi
- Fundación Pública Galega de Medicina Xenómica (FPGMX), 15706 Santiago de Compostela, Spain; (P.S.-R.); (L.L.)
| | - María José Blanco-Teijeiro
- Grupo de Oftalmología Traslacional, Área Oncología, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), 15706 Santiago de Compostela, Spain;
- Department of Ophthalmology, Clinical University Hospital of Santiago de Compostela, 15706 Santiago de Compostela, Spain
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3
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Ma B, Wei X, Zhou S, Yang M. MCTS1 enhances the proliferation of laryngeal squamous cell carcinoma via promoting OTUD6B-1 mediated LIN28B deubiquitination. Biochem Biophys Res Commun 2023; 678:128-134. [PMID: 37634410 DOI: 10.1016/j.bbrc.2023.08.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 08/16/2023] [Indexed: 08/29/2023]
Abstract
The aberrant upregulation of MCTS1 Re-Initiation and Release Factor (also known as Malignant T-cell-amplified sequence 1, MCTS1) can promote laryngeal squamous cell carcinoma (LSCC). It might act as a binding partner of multiple proteins. In this study, we further explored the expression of potential interaction between MCTS1 and OTU domain-containing protein 6B (OTUD6B) and its influence on the ubiquitination and degradation of OTUD6B's substrate in LSCC. LSCC cell lines AMC-HN-8 and TU177 were utilized for assessing protein-protein interaction, protein degradation and tumor growth in vitro and in vivo. The results showed that MCTS1 interacts with OUTD6B isoform 1 (OTUD6B-1) in the cell lines. Higher OTUD6B-1 expression is associated with significantly shorter progression-free interval in LSCC patients. OTUD6B positively modulated the expression of cyclin D1, cyclin E1 and c-Myc and LSCC cell proliferation in vitro and in vivo. MCTS1 negatively modulated the degradation of LIN28B in G1/S cells, via enhancing OTUD6B-mediated cleaving of K48-branched ubiquitin chains from LIN28B. OTUD6B or LIN28B shRNA weakened MCTS1 overexpression-induced cyclin D1 and c-Myc protein expression and LSCC cell proliferation. In summary, this study revealed that MCTS1 could enhance LSCC proliferation partially via the OTUD6B-LIN28B axis.
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Affiliation(s)
- Binjuan Ma
- Otorhinolaryngology-Head and Neck Surgery, Gansu Provincial Hospital, Lanzhou, China
| | - Xiaoquan Wei
- Otorhinolaryngology-Head and Neck Surgery, Gansu Provincial Hospital, Lanzhou, China
| | - Shijie Zhou
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Mengsheng Yang
- Otorhinolaryngology-Head and Neck Surgery, Gansu Provincial Hospital, Lanzhou, China.
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4
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Jiang H, Zhu S, Wu B, Su Y, Wang Q, Lei Y, Shao Q, Gao Y, Gao K, Wu G. CDK2 and CDK4 targeted liensinine inhibits the growth of bladder cancer T24 cells. Chem Biol Interact 2023; 382:110624. [PMID: 37423554 DOI: 10.1016/j.cbi.2023.110624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 07/02/2023] [Accepted: 07/05/2023] [Indexed: 07/11/2023]
Abstract
Bladder cancer (BCa) is a urinary tumor with limited treatment options and high mortality. Liensinine (LIEN), a natural bisbenzylisoquinoline alkaloid, has shown excellent anti-tumor effects in numerous preclinical studies. However, the anti-BCa effect of LIEN remains unclear. To the best of our knowledge, this is the first study to investigate the molecular mechanism of LIEN in the management of BCa. First, we identified the treatment-related targets of BCa; those that repeatedly occur in more than two databases, including GeneCards, Online Mendelian Inheritance in Man, DisGeNET, Therapeutic Target Database, and Drugbank. The SwissTarget database was used to screen LIEN-related targets, and those with a probability >0 were possible LIEN targets. The prospective targets of LIEN in the treatment of BCa were then determined using a Venn diagram. Second, we discovered that the PI3K/AKT pathway and senescence mediated the anti-BCa action of LIEN by using GO and KEGG enrichment analysis to explore the function of LIEN therapeutic targets. A protein-protein interaction network was created using the String website, and six algorithms of the CytoHubba plug-in were then used in Cytoscape to assess the core targets of LIEN for the therapy of BCa. The outcomes of molecular docking and dynamics simulation demonstrated that CDK2 and CDK4 proteins were the direct targets of LIEN in the management of BCa, among which CDK2 was more stable in binding to LIEN than CDK4. Finally, in vitro experiments showed that LIEN inhibited the activity and proliferation of T24 cells. The expression of p-/AKT, CDK2, and CDK4 proteins progressively decreased, while the expression and fluorescence intensity of the senescence-related protein, γH2AX, gradually increased with increasing LIEN concentration in T24 cells. Therefore, our data suggest that LIEN may promote senescence and inhibit proliferation by inhibiting the CDK2/4 and PI3K/AKT pathways in BCa.
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Affiliation(s)
- Hanbing Jiang
- Department of Radiation Oncology, Tangdu Hospital, The Second Affiliated Hospital of Air Force Military Medical University, Xi'an, 710038, China
| | - Siying Zhu
- Department of Radiation Oncology, Tangdu Hospital, The Second Affiliated Hospital of Air Force Military Medical University, Xi'an, 710038, China
| | - Bin Wu
- Department of Urology, Xi'an People's Hospital(Xi'an Fourth Hospital), School of Life Sciences and Medicine, Northwest University, Xi'an, 710199, China
| | - Yinyin Su
- Department of Emergency, Tangdu Hospital, The Second Affiliated Hospital of Air Force Military Medical University, Xi'an, 710038, China
| | - Qiming Wang
- Department of Radiation Oncology, Tangdu Hospital, The Second Affiliated Hospital of Air Force Military Medical University, Xi'an, 710038, China
| | - Yonghua Lei
- Department of Urology, Xi'an People's Hospital(Xi'an Fourth Hospital), School of Life Sciences and Medicine, Northwest University, Xi'an, 710199, China
| | - Qiuju Shao
- Department of Radiation Oncology, Tangdu Hospital, The Second Affiliated Hospital of Air Force Military Medical University, Xi'an, 710038, China
| | - Yun Gao
- Department of Neurosurgery, 521 Hospital of Norinco Group, Xi'an, Shaanxi, 710065, China
| | - Ke Gao
- Department of Urology, Xi'an People's Hospital(Xi'an Fourth Hospital), School of Life Sciences and Medicine, Northwest University, Xi'an, 710199, China.
| | - Guojun Wu
- Department of Urology, Xi'an People's Hospital(Xi'an Fourth Hospital), School of Life Sciences and Medicine, Northwest University, Xi'an, 710199, China.
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5
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Kai K, Han-bing J, Bing-lin C, Shu-jun Z. Network pharmacology, molecular docking and experimental verification help unravel chelerythrine's potential mechanism in the treatment of gastric cancer. Heliyon 2023; 9:e17393. [PMID: 37449157 PMCID: PMC10336441 DOI: 10.1016/j.heliyon.2023.e17393] [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: 03/17/2023] [Revised: 06/11/2023] [Accepted: 06/15/2023] [Indexed: 07/18/2023] Open
Abstract
Gastric cancer (GC) is a deadly malignant tumor with a high fatality rate and limited curative options. A growing body of research suggests that network pharmacology can replace traditional methods for determining the precise mechanism of action of medicinal substances in conditions such as cancer. The goal of this study was to clarify the biological mechanism of chelerythrine (CHE) and develop a prediction target for CHE against GC using network pharmacology. First, the genes related to GC were identified from the databases Genecards, Disgenet, Online Mendelian Inheritance in Man, Therapeutic Target Database, and Drugbank, and the targets of CHE were obtained from the SwissTargetPrediction database. Fifty linked targets were identified as anti-GC targets of CHE. Functional enrichment and pathway analyses revealed important biological mechanisms mediated by these targets. The core target PIK3CA of CHE anti-GC was obtained using the protein-protein interaction network, CytoHubba plug-in, and Human Protein Atlas. Molecular docking studies revealed that CHE has a strong affinity for PIK3CA (-10.5 kcal/mol). In addition, we used MTT, colony formation, wound-healing, Transwell®, and flow cytometry experiments to confirm that CHE inhibited the proliferation and migration of GC cells and induced cell cycle arrest and apoptosis. Finally, western blotting results showed that CHE downregulated the expression of the PIK3CA protein and inhibited the activation of the PI3K/AKT signaling pathway. Therefore, we concluded that CHE inhibited GC cell proliferation and migration and induced cell cycle arrest and apoptosis by targeting the PIK3CA protein to inhibit the PI3K/AKT pathway activity.
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Affiliation(s)
- Kang Kai
- Department of Integrated Traditional Chinese and Western Medicine Oncology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, 150000, PR China
| | - Jiang Han-bing
- Department of Integrated Traditional Chinese and Western Medicine Oncology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, 150000, PR China
- Department of Radiation Oncology, Tangdu Hospital, The Second Affiliated Hospital of Air Force Military Medical University, Xi'an, 710038, China
| | - Cheng Bing-lin
- Department of Integrated Traditional Chinese and Western Medicine Oncology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, 150000, PR China
| | - Zhang Shu-jun
- Department of Pathology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, 150000, PR China
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6
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Li S, Zhu J, Lubman DM, Zhou H, Tang H. GlycoSLASH: Concurrent Glycopeptide Identification from Multiple Related LC-MS/MS Data Sets by Using Spectral Clustering and Library Searching. J Proteome Res 2023; 22:1501-1509. [PMID: 36802412 PMCID: PMC10164058 DOI: 10.1021/acs.jproteome.3c00066] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Liquid chromatography coupled with tandem mass spectrometry is commonly adopted in large-scale glycoproteomic studies involving hundreds of disease and control samples. The software for glycopeptide identification in such data (e.g., the commercial software Byonic) analyzes the individual data set and does not exploit the redundant spectra of glycopeptides presented in the related data sets. Herein, we present a novel concurrent approach for glycopeptide identification in multiple related glycoproteomic data sets by using spectral clustering and spectral library searching. The evaluation on two large-scale glycoproteomic data sets showed that the concurrent approach can identify 105%-224% more spectra as glycopeptides compared to the glycopeptide identification on individual data sets using Byonic alone. The improvement of glycopeptide identification also enabled the discovery of several potential biomarkers of protein glycosylations in hepatocellular carcinoma patients.
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Affiliation(s)
- Sujun Li
- Department of Blood Transfusion, The First Affiliated Hospital of Nanchang University, Nanchang 330000, China.,JiangXi Key Laboratory of Transfusion Medicine, Nanchang 330000, China.,Luddy School of Informatics, Computing and Engineering, Indiana University, Bloomington, Indiana 47408, United States
| | - Jianhui Zhu
- Department of Surgery, University of Michigan, Medical Center, Ann Arbor, Michigan 48109, United States
| | - David M Lubman
- Department of Surgery, University of Michigan, Medical Center, Ann Arbor, Michigan 48109, United States
| | - He Zhou
- Shenzhen Dengding Biopharma Co. Ltd., Shenzhen 518000, China
| | - Haixu Tang
- Luddy School of Informatics, Computing and Engineering, Indiana University, Bloomington, Indiana 47408, United States
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7
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Liu NQ, Cao WH, Wang X, Chen J, Nie J. Cyclin genes as potential novel prognostic biomarkers and therapeutic targets in breast cancer. Oncol Lett 2022; 24:374. [PMID: 36238849 PMCID: PMC9494629 DOI: 10.3892/ol.2022.13494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 08/15/2022] [Indexed: 11/06/2022] Open
Affiliation(s)
- Nian-Qiu Liu
- Department of Breast Surgery, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Center, Kunming, Yunnan 650000, P.R. China
| | - Wei-Han Cao
- Department of Ultrasound, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650000, P.R. China
| | - Xing Wang
- Department of Breast Surgery, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Center, Kunming, Yunnan 650000, P.R. China
| | - Junyao Chen
- Department of Breast Surgery, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Center, Kunming, Yunnan 650000, P.R. China
| | - Jianyun Nie
- Department of Breast Surgery, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Center, Kunming, Yunnan 650000, P.R. China
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8
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Huang X, Wang H, Xu F, Lv L, Wang R, Jiang B, Liu T, Hu H, Jiang Y. Overexpression of chaperonin containing TCP1 subunit 7 has diagnostic and prognostic value for hepatocellular carcinoma. Aging (Albany NY) 2022; 14:747-769. [PMID: 35073517 PMCID: PMC8833116 DOI: 10.18632/aging.203809] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 12/20/2021] [Indexed: 11/25/2022]
Abstract
Chaperonin containing TCP1 subunit 7 (CCT7) regulates the expression of many tumor-related proteins. We investigated the diagnostic and prognostic value of CCT7 expression for hepatocellular carcinoma (HCC). In datasets from The Cancer Genome Atlas and the Gene Expression Omnibus, CCT7 mRNA levels were greater in HCC tissues than adjacent normal tissues, and these results were validated using immunohistochemistry. In patients with early-stage disease and low alpha-fetoprotein expression, CCT7 expression was still higher in HCC tissues than normal tissues. Receiver operating characteristic curve analyses indicated that CCT7 expression had better diagnostic value than alpha-fetoprotein for HCC patients with early-stage disease and low alpha-fetoprotein expression. The positive predictive value of CCT7 expression was higher than that of alpha-fetoprotein expression. Higher CCT7 mRNA and protein levels were independent risk factors for poorer overall and recurrence-free survival in HCC patients. Greater methylation of the CpG site cg19515186 was associated with better overall survival in HCC patients. Genes co-expressed with CCT7 were upregulated in HCC and associated with poorer overall survival. Gene Ontology, Kyoto Encyclopedia of Genes and Genomes and Gene Set Enrichment Analyses demonstrated that CCT7 expression correlated with spliceosome signaling. These findings demonstrate that CCT7 has diagnostic and prognostic value for HCC.
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Affiliation(s)
- Xinghua Huang
- The Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, Fujian 350025, PR China.,Department of Hepatobiliary Surgery, 900th Hospital of the Joint Logistics Team, Fuzhou, Fujian 350025, PR China
| | - Huaxiang Wang
- The Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, Fujian 350025, PR China.,Department of Hepatobiliary and Pancreatic Surgery, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, PR China
| | - Fengfeng Xu
- The Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, Fujian 350025, PR China.,Department of Hepatobiliary Surgery, 900th Hospital of the Joint Logistics 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, 900th Hospital of the Joint Logistics Team, Fuzhou, Fujian 350025, PR China
| | - Ruling Wang
- Department of Hepatobiliary and Pancreatic Surgery, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, PR China
| | - Bin Jiang
- Department of Hepatobiliary and Pancreatic Surgery, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, PR China
| | - Tingting Liu
- Department of Hepatobiliary Surgery, 900th Hospital of the Joint Logistics Team, Fuzhou, Fujian 350025, PR China.,Graduate School of Fujian University of Traditional Chinese Medicine, 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, 900th Hospital of the Joint Logistics 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, 900th Hospital of the Joint Logistics Team, Fuzhou, Fujian 350025, PR China
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Verma HK, Bhaskar LVKS. SARS-CoV-2 infection in people with pre-existing liver disease: Further research is warranted. World J Gastroenterol 2021; 27:7855-7858. [PMID: 34963747 PMCID: PMC8661380 DOI: 10.3748/wjg.v27.i45.7855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 06/13/2021] [Accepted: 09/08/2021] [Indexed: 02/06/2023] Open
Abstract
Patients with severe liver disease who have been infected with severe acute respiratory syndrome coronavirus-2 (coronavirus disease 2019) frequently develop acute respiratory distress syndrome and multiple organ failure, with a high mortality rate, as a result of the hyper-proinflammatory state known as the cytokine storm. Clinicians must recognize cytokine storms earlier to avoid intensive care admission and multi-organ damage, a critical life-threatening condition with prognostic and therapeutic implications
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Affiliation(s)
- Henu Kumar Verma
- Department of Immunopathology, Institute of lungs Biology and Disease, Comprehensive Pneumology Center, Neuherberg 85764, Munich, Germany
| | - LVKS Bhaskar
- Zoology, Guru Ghasidas Vishwavidyalaya, Bilaspur 495001, Chhattisgarh, India
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10
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Tang W, Xu F, Zhao M, Zhang S. Ferroptosis regulators, especially SQLE, play an important role in prognosis, progression and immune environment of breast cancer. BMC Cancer 2021; 21:1160. [PMID: 34715817 PMCID: PMC8555209 DOI: 10.1186/s12885-021-08892-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 10/20/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Ferroptosis, a new form of programmed cell death, has great potential for cancer treatment. However, the roles of ferroptosis-related (FR) genes in breast cancer (BC) remain elusive. MATERIALS AND METHODS Using TCGA database, a novel FR risk signature was constructed through the Lasso regression analysis. Meanwhile, its prognostic value was assessed by a series of survival analyses. Besides, a nomogram was constructed to predict the overall survival rate (OSR) of individual at 1,3,5 year. Four validation cohorts (n = 2248), including METABRIC, GSE58812, GSE20685 and ICGC-KR datasets, were employed to test the prognostic value of FR risk signature. The effects of FR risk signature on BC immune microenvironment were explored by CIBERSORT algorithm and ssGSEA method. The histological expressions of FR risk genes were presented by HPA database. The biofunctions of SQLE were determined by qPCR, MTT, wound-healing and Transwell assays. RESULTS We constructed a novel FR risk signature consisting of eight genes. High FR risk led a poor prognosis and was identified as an independent prognostic factor. Besides, A higher proportion of patients with luminal A type was observed in low-risk group (53%), while a higher proportion of patients with basal type in high-risk group (24%). FR risk score could discriminate the prognostic difference of most clinical subgroups, except for M1 stage, HER2 and basal types. Moreover, its prognostic value was successfully validated in other four cohorts. Through immune analyses, we found that the reduced infiltration levels of CD8+ and NK cells, whereas the enhanced activity of antigen presentation process appeared in high FR risk. Then, FR risk score was found to weakly correlate with the expressions of six immune checkpoints. Through the experiments in vitro, we confirmed that overexpression of SQLE could promote, whereas blocking SQLE could inhibit the proliferative, migrative and invasive abilities of BC cells. CONCLUSIONS FR risk signature was conducive to BC prognostic assessment. High FR risk level was closely associated with BC immunosuppression, but may not predict ICIs efficacy. Moreover, SQLE was identified as a crucial cancer-promoting gene in BC. Our findings provide new insights into prognostic assessment and molecular mechanism of BC.
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Affiliation(s)
- Wenqing Tang
- Department of Medicine, Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China.,Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157, West Five Road, Xi'an, 710000, Shaanxi, China
| | - Fangshi Xu
- Department of Medicine, Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
| | - Meng Zhao
- Department of Medicine, Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
| | - Shuqun Zhang
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157, West Five Road, Xi'an, 710000, Shaanxi, China.
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11
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Xu F, Zhang Z, Zhao Y, Zhou Y, Pei H, Bai L. Bioinformatic mining and validation of the effects of ferroptosis regulators on the prognosis and progression of pancreatic adenocarcinoma. Gene 2021; 795:145804. [PMID: 34175402 DOI: 10.1016/j.gene.2021.145804] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 05/06/2021] [Accepted: 06/22/2021] [Indexed: 02/07/2023]
Abstract
Ferroptosis, a new form of programmed cell death, provides a new option for anti-tumor treatment. However, the roles of ferroptosis-related (FR) genes in pancreatic adenocarcinoma (PAAD) were not fully elaborated. In the present study, 185 TCGA samples and 81 ICGC samples were used as training and validation cohorts, respectively. A novel FR risk signature (ALOX5, ALOX12, PTGS2, SAT1, STEAP3 and SQLE) was constructed via the Lasso regression analysis. In TCGA cohort, the risk signature was identified as an independent prognostic factor. Decision curve analysis (DCA) indicated that FR risk score could increase the net benefit when making clinical-decision. In addition, we constructed a nomogram to predict the overall survival rate (OSR) of individual at 1,2,3 year. Meanwhile, the prognostic value was partly validated in ICGC cohort. Through immune analyses, we found that high FR risk could affect the immune abundances of five lymphocytes but not effectively affect the activities of immune-related pathways. The expressions of most FR risk genes did not correlate with that of PD-L1(CD274) and CTLA4. Further, through RT-qPCR tests, the expressions of PTGS2 and SQLE were proven to be significantly upregulated in normal pancreatic duct epithelia cell (HPDE6-C7) compared to pancreatic cancer cells (SW1990 and BxPC-3). MTT, wound-healing and transwell assays revealed that silencing PTGS2 and SQLE could inhibit the proliferation, migration and invasion of pancreatic cancer cells. Besides, western-blot assays showed that blocking PTGS2 and SQLE expressions could suppress the protein expressions of cyclin D1 and N-cadherin, but facilitate that of E-cadherin, which suggested that they were involved in the epithelial to mesenchymal transition (EMT). Collectively, FR risk signature provides an important complement for PAAD prognostic analysis. High FR risk level can adversely affect anti-tumor immune process, but may not serve as a predictive marker of ICIs efficacy. PTGS2 and SQLE are proven to possess cancer-promoting abilities in PAAD.
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Affiliation(s)
- Fangshi Xu
- Department of Emergency, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710000, Shaanxi Province, China; Department of Medicine, Xi'an Jiaotong University, Xi'an 710000, Shaanxi Province, China.
| | - Zhengliang Zhang
- Department of Emergency, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710000, Shaanxi Province, China.
| | - Yidi Zhao
- Department of Emergency, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710000, Shaanxi Province, China.
| | - Yang Zhou
- Department of Emergency, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710000, Shaanxi Province, China.
| | - Honghong Pei
- Department of Emergency, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710000, Shaanxi Province, China.
| | - Ling Bai
- Department of Emergency, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710000, Shaanxi Province, China.
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12
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Tan M, Meng J, Sun X, Fu X, Wang R. EPS8 supports pancreatic cancer growth by inhibiting BMI1 mediated proteasomal degradation of ALDH7A1. Exp Cell Res 2021; 407:112782. [PMID: 34391775 DOI: 10.1016/j.yexcr.2021.112782] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/11/2021] [Accepted: 07/17/2021] [Indexed: 01/29/2023]
Abstract
Aldehyde dehydrogenase 7 family member A1 (ALDH7A1) is an enzyme catalyzing lipid peroxidation of fatty aldehydes. It plays a critical role in sustaining high oxygen consumption rate (OCR) and ATP production in pancreatic ductal adenocarcinoma (PADC). However, why PADC cells maintain a relatively high level of ALDH7A1 concentration is still not well understood. In the current study, we explored the interplay between epidermal growth factor receptor kinase substrate 8 (EPS8) and ALDH7A1 in PADC cells. PADC cell lines MIA PaCa-2 and AsPANC-1 were used for in vitro and in vivo studies. The co-IP assay showed mutual interactions between Flag-EPS8 and Myc-ALDH7A1 in both MIA PaCa-2 and AsPANC-1 cells. EPS8 knockdown resulted in decreased ALDH7A1 protein levels and increased poly-ubiquitination. An interaction was observed between ALDH7A1 and BMI1 but not between BMI1 and EPS8. BMI1 knockdown reduced ALDH7A1 poly-ubiquitination and degradation caused by EPS8 knockdown. Dual EPS8 and ALDH7A1 knockdown had a synergistic effect on suppressing PADC cell proliferation in vitro and in vivo. In conclusion, this study revealed that EPS8 supports PADC growth by interacting with ALDH7A1 and inhibiting BMI1 mediated proteasomal degradation of ALDH7A1.
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Affiliation(s)
- Mingzhu Tan
- Internal Medicine, Weifang People's Hospital Brain Hospital, Weifang, Shandong, 261000, China
| | - Jun Meng
- Occupational Medicine, Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Xiaojuan Sun
- Occupational Medicine, Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Xiaowei Fu
- Department of Neonatology, Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Ruihao Wang
- Internal Medicine, Weifang People's Hospital Brain Hospital, Weifang, Shandong, 261000, China.
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13
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Madda R, Chen CM, Chen CF, Wang JY, Wu PK, Chen WM. Effect of Cryoablation Treatment on the Protein Expression Profile of Low-Grade Central Chondrosarcoma Identified by LC-ESI-MS/MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1469-1489. [PMID: 34003650 DOI: 10.1021/jasms.1c00068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The use of cryoablation/cryosurgery in treating solid tumors has been proven as a unique technique that uses lethal temperatures to destroy the tumors and impart better functions for the affected organs. This novel technique recently demonstrated the best clinical results in chondrosarcoma (CSA) with faster recovery, less recurrence, and metastasis. Due to the resistant nature of CSA to chemo and radiation therapy, cryoablation comes to light as the best alternative approach. Therefore, for the first time, we aimed to compare CSA-untreated with cryoablation treated samples to discover some potential markers that may provide various clues in terms of diagnosis and pathophysiology and may facilitate the development of novel methods to treat sarcoma efficiently. To find the altered proteins among both groups, a mass-based label-free approach was employed and identified a total of 160 significantly altered proteins. Among these, 138 proteins were dysregulated with <1- to -0.1-fold, 18 proteins were up-regulated with >3 folds, and four proteins were similarly expressed in the untreated group compared to the treated. Interestingly, the differential expressions of proteins from the untreated group showed contrast expressions in the treated group. Furthermore, the functional enrichment analysis revealed that most of the identified proteins from this study were associated with various significant pathways such as glycolysis, MAPK activation, PI3K-Akt signaling, extracellular matrix degradation, etc. In addition, two protein expressions, such as fibronectin and annexin-1, were validated by immunoblot analysis. Therefore, this study signifies the most comprehensive discovery of altered protein expressions to date and the first large-scale detection of protein profiles from CSA-cryoablation treated compared to untreated. This work may serve as the basis for future research to open novel treatment options for chondrosarcoma.
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Affiliation(s)
- Rashmi Madda
- Department of Orthopedics & Traumatology, Taipei Veterans General Hospital, Taipai 11217 Taiwan
- Department of orthopedics, Therapeutical and Musculoskeletal Tumor Research Center, Taipei Veterans General Hospital, Taipai 11217 Taiwan
- Orthopedic Department, School of Medicine, National Yang-Ming University, Taipai 11221 Taiwan
- Institute of Clinical Medicine, School of Medicine, National Yang-Ming University, Taipai 11221 Taiwan
| | - Chao-Ming Chen
- Department of Orthopedics & Traumatology, Taipei Veterans General Hospital, Taipai 11217 Taiwan
- Department of orthopedics, Therapeutical and Musculoskeletal Tumor Research Center, Taipei Veterans General Hospital, Taipai 11217 Taiwan
- Orthopedic Department, School of Medicine, National Yang-Ming University, Taipai 11221 Taiwan
- Institute of Clinical Medicine, School of Medicine, National Yang-Ming University, Taipai 11221 Taiwan
| | - Cheng-Fong Chen
- Department of Orthopedics & Traumatology, Taipei Veterans General Hospital, Taipai 11217 Taiwan
- Department of orthopedics, Therapeutical and Musculoskeletal Tumor Research Center, Taipei Veterans General Hospital, Taipai 11217 Taiwan
- Orthopedic Department, School of Medicine, National Yang-Ming University, Taipai 11221 Taiwan
| | - Jir-You Wang
- Department of Orthopedics & Traumatology, Taipei Veterans General Hospital, Taipai 11217 Taiwan
- Department of orthopedics, Therapeutical and Musculoskeletal Tumor Research Center, Taipei Veterans General Hospital, Taipai 11217 Taiwan
- Orthopedic Department, School of Medicine, National Yang-Ming University, Taipai 11221 Taiwan
- Institute of Clinical Medicine, School of Medicine, National Yang-Ming University, Taipai 11221 Taiwan
| | - Po-Kuei Wu
- Department of Orthopedics & Traumatology, Taipei Veterans General Hospital, Taipai 11217 Taiwan
- Department of orthopedics, Therapeutical and Musculoskeletal Tumor Research Center, Taipei Veterans General Hospital, Taipai 11217 Taiwan
- Orthopedic Department, School of Medicine, National Yang-Ming University, Taipai 11221 Taiwan
- Institute of Clinical Medicine, School of Medicine, National Yang-Ming University, Taipai 11221 Taiwan
| | - Wei-Ming Chen
- Department of Orthopedics & Traumatology, Taipei Veterans General Hospital, Taipai 11217 Taiwan
- Department of orthopedics, Therapeutical and Musculoskeletal Tumor Research Center, Taipei Veterans General Hospital, Taipai 11217 Taiwan
- Orthopedic Department, School of Medicine, National Yang-Ming University, Taipai 11221 Taiwan
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14
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Girousse A, Mathieu M, Sastourné-Arrey Q, Monferran S, Casteilla L, Sengenès C. Endogenous Mobilization of Mesenchymal Stromal Cells: A Pathway for Interorgan Communication? Front Cell Dev Biol 2021; 8:598520. [PMID: 33490065 PMCID: PMC7820193 DOI: 10.3389/fcell.2020.598520] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 11/18/2020] [Indexed: 12/16/2022] Open
Abstract
To coordinate specialized organs, inter-tissue communication appeared during evolution. Consequently, individual organs communicate their states via a vast interorgan communication network (ICN) made up of peptides, proteins, and metabolites that act between organs to coordinate cellular processes under homeostasis and stress. However, the nature of the interorgan signaling could be even more complex and involve mobilization mechanisms of unconventional cells that are still poorly described. Mesenchymal stem/stromal cells (MSCs) virtually reside in all tissues, though the biggest reservoir discovered so far is adipose tissue where they are named adipose stromal cells (ASCs). MSCs are thought to participate in tissue maintenance and repair since the administration of exogenous MSCs is well known to exert beneficial effects under several pathological conditions. However, the role of endogenous MSCs is barely understood. Though largely debated, the presence of circulating endogenous MSCs has been reported in multiple pathophysiological conditions, but the significance of such cell circulation is not known and therapeutically untapped. In this review, we discuss current knowledge on the circulation of native MSCs, and we highlight recent findings describing MSCs as putative key components of the ICN.
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Affiliation(s)
- Amandine Girousse
- Stromalab, Université de Toulouse, CNRS ERL5311, EFS, INP-ENVT, INSERM U1031, Université Paul Sabatier, Toulouse, France
| | - Maxime Mathieu
- Stromalab, Université de Toulouse, CNRS ERL5311, EFS, INP-ENVT, INSERM U1031, Université Paul Sabatier, Toulouse, France
| | - Quentin Sastourné-Arrey
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Sylvie Monferran
- Stromalab, Université de Toulouse, CNRS ERL5311, EFS, INP-ENVT, INSERM U1031, Université Paul Sabatier, Toulouse, France
| | - Louis Casteilla
- Stromalab, Université de Toulouse, CNRS ERL5311, EFS, INP-ENVT, INSERM U1031, Université Paul Sabatier, Toulouse, France
| | - Coralie Sengenès
- Stromalab, Université de Toulouse, CNRS ERL5311, EFS, INP-ENVT, INSERM U1031, Université Paul Sabatier, Toulouse, France
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15
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Di Meo A, Sohaei D, Batruch I, Alexandrou P, Prassas I, Diamandis EP. Proteomic Profiling of the Human Tissue and Biological Fluid Proteome. J Proteome Res 2020; 20:444-452. [PMID: 33107741 DOI: 10.1021/acs.jproteome.0c00502] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
In-depth analysis of the human genome sequence has led to the annotation of approximately 20,000 human protein-coding genes. Although mass spectrometry (MS)-based workflows have made a great headway in achieving near genome-wide coverage, an equivalent complete map of the human proteome remains elusive. Delineating the spatial distribution of all human proteins at the organ, tissue, and cellular level can offer insight into health and disease and represents an excellent reference for the discovery of biomarkers and therapeutic targets. Here, we performed label-free liquid chromatography coupled to tandem MS (LC-MS/MS) to profile the normal human proteome. In total, we analyzed 117 samples from 46 normal tissues and organs at autopsy. Our high-resolution MS approach allowed for the quantification of 10,438 unique proteins. In order to expand our coverage of the human proteome, we combined our previously published biological fluid proteomic data from healthy individuals. We considered data from seven biological fluids, including urine, cerebrospinal fluid, synovial fluid, seminal plasma, sweat, cervical vaginal fluid, and nipple aspirate fluid. Overall, we generated tandem mass spectra corresponding to 13,028 unique human protein-coding genes. Although our analysis did not accomplish complete proteome coverage, it should be an important complementary resource for future biomarker discovery.
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Affiliation(s)
- Ashley Di Meo
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto M5T 3L9, Canada
| | - Dorsa Sohaei
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto M5T 3L9, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto ON M5S, Canada
| | - Ihor Batruch
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto M5T 3L9, Canada
| | - Pantelis Alexandrou
- Department of Forensic Medicine and Toxicology, School of Medicine, University of Athens, Athens 157 72, Greece
| | - Ioannis Prassas
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto M5T 3L9, Canada.,Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto M5T 3L9, Canada
| | - Eleftherios P Diamandis
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto M5T 3L9, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto ON M5S, Canada.,Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto M5T 3L9, Canada.,Department of Clinical Biochemistry, University Health Network, Toronto M5G 2C4, Canada
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16
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Patel M, Patel D, Datta S, Singh U. An immunochemistry-based screen for chemical inhibitors of DNA-protein interactions and its application to human CGGBP1. BMC Cancer 2020; 20:1016. [PMID: 33081720 PMCID: PMC7576722 DOI: 10.1186/s12885-020-07526-5] [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: 01/14/2020] [Accepted: 10/14/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Inhibition of DNA-binding of proteins by small-molecule chemicals holds immense potential in manipulating the activities of DNA-binding proteins. Such a chemical inhibition of DNA-binding of proteins can be used to modulate processes such as replication, transcription, DNA repair and maintenance of epigenetic states. This prospect is currently challenged with the absence of robust and generic protocols to identify DNA-protein interactions. Additionally, much of the current approaches to designing inhibitors requires structural information of the target proteins. METHODS We have developed a simple dot blot and immunodetection-based assay to screen chemical libraries for inhibitors of DNA-protein interactions. The assay has been applied to a library of 1685 FDA-approved chemicals to discover inhibitors of CGGBP1, a multifunctional DNA-binding protein with no known structure. Additional in vitro and in cellulo assays have been performed to verify and supplement the findings of the screen. RESULTS Our primary screen has identified multiple inhibitors of direct or indirect interactions between CGGBP1 and genomic DNA. Of these, one inhibitor, Givinostat, was found to inhibit direct DNA-binding of CGGBP1 in the secondary screen using purified recombinant protein as the target. DNA and chromatin immunoprecipitation assays reinforced the findings of the screen that Givinostat inhibits CGGBP1-DNA binding. CONCLUSIONS The assay we have described successfully identifies verifiable inhibitors of DNA-binding of protein; in this example, the human CGGBP1. This assay is customizable for a wide range of targets for which primary antibodies are available. It works with different sources of the target protein, cell lysates or purified recombinant preparations and does not require special equipment, DNA modifications or protein structural data. This assay is scalable and highly adaptable with the potential to discover inhibitors of transcription factors with implications in cancer biology.
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Affiliation(s)
- Manthan Patel
- HoMeCell Lab, Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat, 382355, India
| | - Divyesh Patel
- HoMeCell Lab, Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat, 382355, India
| | - Subhamoy Datta
- HoMeCell Lab, Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat, 382355, India
| | - Umashankar Singh
- HoMeCell Lab, Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat, 382355, India.
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17
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Alternative Polyadenylation Modification Patterns Reveal Essential Posttranscription Regulatory Mechanisms of Tumorigenesis in Multiple Tumor Types. BIOMED RESEARCH INTERNATIONAL 2020; 2020:6384120. [PMID: 32626751 PMCID: PMC7315320 DOI: 10.1155/2020/6384120] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/26/2020] [Accepted: 05/30/2020] [Indexed: 12/11/2022]
Abstract
Among various risk factors for the initiation and progression of cancer, alternative polyadenylation (APA) is a remarkable endogenous contributor that directly triggers the malignant phenotype of cancer cells. APA affects biological processes at a transcriptional level in various ways. As such, APA can be involved in tumorigenesis through gene expression, protein subcellular localization, or transcription splicing pattern. The APA sites and status of different cancer types may have diverse modification patterns and regulatory mechanisms on transcripts. Potential APA sites were screened by applying several machine learning algorithms on a TCGA-APA dataset. First, a powerful feature selection method, minimum redundancy maximum relevancy, was applied on the dataset, resulting in a feature list. Then, the feature list was fed into the incremental feature selection, which incorporated the support vector machine as the classification algorithm, to extract key APA features and build a classifier. The classifier can classify cancer patients into cancer types with perfect performance. The key APA-modified genes had a potential prognosis ability because of their significant power in the survival analysis of TCGA pan-cancer data.
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18
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Wang X, Yu Q, Ghareeb WM, Zhang Y, Lu X, Huang Y, Huang S, Sun Y, Lin J, Liu J, Chi P. Downregulated SPINK4 is associated with poor survival in colorectal cancer. BMC Cancer 2019; 19:1258. [PMID: 31888570 PMCID: PMC6938003 DOI: 10.1186/s12885-019-6484-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 12/18/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND SPINK4 is known as a gastrointestinal peptide in the gastrointestinal tract and is abundantly expressed in human goblet cells. The clinical significance of SPINK4 in colorectal cancer (CRC) is largely unknown. METHODS We retrieved the expression data of 1168 CRC patients from 3 Gene Expression Omnibus (GEO) datasets (GSE24551, GSE39582, GSE32323) and The Cancer Genome Atlas (TCGA) to compare the expression level of SPINK4 between CRC tissues and normal colorectal tissues and to evaluate its value in predicting the survival of CRC patients. At the protein level, these results were further confirmed by data mining in the Human Protein Atlas and by immunohistochemical staining of samples from 81 CRC cases in our own center. RESULTS SPINK4 expression was downregulated in CRC compared with that in normal tissues, and decreased SPINK4 expression at both the mRNA and protein levels was associated with poor prognosis in CRC patients from all 3 GEO datasets, the TCGA database and our cohort. Additionally, lower SPINK4 expression was significantly related to higher TNM stage. Moreover, in multivariate regression, SPINK4 was confirmed as an independent indicator of poor survival in CRC patients in all databases and in our own cohort. CONCLUSIONS We concluded that reduced expression of SPINK4 relates to poor survival in CRC, functioning as a novel indicator.
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Affiliation(s)
- Xiaojie Wang
- Department of Colorectal Surgery, Union Hospital, Fujian Medical University, 29 Xin-Quan Road, Fuzhou, Fujian, 350001, People's Republic of China
| | - Qian Yu
- Department of Pathology, Union Hospital, Fujian Medical University, Fuzhou, People's Republic of China
| | - Waleed M Ghareeb
- Department of Colorectal Surgery, Union Hospital, Fujian Medical University, 29 Xin-Quan Road, Fuzhou, Fujian, 350001, People's Republic of China.,Department of General and Gastrointestinal Surgery, Suez Canal University, Suez, Egypt
| | - Yiyi Zhang
- Department of Colorectal Surgery, Union Hospital, Fujian Medical University, 29 Xin-Quan Road, Fuzhou, Fujian, 350001, People's Republic of China
| | - Xingrong Lu
- Department of Colorectal Surgery, Union Hospital, Fujian Medical University, 29 Xin-Quan Road, Fuzhou, Fujian, 350001, People's Republic of China
| | - Ying Huang
- Department of Colorectal Surgery, Union Hospital, Fujian Medical University, 29 Xin-Quan Road, Fuzhou, Fujian, 350001, People's Republic of China
| | - Shenghui Huang
- Department of Colorectal Surgery, Union Hospital, Fujian Medical University, 29 Xin-Quan Road, Fuzhou, Fujian, 350001, People's Republic of China
| | - Yanwu Sun
- Department of Colorectal Surgery, Union Hospital, Fujian Medical University, 29 Xin-Quan Road, Fuzhou, Fujian, 350001, People's Republic of China
| | - Jiayi Lin
- Clinical Laboratory, Union Hospital, Fujian Medical University, Fuzhou, People's Republic of China
| | - Jin Liu
- Clinical Laboratory, Union Hospital, Fujian Medical University, Fuzhou, People's Republic of China
| | - Pan Chi
- Department of Colorectal Surgery, Union Hospital, Fujian Medical University, 29 Xin-Quan Road, Fuzhou, Fujian, 350001, People's Republic of China.
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19
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Liu J, Meng H, Li S, Shen Y, Wang H, Shan W, Qiu J, Zhang J, Cheng W. Identification of Potential Biomarkers in Association With Progression and Prognosis in Epithelial Ovarian Cancer by Integrated Bioinformatics Analysis. Front Genet 2019; 10:1031. [PMID: 31708970 PMCID: PMC6822059 DOI: 10.3389/fgene.2019.01031] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 09/25/2019] [Indexed: 02/03/2023] Open
Abstract
Epithelial ovarian cancer (EOC) is one of the malignancies in women, which has the highest mortality. However, the microlevel mechanism has not been discussed in detail. The expression profiles GSE27651, GSE38666, GSE40595, and GSE66957 including 188 tumor and 52 nontumor samples were downloaded from the Gene Expression Omnibus database. The differentially expressed genes (DEGs) were filtered using R software, and we performed functional analysis using the clusterProfiler. Cytoscape software, the molecular complex detection plugin and database STRING analyzed DEGs to construct protein-protein interaction network. We identified 116 DEGs including 81 upregulated and 35 downregulated DEGs. Functional analysis revealed that they were significantly enriched in the extracellular region and biosynthesis of amino acids. We next identified four bioactive compounds (vorinostat, LY-294002,trichostatin A, and tanespimycin) based on ConnectivityMap. Then 114 nodes were obtained in protein-protein interaction. The three most relevant modules were detected. In addition, according to degree ≥ 10, 14 core genes including FOXM1, CXCR4, KPNA2, NANOG, UBE2C, KIF11, ZWINT, CDCA5, DLGAP5, KIF15, MCM2, MELK, SPP1, and TRIP13 were identified. Kaplan-Meier analysis, Oncomine, and Gene Expression Profiling Interactive Analysis showed that overexpression of FOXM1, SPP1, UBE2C, KIF11, ZWINT, CDCA5, UBE2C, and KIF15 was related to bad prognosis of EOC patients. CDCA5, FOXM1, KIF15, MCM2, and ZWINT were associated with stage. Receiver operating characteristic (ROC) curve showed that messenger RNA levels of these five genes exhibited better diagnostic efficiency for normal and tumor tissues. The Human Protein Atlas database was performed. The protein levels of these five genes were significantly higher in tumor tissues compared with normal tissues. Functional enrichment analysis suggested that all the hub genes played crucial roles in citrate cycle tricarboxylic acid cycle. Furthermore, the univariate and multivariate Cox proportional hazards regression showed that ZWINT was independent prognostic indictor among EOC patients. The genes and pathways discovered in the above studies may open a new direction for EOC treatment.
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Affiliation(s)
- Jinhui Liu
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Huangyang Meng
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Siyue Li
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yujie Shen
- Department of Otorhinolaryngology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Hui Wang
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Wu Shan
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jiangnan Qiu
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jie Zhang
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Wenjun Cheng
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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20
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Castillo‐Armengol J, Fajas L, Lopez‐Mejia IC. Inter-organ communication: a gatekeeper for metabolic health. EMBO Rep 2019; 20:e47903. [PMID: 31423716 PMCID: PMC6726901 DOI: 10.15252/embr.201947903] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 05/21/2019] [Accepted: 05/24/2019] [Indexed: 12/17/2022] Open
Abstract
Multidirectional interactions between metabolic organs in the periphery and the central nervous system have evolved concomitantly with multicellular organisms to maintain whole-body energy homeostasis and ensure the organism's adaptation to external cues. These interactions are altered in pathological conditions such as obesity and type 2 diabetes. Bioactive peptides and proteins, such as hormones and cytokines, produced by both peripheral organs and the central nervous system, are key messengers in this inter-organ communication. Despite the early discovery of the first hormones more than 100 years ago, recent studies taking advantage of novel technologies have shed light on the multiple ways used by cells in the body to communicate and maintain energy balance. This review briefly summarizes well-established concepts and focuses on recent advances describing how specific proteins and peptides mediate the crosstalk between gut, brain, and other peripheral metabolic organs in order to maintain energy homeostasis. Additionally, this review outlines how the improved knowledge about these inter-organ networks is helping us to redefine therapeutic strategies in an effort to promote healthy living and fight metabolic disorders and other diseases.
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Affiliation(s)
| | - Lluis Fajas
- Center for Integrative GenomicsUniversity of LausanneLausanneSwitzerland
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21
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Mallam AL, Marcotte EM. Systems-wide Studies Uncover Commander, a Multiprotein Complex Essential to Human Development. Cell Syst 2019; 4:483-494. [PMID: 28544880 DOI: 10.1016/j.cels.2017.04.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 01/25/2017] [Accepted: 03/23/2017] [Indexed: 11/27/2022]
Abstract
Recent mass spectrometry maps of the human interactome independently support the existence of a large multiprotein complex, dubbed "Commander." Broadly conserved across animals and ubiquitously expressed in nearly every human cell type examined thus far, Commander likely plays a fundamental cellular function, akin to other ubiquitous machines involved in expression, proteostasis, and trafficking. Experiments on individual subunits support roles in endosomal protein sorting, including the trafficking of Notch proteins, copper transporters, and lipoprotein receptors. Commander is critical for vertebrate embryogenesis, and defects in the complex and its interaction partners disrupt craniofacial, brain, and heart development. Here, we review the synergy between large-scale proteomic efforts and focused studies in the discovery of Commander, describe its composition, structure, and function, and discuss how it illustrates the power of systems biology. Based on 3D modeling and biochemical data, we draw strong parallels between Commander and the retromer cargo-recognition complex, laying a foundation for future research into Commander's role in human developmental disorders.
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Affiliation(s)
- Anna L Mallam
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA.
| | - Edward M Marcotte
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA.
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22
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Rapid evolution of protein diversity by de novo origination in Oryza. Nat Ecol Evol 2019; 3:679-690. [PMID: 30858588 DOI: 10.1038/s41559-019-0822-5] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 01/23/2019] [Indexed: 12/22/2022]
Abstract
New protein-coding genes that arise de novo from non-coding DNA sequences contribute to protein diversity. However, de novo gene origination is challenging to study as it requires high-quality reference genomes for closely related species, evidence for ancestral non-coding sequences, and transcription and translation of the new genes. High-quality genomes of 13 closely related Oryza species provide unprecedented opportunities to understand de novo origination events. Here, we identify a large number of young de novo genes with discernible recent ancestral non-coding sequences and evidence of translation. Using pipelines examining the synteny relationship between genomes and reciprocal-best whole-genome alignments, we detected at least 175 de novo open reading frames in the focal species O. sativa subspecies japonica, which were all detected in RNA sequencing-based transcriptomes. Mass spectrometry-based targeted proteomics and ribosomal profiling show translational evidence for 57% of the de novo genes. In recent divergence of Oryza, an average of 51.5 de novo genes per million years were generated and retained. We observed evolutionary patterns in which excess indels and early transcription were favoured in origination with a stepwise formation of gene structure. These data reveal that de novo genes contribute to the rapid evolution of protein diversity under positive selection.
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23
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van Keulen BJ, Rotteveel J, Finken MJJ. Unexplained death in patients with NGLY1 mutations may be explained by adrenal insufficiency. Physiol Rep 2019; 7:e13979. [PMID: 30740912 PMCID: PMC6369059 DOI: 10.14814/phy2.13979] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 12/18/2018] [Accepted: 12/23/2018] [Indexed: 11/24/2022] Open
Abstract
Homozygous mutations in NGLY1 were recently found to cause a condition characterized by a complex neurological syndrome, hypo- or alacrimia, and elevated liver transaminases. For yet unknown reasons, mortality is increased in patients with this condition. NGLY1 encodes the cytosolic enzyme N-glycanase 1, which is responsible for the deglycosylation of misfolded N-glycosylated proteins. Disruption of this process is hypothesized to lead to an accumulation of misfolded proteins in the cytosol. Here, we describe the disease course of a girl with a homozygous mutation in NGLY1, namely c.1837del (p.Gln613 fs). In addition to the previously described symptoms, at the age of 8 she presented with recurrent infections and hyperpigmentation, and, subsequently, a diagnosis of primary adrenal insufficiency was made. There are no previous reports describing adrenal insufficiency in such patients. We postulate that patients with NGLY1 deficiency may develop adrenal insufficiency as a consequence of impaired proteostasis, and the accompanying proteotoxic stress-induced cell death, through defective Nrf1 function. We recommend an annual evaluation of adrenal function in all patients with NGLY1 mutations in order to prevent unnecessary deaths.
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Affiliation(s)
- Britt J. van Keulen
- Emma Children's HospitalAmsterdam UMCVrije Universiteit AmsterdamPediatric EndocrinologyAmsterdamThe Netherlands
| | - Joost Rotteveel
- Emma Children's HospitalAmsterdam UMCVrije Universiteit AmsterdamPediatric EndocrinologyAmsterdamThe Netherlands
| | - Martijn J. J. Finken
- Emma Children's HospitalAmsterdam UMCVrije Universiteit AmsterdamPediatric EndocrinologyAmsterdamThe Netherlands
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Smith SM, Melrose J. A Retrospective Analysis of the Cartilage Kunitz Protease Inhibitory Proteins Identifies These as Members of the Inter-α-Trypsin Inhibitor Superfamily with Potential Roles in the Protection of the Articulatory Surface. Int J Mol Sci 2019; 20:ijms20030497. [PMID: 30678366 PMCID: PMC6387120 DOI: 10.3390/ijms20030497] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 01/17/2019] [Accepted: 01/21/2019] [Indexed: 02/06/2023] Open
Abstract
Aim: The aim of this study was to assess if the ovine articular cartilage serine proteinase inhibitors (SPIs) were related to the Kunitz inter-α-trypsin inhibitor (ITI) family. Methods: Ovine articular cartilage was finely diced and extracted in 6 M urea and SPIs isolated by sequential anion exchange, HA affinity and Sephadex G100 gel permeation chromatography. Selected samples were also subjected to chymotrypsin and concanavalin-A affinity chromatography. Eluant fractions from these isolation steps were monitored for protein and trypsin inhibitory activity. Inhibitory fractions were assessed by affinity blotting using biotinylated trypsin to detect SPIs and by Western blotting using antibodies to α1-microglobulin, bikunin, TSG-6 and 2-B-6 (+) CS epitope generated by chondroitinase-ABC digestion. Results: 2-B-6 (+) positive 250, 220,120, 58 and 36 kDa SPIs were detected. The 58 kDa SPI contained α1-microglobulin, bikunin and chondroitin-4-sulfate stub epitope consistent with an identity of α1-microglobulin-bikunin (AMBP) precursor and was also isolated by concanavalin-A lectin affinity chromatography indicating it had N-glycosylation. Kunitz protease inhibitor (KPI) species of 36, 26, 12 and 6 kDa were autolytically generated by prolonged storage of the 120 and 58 kDa SPIs; chymotrypsin affinity chromatography generated the 6 kDa SPI. KPI domain 1 and 2 SPIs were separated by concanavalin lectin affinity chromatography, domain 1 displayed affinity for this lectin indicating it had N-glycosylation. KPI 1 and 2 displayed potent inhibitory activity against trypsin, chymotrypsin, kallikrein, leucocyte elastase and cathepsin G. Localisation of versican, lubricin and hyaluronan (HA) in the surface regions of articular cartilage represented probable binding sites for the ITI serine proteinase inhibitors (SPIs) which may preserve articulatory properties and joint function. Discussion/Conclusions: The Kunitz SPI proteins synthesised by articular chondrocytes are members of the ITI superfamily. By analogy with other tissues in which these proteins occur we deduce that the cartilage Kunitz SPIs may be multifunctional proteins. Binding of the cartilage Kunitz SPIs to HA may protect this polymer from depolymerisation by free radical damage and may also protect other components in the cartilage surface from proteolytic degradation preserving joint function.
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Affiliation(s)
- Susan M Smith
- Raymond Purves Bone and Joint Research Laboratory, Kolling Institute, Northern Sydney Local Health District, St. Leonards, NSW 2065, Australia.
| | - James Melrose
- Raymond Purves Bone and Joint Research Laboratory, Kolling Institute, Northern Sydney Local Health District, St. Leonards, NSW 2065, Australia.
- Graduate School of Biomedical Engineering, University of New South Wales, Sydney, NSW 2052, Australia.
- Sydney Medical School, Northern, The University of Sydney, Royal North Shore Hospital, St. Leonards, NSW 2065, Australia.
- Faculty of Medicine and Health, University of Sydney, Royal North Shore Hospital, St. Leonards, NSW 2065, Australia.
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25
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Song H, Liu L, Song Z, Ren Y, Li C, Huo J. P4HA3 is Epigenetically Activated by Slug in Gastric Cancer and its Deregulation is Associated With Enhanced Metastasis and Poor Survival. Technol Cancer Res Treat 2019; 17:1533033818796485. [PMID: 30198421 PMCID: PMC6131293 DOI: 10.1177/1533033818796485] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Prolyl 4-hydroxylase alpha subunit is the enzymic active site of prolyl 4-hydroxylase, which is a critical enzyme to maintain the stability of newly synthesized collagens. The expression profile and functional role of P4HA3 in gastric cancer have not been explored. In the Cancer Genome Atlas-Stomach Cancer, P4HA3 RNA is significantly upregulated in gastric cancer than in normal stomach tissues. In the Human Protein Atlas, Prolyl 4-hydroxylase alpha subunit is not detectable by immunohistochemistry staining in normal stomach tissues, but it has weak staining in 7 of 12 gastric cancer tissues. Further study showed that SNAI2 (encoding Slug) is highly coexpressed with P4HA3 (Pearson r = 0.70) in Cancer Genome Atlas-Stomach Cancer. In vitro cell assay showed that Slug could efficiently bind to the P4HA3 promoter and increase its transcription. P4HA3 exon array data in Cancer Genome Atlas-Stomach Cancer revealed that 2 exons are significantly upregulated in M1 (N = 27) cases than in M0 (N = 367) cases. In MKN-45 and AGS cells, P4HA3 upregulation could enhance cell motility and invasiveness. In Cancer Genome Atlas-Stomach Cancer, high P4HA3 exon expression is associated with significantly worse 5-year and 10-year overall survival (P = .007 and .009, respectively). Data mining in Kaplan-Meier plotter also showed that high P4HA3 expression is related to unfavorable overall survival (hazard ratio: 1.54, 95% confidence interval: 1.23-1.93, P < .001) and first progression-free survival (hazard ratio: 1.64, 95% confidence interval: 1.29-2.1, P < .001). Based on findings above, we infer that P4HA3 is epigenetically activated by Slug, and its deregulation is associated with enhanced metastasis and poor survival of gastric cancer.
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Affiliation(s)
- Hu Song
- 1 Department of Gastrointestinal Surgery, the Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Lingling Liu
- 2 Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong, China
| | - Zhaoquan Song
- 3 Clinical Laboratory, Linyi Luozhuang Central Hospital, Linyi, Shandong, China
| | - Yongqiang Ren
- 4 Clinical Laboratory, Linyi Central Hospital, Linyi, Shandong, China
| | - Chao Li
- 5 Department of NMR, Heilongjiang Provincial Hospital, Harbin, Heilongjiang, China
| | - Jiege Huo
- 6 Department of Oncology, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
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26
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Ghosh D, Bernstein JA, Khurana Hershey GK, Rothenberg ME, Mersha TB. Leveraging Multilayered "Omics" Data for Atopic Dermatitis: A Road Map to Precision Medicine. Front Immunol 2018; 9:2727. [PMID: 30631320 PMCID: PMC6315155 DOI: 10.3389/fimmu.2018.02727] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 11/05/2018] [Indexed: 12/14/2022] Open
Abstract
Atopic dermatitis (AD) is a complex multifactorial inflammatory skin disease that affects ~280 million people worldwide. About 85% of AD cases begin in childhood, a significant portion of which can persist into adulthood. Moreover, a typical progression of children with AD to food allergy, asthma or allergic rhinitis has been reported (“allergic march” or “atopic march”). AD comprises highly heterogeneous sub-phenotypes/endotypes resulting from complex interplay between intrinsic and extrinsic factors, such as environmental stimuli, and genetic factors regulating cutaneous functions (impaired barrier function, epidermal lipid, and protease abnormalities), immune functions and the microbiome. Though the roles of high-throughput “omics” integrations in defining endotypes are recognized, current analyses are primarily based on individual omics data and using binary clinical outcomes. Although individual omics analysis, such as genome-wide association studies (GWAS), can effectively map variants correlated with AD, the majority of the heritability and the functional relevance of discovered variants are not explained or known by the identified variants. The limited success of singular approaches underscores the need for holistic and integrated approaches to investigate complex phenotypes using trans-omics data integration strategies. Integrating omics layers (e.g., genome, epigenome, transcriptome, proteome, metabolome, lipidome, exposome, microbiome), which often have complementary and synergistic effects, might provide the opportunity to capture the flow of information underlying AD disease manifestation. Overlapping genes/candidates derived from multiple omics types include FLG, SPINK5, S100A8, and SERPINB3 in AD pathogenesis. Overlapping pathways include macrophage, endothelial cell and fibroblast activation pathways, in addition to well-known Th1/Th2 and NFkB activation pathways. Interestingly, there was more multi-omics overlap at the pathway level than gene level. Further analysis of multi-omics overlap at the tissue level showed that among 30 tissue types from the GTEx database, skin and esophagus were significantly enriched, indicating the biological interconnection between AD and food allergy. The present work explores multi-omics integration and provides new biological insights to better define the biological basis of AD etiology and confirm previously reported AD genes/pathways. In this context, we also discuss opportunities and challenges introduced by “big omics data” and their integration.
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Affiliation(s)
- Debajyoti Ghosh
- Division of Immunology, Allergy & Rheumatology, Department of Internal Medicine, University of Cincinnati, Cincinnati, OH, United States
| | - Jonathan A Bernstein
- Division of Immunology, Allergy & Rheumatology, Department of Internal Medicine, University of Cincinnati, Cincinnati, OH, United States
| | - Gurjit K Khurana Hershey
- Division of Asthma Research, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, United States
| | - Marc E Rothenberg
- Division of Allergy and Immunology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, United States
| | - Tesfaye B Mersha
- Division of Asthma Research, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, United States
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27
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Seldin MM, Koplev S, Rajbhandari P, Vergnes L, Rosenberg GM, Meng Y, Pan C, Phuong TMN, Gharakhanian R, Che N, Mäkinen S, Shih DM, Civelek M, Parks BW, Kim ED, Norheim F, Chella Krishnan K, Hasin-Brumshtein Y, Mehrabian M, Laakso M, Drevon CA, Koistinen HA, Tontonoz P, Reue K, Cantor RM, Björkegren JLM, Lusis AJ. A Strategy for Discovery of Endocrine Interactions with Application to Whole-Body Metabolism. Cell Metab 2018; 27:1138-1155.e6. [PMID: 29719227 PMCID: PMC5935137 DOI: 10.1016/j.cmet.2018.03.015] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 12/14/2017] [Accepted: 03/24/2018] [Indexed: 12/16/2022]
Abstract
Inter-tissue communication via secreted proteins has been established as a vital mechanism for proper physiologic homeostasis. Here, we report a bioinformatics framework using a mouse reference population, the Hybrid Mouse Diversity Panel (HMDP), which integrates global multi-tissue expression data and publicly available resources to identify and functionally annotate novel circuits of tissue-tissue communication. We validate this method by showing that we can identify known as well as novel endocrine factors responsible for communication between tissues. We further show the utility of this approach by identification and mechanistic characterization of two new endocrine factors. Adipose-derived Lipocalin-5 is shown to enhance skeletal muscle mitochondrial function, and liver-secreted Notum promotes browning of white adipose tissue, also known as "beiging." We demonstrate the general applicability of the method by providing in vivo evidence for three additional novel molecules mediating tissue-tissue interactions.
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Affiliation(s)
- Marcus M Seldin
- Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Simon Koplev
- Department of Genetics and Genomic Sciences, The Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Integrated Cardio Metabolic Centre, Department of Medicine, Karolinska Institutet, Karolinska Universitetssjukhuset, Huddinge, Sweden
| | - Prashant Rajbhandari
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Laurent Vergnes
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Gregory M Rosenberg
- Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Yonghong Meng
- Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Calvin Pan
- Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Thuy M N Phuong
- Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Raffi Gharakhanian
- Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Nam Che
- Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Selina Mäkinen
- Department of Medicine, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland; Minerva Foundation Institute for Medical Research, Biomedicum 2U, Helsinki, Finland
| | - Diana M Shih
- Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Mete Civelek
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
| | - Brian W Parks
- Department of Nutritional Sciences, University of Wisconsin, Madison, WI, USA
| | - Eric D Kim
- Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Frode Norheim
- Department of Nutrition, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
| | | | | | - Margarete Mehrabian
- Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Markku Laakso
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Christian A Drevon
- Department of Nutrition, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Heikki A Koistinen
- Department of Medicine, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland; Minerva Foundation Institute for Medical Research, Biomedicum 2U, Helsinki, Finland
| | - Peter Tontonoz
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Karen Reue
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Rita M Cantor
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Johan L M Björkegren
- Department of Genetics and Genomic Sciences, The Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Integrated Cardio Metabolic Centre, Department of Medicine, Karolinska Institutet, Karolinska Universitetssjukhuset, Huddinge, Sweden
| | - Aldons J Lusis
- Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, USA.
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28
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Zhao P, Zheng X, Feng W, Wang H, Kang H, Ning C, Du H, Yu Y, Li B, Zhao Y, Liu JF. Profiling long noncoding RNA of multi-tissue transcriptome enhances porcine noncoding genome annotation. Epigenomics 2018; 10:301-320. [DOI: 10.2217/epi-2017-0149] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Aim: To construct a comprehensive pig noncoding transcriptome and further enhance porcine noncoding genome annotation. Materials & methods: We performed a tissue-based long noncoding RNA (lncRNA) profiling via exploiting 32,212 nonredundant lncRNA isoforms corresponding to 18,676 lncRNA loci across 34 normal pig tissues using high-throughput sequencing. Furthermore, the potential relationship between our identified lncRNAs and known protein-coding genes were globally assessed via a comprehensive computation-based strategy, developing a genome-wide lncRNA-targeted genome draft for further functional studies on noncoding genes. Results & conclusion: Among these lncRNAs, ubiquitously expressed lncRNA appeared at a higher level compared with tissue-specific one. Findings herein provide insight into comprehensive knowledge of porcine noncoding RNAs and further enhance pig noncoding annotation. For ease of accessing the information of the identified lncRNAs, we deposited those with high confidence in the publicly available NONCODE database, providing a valuable resource for facilitating pig noncoding genomic studies.
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Affiliation(s)
- Pengju Zhao
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding & Reproduction, Ministry of Agriculture, College of Animal Science & Technology, China Agricultural University, Beijing 100193, China
| | - Xianrui Zheng
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding & Reproduction, Ministry of Agriculture, College of Animal Science & Technology, China Agricultural University, Beijing 100193, China
| | - Wen Feng
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding & Reproduction, Ministry of Agriculture, College of Animal Science & Technology, China Agricultural University, Beijing 100193, China
| | - Haifei Wang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding & Reproduction, Ministry of Agriculture, College of Animal Science & Technology, China Agricultural University, Beijing 100193, China
| | - Huimin Kang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding & Reproduction, Ministry of Agriculture, College of Animal Science & Technology, China Agricultural University, Beijing 100193, China
| | - Chao Ning
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding & Reproduction, Ministry of Agriculture, College of Animal Science & Technology, China Agricultural University, Beijing 100193, China
| | - Heng Du
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding & Reproduction, Ministry of Agriculture, College of Animal Science & Technology, China Agricultural University, Beijing 100193, China
| | - Ying Yu
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding & Reproduction, Ministry of Agriculture, College of Animal Science & Technology, China Agricultural University, Beijing 100193, China
| | - Bugao Li
- Department of Animal Sciences & Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, China
| | - Yi Zhao
- School of Medicine, MOE Key Laboratory of Bioinformatics & Bioinformatics Division, Center for Synthetic & System Biology, TNLIST/Department of Automation, Tsinghua University, Beijing 100084, China
| | - Jian-Feng Liu
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding & Reproduction, Ministry of Agriculture, College of Animal Science & Technology, China Agricultural University, Beijing 100193, China
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Chen J, Chen H, Yang H, Dai H. SPC25 upregulation increases cancer stem cell properties in non-small cell lung adenocarcinoma cells and independently predicts poor survival. Biomed Pharmacother 2018; 100:233-239. [PMID: 29432994 DOI: 10.1016/j.biopha.2018.02.015] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Revised: 02/01/2018] [Accepted: 02/02/2018] [Indexed: 11/15/2022] Open
Abstract
In this study, we investigated the functional role and prognostic value of spindle pole body component 25 (SPC25) in non-small cell lung cancer (NSCLC). SPC25 expression profile in lung adenocarcinoma (LUAD), lung squamous cell carcinoma (LUSC) and normal lung tissues was examined by using data from the Cancer Genome Atlas (TCGA) and the Human Protein Atlas (HPA). LUAD A549 cells and LUSC H520 cells were used to investigate the influence of SPC25 on cancer stem cell (CSC) properties in terms of the proportion of CD133+ cells, tumorsphere formation and CSC markers, including CD133, ALDH1 and Sox2. Data mining was also performed in the Kaplan-Meier plotter and TCGA-NSCLC to assess the independent prognostic value of SPC25. Results showed SPC25 was significantly upregulated in LUAD and LUSC tissues compared with normal lung tissues. SPC25 overexpression significantly increased the CSC properties and invasion of A549 cells, but not H520 cells. In comparison, SPC25 knockdown impaired the CSC properties and invasion of A549 cells, but not H520 cells. Univariate and multivariate analysis confirmed that high SPC25 expression was an independent prognostic factor for poor overall survival (OS) (HR: 1.622, 95%CI: 1.207-2.178, p = .001) and recurrence-free survival (RFS) (HR: 1.726, 95%CI: 1.242-2.399, p = .001) in LUAD patients. However, no independent prognostic value of SPC25 was observed in LUSC patients even under the best cut-off model. Based on these findings, we infer that SPC25 upregulation can increase CSC properties in LUAD and independently predict poor survival in this histological subtype.
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Affiliation(s)
- Jingxia Chen
- Department of Emergency Medicine, The Affiliated Hospital of Weifang Medical University, Weifang, Shandong, 261031, China
| | - Hongfen Chen
- Department of Emergency Medicine, The Affiliated Hospital of Weifang Medical University, Weifang, Shandong, 261031, China.
| | - Hanbing Yang
- Department of Emergency Medicine, The Affiliated Hospital of Weifang Medical University, Weifang, Shandong, 261031, China
| | - Huizhen Dai
- Department of Emergency Medicine, The Affiliated Hospital of Weifang Medical University, Weifang, Shandong, 261031, China
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30
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Cui J, Liu Y, Zhang H, Wang Y, Liu G, Zhang W, Zhang C. Low BIN3 Expression is an Independent Predictor of Unfavorable Survival in Patients With Primary Colorectal Cancer. Technol Cancer Res Treat 2017. [PMCID: PMC5762098 DOI: 10.1177/1533034617747774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
This study aimed to explore the mechanisms of bridging integrator-3 dysregulation, its prognostic value, and related signaling pathways in colorectal cancer . Bioinformatic analysis was performed based on the data from The Cancer Genome Atlas–colorectal cancer and Human Protein Atlas. Colorectal cancer cell lines, LoVo and HT29 cells, were used as in vitro cell model to assess the effect of demethylation on bridging integrator-3 expression. Results showed that bridging integrator-3 was downregulated in colorectal cancer tissues compared to normal colon and rectum tissues. Heatmap of bridging integrator-3 messenger RNA expression, exon expression, and DNA methylation indicated a negative correlation between bridging integrator-3 expression and methylation of some CpG sites within the coding sequence. Demethylation treatment significantly increased bridging integrator-3 expression in LoVo and HT29 cells. Low bridging integrator-3 messenger RNA and exon expression were associated with significantly worse overall survival (P = .015 and .013, respectively). Multivariate analysis confirmed that low bridging integrator-3 messenger RNA expression was an independent prognostic factor of unfavorable overall survival (Hazard Ratio (HR) = 1.596, 95% confidence interval: 1.024-2.486; P = .039). High bridging integrator-3 DNA methylation was also associated with significantly worse overall survival (P = .013). Kyoto Encyclopedia of Genes and Genomes analysis indicated that the genes correlated with bridging integrator-3 (absolute Pearson r ≥ 0.3, n = 121) were enriched in sphingolipid signaling pathway, natural killer cell-mediated cytotoxicity, p53 signaling pathway, and apoptosis. Based on these findings, we infer that DNA hypermethylation might be an important mechanism of suppressed bridging integrator-3 expression in colorectal cancer . Its low expression is an independent predictor of unfavorable survival in patients with primary colorectal cancer . Bridging integrator-3 might act as a tumor suppressor via modulating natural killer cell-mediated cytotoxicity, p53 signaling pathway, and apoptosis.
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Affiliation(s)
- Jifang Cui
- Department of Gastroenterology, Tianjin Union Medical Center, Tianjin, China
| | - Yandi Liu
- Department of Gastroenterology, Tianjin Union Medical Center, Tianjin, China
| | - Heng Zhang
- Medical Oncology, Tianjin Union Medical Center, Tianjin, China
| | - Yijia Wang
- Department of Pathology, Tianjin Union Medical Center, Tianjin, China
| | - Guang Liu
- Department of Pathology, Tianjin Union Medical Center, Tianjin, China
| | - Weihua Zhang
- Department of Colorectal Surgery, Tianjin Union Medical Center, Tianjin, China
| | - Chunze Zhang
- Department of Colorectal Surgery, Tianjin Union Medical Center, Tianjin, China
- Chunze Zhang, MD, No. 190, Jieyuan Road, Tianjin 300121, China.
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Goodin MM. Protein Localization and Interaction Studies in Plants: Toward Defining Complete Proteomes by Visualization. Adv Virus Res 2017; 100:117-144. [PMID: 29551133 DOI: 10.1016/bs.aivir.2017.10.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Protein interaction and localization studies in plants are a fundamental component of achieving mechanistic understanding of virus:plant interactions at the systems level. Many such studies are conducted using transient expression assays in leaves of Nicotiana benthamiana, the most widely used experimental plant host in virology, examined by laser-scanning confocal microscopy. This chapter provides a workflow for protein interaction and localization experiments, with particular attention to the many control and supporting assays that may also need to be performed. Basic principles of microscopy are introduced to aid researchers in the early stages of adding imaging techniques to their experimental repertoire. Three major types of imaging-based experiments are discussed in detail: (i) protein localization using autofluorescent proteins, (ii) colocalization studies, and (iii) bimolecular fluorescence complementation, with emphasis on judicious interpretation of the data obtained from these approaches. In addition to establishing a general framework for protein localization experiments in plants, the need for proteome-scale localization projects is discussed, with emphasis on nuclear-localized proteins.
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Thul PJ, Lindskog C. The human protein atlas: A spatial map of the human proteome. Protein Sci 2017; 27:233-244. [PMID: 28940711 DOI: 10.1002/pro.3307] [Citation(s) in RCA: 627] [Impact Index Per Article: 89.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 09/14/2017] [Accepted: 09/18/2017] [Indexed: 12/15/2022]
Abstract
The correct spatial distribution of proteins is vital for their function and often mis-localization or ectopic expression leads to diseases. For more than a decade, the Human Protein Atlas (HPA) has constituted a valuable tool for researchers studying protein localization and expression in human tissues and cells. The centerpiece of the HPA is its unique antibody collection for mapping the entire human proteome by immunohistochemistry and immunocytochemistry. By these approaches, more than 10 million images showing protein expression patterns at a single-cell level were generated and are publicly available at www.proteinatlas.org. The antibody-based approach is combined with transcriptomics data for an overview of global expression profiles. The present article comprehensively describes the HPA database functions and how users can utilize it for their own research as well as discusses the future path of spatial proteomics.
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Affiliation(s)
- Peter J Thul
- Science for Life Laboratory, School of Biotechnology, KTH - Royal Institute of Technology, Stockholm, SE, 171 21, Sweden
| | - Cecilia Lindskog
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Uppsala, SE, 751 85, Sweden
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Reubi JC. In Vitro Evaluation of Molecular Tumor Targets in Nuclear Medicine: Immunohistochemistry Is One Option, but Under Which Conditions? J Nucl Med 2017; 58:1885-1887. [PMID: 28912151 DOI: 10.2967/jnumed.117.197582] [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: 06/14/2017] [Accepted: 08/10/2017] [Indexed: 11/16/2022] Open
Abstract
The identification of new molecular targets for diagnostic and therapeutic applications using in vitro methods is an important challenge in nuclear medicine. One such method is immunohistochemistry, increasingly popular because it is easy to perform. This review presents the case for conducting receptor immunohistochemistry to evaluate potential molecular targets in human tumor tissue sections. The focus is on the immunohistochemistry of G-protein-coupled receptors, one of the largest families of cell surface proteins, representing a major class of drug targets and thus playing an important role in nuclear medicine. This review identifies common pitfalls and challenges and provides guidelines on performing such immunohistochemical studies. An appropriate validation of the target is a prerequisite for developing robust and informative new molecular probes.
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Saidijam M, Azizpour S, Patching SG. Comprehensive analysis of the numbers, lengths and amino acid compositions of transmembrane helices in prokaryotic, eukaryotic and viral integral membrane proteins of high-resolution structure. J Biomol Struct Dyn 2017; 36:443-464. [PMID: 28150531 DOI: 10.1080/07391102.2017.1285725] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We report a comprehensive analysis of the numbers, lengths and amino acid compositions of transmembrane helices in 235 high-resolution structures of integral membrane proteins. The properties of 1551 transmembrane helices in the structures were compared with those obtained by analysis of the same amino acid sequences using topology prediction tools. Explanations for the 81 (5.2%) missing or additional transmembrane helices in the prediction results were identified. Main reasons for missing transmembrane helices were mis-identification of N-terminal signal peptides, breaks in α-helix conformation or charged residues in the middle of transmembrane helices and transmembrane helices with unusual amino acid composition. The main reason for additional transmembrane helices was mis-identification of amphipathic helices, extramembrane helices or hairpin re-entrant loops. Transmembrane helix length had an overall median of 24 residues and an average of 24.9 ± 7.0 residues and the most common length was 23 residues. The overall content of residues in transmembrane helices as a percentage of the full proteins had a median of 56.8% and an average of 55.7 ± 16.0%. Amino acid composition was analysed for the full proteins, transmembrane helices and extramembrane regions. Individual proteins or types of proteins with transmembrane helices containing extremes in contents of individual amino acids or combinations of amino acids with similar physicochemical properties were identified and linked to structure and/or function. In addition to overall median and average values, all results were analysed for proteins originating from different types of organism (prokaryotic, eukaryotic, viral) and for subgroups of receptors, channels, transporters and others.
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Affiliation(s)
- Massoud Saidijam
- a Department of Molecular Medicine and Genetics, Research Centre for Molecular Medicine, School of Medicine , Hamadan University of Medical Sciences , Hamadan , Iran
| | - Sonia Azizpour
- a Department of Molecular Medicine and Genetics, Research Centre for Molecular Medicine, School of Medicine , Hamadan University of Medical Sciences , Hamadan , Iran
| | - Simon G Patching
- b School of BioMedical Sciences and the Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds , UK
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Abstract
Medical diagnostics and treatment has advanced from a one size fits all science to treatment of the patient as a unique individual. Currently, this is limited solely to genetic analysis. However, epigenetic, transcriptional, proteomic, posttranslational modifications, metabolic, and environmental factors influence a patient’s response to disease and treatment. As more analytical and diagnostic techniques are incorporated into medical practice, the personalized medicine initiative transitions to precision medicine giving a holistic view of the patient’s condition. The high accuracy and sensitivity of mass spectrometric analysis of proteomes is well suited for the incorporation of proteomics into precision medicine. This review begins with an overview of the advance to precision medicine and the current state of the art in technology and instrumentation for mass spectrometry analysis. Thereafter, it focuses on the benefits and potential uses for personalized proteomic analysis in the diagnostic and treatment of individual patients. In conclusion, it calls for a synthesis between basic science and clinical researchers with practicing clinicians to design proteomic studies to generate meaningful and applicable translational medicine. As clinical proteomics is just beginning to come out of its infancy, this overview is provided for the new initiate.
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Saidijam M, Azizpour S, Patching SG. Amino acid composition analysis of human secondary transport proteins and implications for reliable membrane topology prediction. J Biomol Struct Dyn 2016; 35:929-949. [PMID: 27159787 DOI: 10.1080/07391102.2016.1167622] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Secondary transporters in humans are a large group of proteins that transport a wide range of ions, metals, organic and inorganic solutes involved in energy transduction, control of membrane potential and osmotic balance, metabolic processes and in the absorption or efflux of drugs and xenobiotics. They are also emerging as important targets for development of new drugs and as target sites for drug delivery to specific organs or tissues. We have performed amino acid composition (AAC) and phylogenetic analyses and membrane topology predictions for 336 human secondary transport proteins and used the results to confirm protein classification and to look for trends and correlations with structural domains and specific substrates and/or function. Some proteins showed statistically high contents of individual amino acids or of groups of amino acids with similar physicochemical properties. One recurring trend was a correlation between high contents of charged and/or polar residues with misleading results in predictions of membrane topology, which was especially prevalent in Mitochondrial Carrier family proteins. We demonstrate how charged or polar residues located in the middle of transmembrane helices can interfere with their identification by membrane topology tools resulting in missed helices in the prediction. Comparison of AAC in the human proteins with that in 235 secondary transport proteins from Escherichia coli revealed similar overall trends along with differences in average contents for some individual amino acids and groups of similar amino acids that are presumed to result from a greater number of functions and complexity in the higher organism.
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Affiliation(s)
- Massoud Saidijam
- a Department of Molecular Medicine and Genetics, Research Centre for Molecular Medicine, School of Medicine , Hamadan University of Medical Sciences , Hamadan , Iran
| | - Sonia Azizpour
- a Department of Molecular Medicine and Genetics, Research Centre for Molecular Medicine, School of Medicine , Hamadan University of Medical Sciences , Hamadan , Iran
| | - Simon G Patching
- b School of BioMedical Sciences and the Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , UK
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Gavasso S, Gullaksen SE, Skavland J, Gjertsen BT. Single-cell proteomics: potential implications for cancer diagnostics. Expert Rev Mol Diagn 2016; 16:579-89. [DOI: 10.1586/14737159.2016.1156531] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Sonia Gavasso
- Department of Neurology, Haukeland University Hospital, Bergen, Norway
| | | | - Jørn Skavland
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Bjørn T. Gjertsen
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Translational Hemato-Oncology Group, University of Bergen, Bergen, Norway
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Zhou L, Wang K, Li Q, Nice EC, Zhang H, Huang C. Clinical proteomics-driven precision medicine for targeted cancer therapy: current overview and future perspectives. Expert Rev Proteomics 2016; 13:367-81. [PMID: 26923776 DOI: 10.1586/14789450.2016.1159959] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Cancer is a common disease that is a leading cause of death worldwide. Currently, early detection and novel therapeutic strategies are urgently needed for more effective management of cancer. Importantly, protein profiling using clinical proteomic strategies, with spectacular sensitivity and precision, offer excellent promise for the identification of potential biomarkers that would direct the development of targeted therapeutic anticancer drugs for precision medicine. In particular, clinical sample sources, including tumor tissues and body fluids (blood, feces, urine and saliva), have been widely investigated using modern high-throughput mass spectrometry-based proteomic approaches combined with bioinformatic analysis, to pursue the possibilities of precision medicine for targeted cancer therapy. Discussed in this review are the current advantages and limitations of clinical proteomics, the available strategies of clinical proteomics for the management of precision medicine, as well as the challenges and future perspectives of clinical proteomics-driven precision medicine for targeted cancer therapy.
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Affiliation(s)
- Li Zhou
- a State Key Laboratory of Biotherapy and Cancer Center, West China Hospital , Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu , P.R. China.,b Department of Neurology , The Affiliated Hospital of Hainan Medical College , Haikou , Hainan , P.R. China
| | - Kui Wang
- a State Key Laboratory of Biotherapy and Cancer Center, West China Hospital , Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu , P.R. China
| | - Qifu Li
- b Department of Neurology , The Affiliated Hospital of Hainan Medical College , Haikou , Hainan , P.R. China
| | - Edouard C Nice
- a State Key Laboratory of Biotherapy and Cancer Center, West China Hospital , Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu , P.R. China.,c Department of Biochemistry and Molecular Biology , Monash University , Clayton , Australia
| | - Haiyuan Zhang
- b Department of Neurology , The Affiliated Hospital of Hainan Medical College , Haikou , Hainan , P.R. China
| | - Canhua Huang
- a State Key Laboratory of Biotherapy and Cancer Center, West China Hospital , Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu , P.R. China.,b Department of Neurology , The Affiliated Hospital of Hainan Medical College , Haikou , Hainan , P.R. China
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Choong WK, Chang HY, Chen CT, Tsai CF, Hsu WL, Chen YJ, Sung TY. Informatics View on the Challenges of Identifying Missing Proteins from Shotgun Proteomics. J Proteome Res 2015; 14:5396-407. [DOI: 10.1021/acs.jproteome.5b00482] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Wai-Kok Choong
- Institute
of Information Science, Academia Sinica, Taipei 11529, Taiwan
| | - Hui-Yin Chang
- Institute
of Information Science, Academia Sinica, Taipei 11529, Taiwan
- Bioinformatics
Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
- Institute
of Biomedical Informatics, National Yang-Ming University, Taipei 11221, Taiwan
| | - Ching-Tai Chen
- Institute
of Information Science, Academia Sinica, Taipei 11529, Taiwan
| | - Chia-Feng Tsai
- Institute
of Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Wen-Lian Hsu
- Institute
of Information Science, Academia Sinica, Taipei 11529, Taiwan
| | - Yu-Ju Chen
- Institute
of Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Ting-Yi Sung
- Institute
of Information Science, Academia Sinica, Taipei 11529, Taiwan
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