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Futosi K, Bajza B, Deli D, Erdélyi A, Tusnády S, Mócsai A. Analysis of intracellular tyrosine phosphorylation in circulating neutrophils as a rapid assay for the in vivo effect of oral tyrosine kinase inhibitors. Front Pharmacol 2023; 14:1056154. [PMID: 37089957 PMCID: PMC10117656 DOI: 10.3389/fphar.2023.1056154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 02/24/2023] [Indexed: 04/08/2023] Open
Abstract
Tyrosine kinases are crucial signaling components of diverse biological processes and are major therapeutic targets in various malignancies and immune-mediated disorders. A critical step of development of novel tyrosine kinase inhibitors is the transition from the confirmation of the in vitro effects of drug candidates to the analysis of their in vivo efficacy. To facilitate this transition, we have developed a rapid in vivo assay for the analysis of the effect of oral tyrosine kinase inhibitors on basal tyrosine phosphorylation of circulating mouse neutrophils. The assay uses a single drop of peripheral blood without sacrificing the mice. Flow cytometry using intracellular staining by fluorescently labeled anti-phosphotyrosine antibodies revealed robust basal tyrosine phosphorylation in resting circulating neutrophils. This signal was abrogated by the use of isotype control antibodies or by pre-saturation of the anti-phosphotyrosine antibodies with soluble phosphotyrosine amino acids or tyrosine-phosphorylated peptides. Basal tyrosine phosphorylation was dramatically reduced in neutrophils of triple knockout mice lacking the Src-family tyrosine kinases Hck, Fgr, and Lyn. Neutrophil tyrosine phosphorylation was also abrogated by oral administration of the Abl/Src-family inhibitor dasatinib, a clinically used anti-leukemic agent. Detailed dose-response and kinetic studies revealed half-maximal reduction of neutrophil tyrosine phosphorylation by 2.9 mg/kg dasatinib, with maximal reduction observed 2 h after inhibitor administration. Taken together, our assay allows highly efficient analysis of the in vivo effect of orally administered tyrosine kinase inhibitors, and may be used as a suitable alternative to other existing approaches.
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Affiliation(s)
- Krisztina Futosi
- Department of Physiology, Semmelweis University School of Medicine, Budapest, Hungary
- ELKH-SE Inflammation Physiology Research Group, Eötvös Loránd Research Network, Budapest, Hungary
- *Correspondence: Krisztina Futosi,
| | - Boglárka Bajza
- Department of Physiology, Semmelweis University School of Medicine, Budapest, Hungary
| | - Dorottya Deli
- Department of Physiology, Semmelweis University School of Medicine, Budapest, Hungary
| | - András Erdélyi
- Department of Physiology, Semmelweis University School of Medicine, Budapest, Hungary
| | - Simon Tusnády
- Department of Physiology, Semmelweis University School of Medicine, Budapest, Hungary
| | - Attila Mócsai
- Department of Physiology, Semmelweis University School of Medicine, Budapest, Hungary
- ELKH-SE Inflammation Physiology Research Group, Eötvös Loránd Research Network, Budapest, Hungary
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152
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Chakraborty A, Mitra S, Bhattacharjee M, De D, Pal AJ. Determining human-coronavirus protein-protein interaction using machine intelligence. Med Nov Technol Devices 2023; 18:100228. [PMID: 37056696 PMCID: PMC10077817 DOI: 10.1016/j.medntd.2023.100228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 03/29/2023] [Accepted: 04/01/2023] [Indexed: 04/08/2023] Open
Abstract
The Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2) virus spread the novel CoronaVirus −19 (nCoV-19) pandemic, resulting in millions of fatalities globally. Recent research demonstrated that the Protein-Protein Interaction (PPI) between SARS-CoV-2 and human proteins is accountable for viral pathogenesis. However, many of these PPIs are poorly understood and unexplored, necessitating a more in-depth investigation to find latent yet critical interactions. This article elucidates the host-viral PPI through Machine Learning (ML) lenses and validates the biological significance of the same using web-based tools. ML classifiers are designed based on comprehensive datasets with five sequence-based features of human proteins, namely Amino Acid Composition, Pseudo Amino Acid Composition, Conjoint Triad, Dipeptide Composition, and Normalized Auto Correlation. A majority voting rule-based ensemble method composed of the Random Forest Model (RFM), AdaBoost, and Bagging technique is proposed that delivers encouraging statistical performance compared to other models employed in this work. The proposed ensemble model predicted a total of 111 possible SARS-CoV-2 human target proteins with a high likelihood factor ≥70%, validated by utilizing Gene Ontology (GO) and KEGG pathway enrichment analysis. Consequently, this research can aid in a deeper understanding of the molecular mechanisms underlying viral pathogenesis and provide clues for developing more efficient anti-COVID medications.
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Affiliation(s)
- Arijit Chakraborty
- Bachelor of Computer Application Department, The Heritage Academy, Kolkata, India
| | - Sajal Mitra
- Department of Computer Science and Engineering, Heritage Institute of Technology, Kolkata, India
| | | | - Debashis De
- Department of Computer Science and Engineering, Maulana Abul Kalam Azad University of Technology, Kolkata, India
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153
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Luther CH, Brandt P, Vylkova S, Dandekar T, Müller T, Dittrich M. Integrated analysis of SR-like protein kinases Sky1 and Sky2 links signaling networks with transcriptional regulation in Candida albicans. Front Cell Infect Microbiol 2023; 13:1108235. [PMID: 37082713 PMCID: PMC10111165 DOI: 10.3389/fcimb.2023.1108235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 03/01/2023] [Indexed: 04/07/2023] Open
Abstract
Fungal infections are a major global health burden where Candida albicans is among the most common fungal pathogen in humans and is a common cause of invasive candidiasis. Fungal phenotypes, such as those related to morphology, proliferation and virulence are mainly driven by gene expression, which is primarily regulated by kinase signaling cascades. Serine-arginine (SR) protein kinases are highly conserved among eukaryotes and are involved in major transcriptional processes in human and S. cerevisiae. Candida albicans harbors two SR protein kinases, while Sky2 is important for metabolic adaptation, Sky1 has similar functions as in S. cerevisiae. To investigate the role of these SR kinases for the regulation of transcriptional responses in C. albicans, we performed RNA sequencing of sky1Δ and sky2Δ and integrated a comprehensive phosphoproteome dataset of these mutants. Using a Systems Biology approach, we study transcriptional regulation in the context of kinase signaling networks. Transcriptomic enrichment analysis indicates that pathways involved in the regulation of gene expression are downregulated and mitochondrial processes are upregulated in sky1Δ. In sky2Δ, primarily metabolic processes are affected, especially for arginine, and we observed that arginine-induced hyphae formation is impaired in sky2Δ. In addition, our analysis identifies several transcription factors as potential drivers of the transcriptional response. Among these, a core set is shared between both kinase knockouts, but it appears to regulate different subsets of target genes. To elucidate these diverse regulatory patterns, we created network modules by integrating the data of site-specific protein phosphorylation and gene expression with kinase-substrate predictions and protein-protein interactions. These integrated signaling modules reveal shared parts but also highlight specific patterns characteristic for each kinase. Interestingly, the modules contain many proteins involved in fungal morphogenesis and stress response. Accordingly, experimental phenotyping shows a higher resistance to Hygromycin B for sky1Δ. Thus, our study demonstrates that a combination of computational approaches with integration of experimental data can offer a new systems biological perspective on the complex network of signaling and transcription. With that, the investigation of the interface between signaling and transcriptional regulation in C. albicans provides a deeper insight into how cellular mechanisms can shape the phenotype.
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Affiliation(s)
- Christian H. Luther
- University of Würzburg, Department of Bioinformatics, Biocenter/Am Hubland 97074, Würzburg, Germany
| | - Philipp Brandt
- Septomics Research Center, Friedrich Schiller University and Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Jena, Germany
| | - Slavena Vylkova
- Septomics Research Center, Friedrich Schiller University and Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Jena, Germany
| | - Thomas Dandekar
- University of Würzburg, Department of Bioinformatics, Biocenter/Am Hubland 97074, Würzburg, Germany
| | - Tobias Müller
- University of Würzburg, Department of Bioinformatics, Biocenter/Am Hubland 97074, Würzburg, Germany
| | - Marcus Dittrich
- University of Würzburg, Department of Bioinformatics, Biocenter/Am Hubland 97074, Würzburg, Germany
- University of Würzburg, Institut of Human Genetics, Biocenter/Am Hubland 97074, Würzburg, Germany
- *Correspondence: Marcus Dittrich,
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154
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Chen Z, Xin Q, Wei W, Wu Y. The pathogenesis and development of targeted drugs in acute T lymphoblastic leukaemia. Br J Pharmacol 2023; 180:1017-1037. [PMID: 36623836 DOI: 10.1111/bph.16029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
Acute lymphoblastic leukaemia (ALL) is mainly classified into acute T- and B-lymphoblastic leukaemia according to the source of its lymphocytes, thymus and bone. Among them, the incidence of adult T-cell accounts for about 25% of adult acute lymphoblastic leukaemia, but the degree of malignancy is high and the treatment rate and prognosis are poor. At this stage, there are few targeted drugs and the commonly used broad-spectrum chemotherapeutic drugs have poor efficacy and many adverse drug reactions. Understanding and investigating the pathogenesis of T-acute lymphoblastic leukaemia is very important for further developing new targeting drugs and improving existing drugs. Dysregulated signalling pathways are the main aetiological factors of T-acute lymphoblastic leukaemia. They play crucial roles in promoting tumour initiation, progression, drug design and therapy responses. This is primarily because signalling pathways are indispensable for many cellular biological processes, including tumour growth, migration, invasion, metastasis and others. As a result, small molecule inhibitors targeting the major kinase components of the signalling pathway have received a lot of attention and have been developed and evaluated in preclinical models and clinical trials. Already marketed drugs are also being repurposed in combination therapies to further improve efficacy and overcome tumour cell resistance. In this review, we have aimed to examine the latest and most classical signalling pathways in the aetiology of T-acute lymphoblastic leukaemia and shed light on potential targets for novel therapeutic agents to act on.
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Affiliation(s)
- Zhaoying Chen
- Institute of Clinical Pharmacology, Anhui Medical University, Key Laboratory of Anti-inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-inflammatory and Immune Medicine, Anhui Provincial Institute of Translational Medicine, Hefei, China
| | - Qianling Xin
- Institute of Clinical Pharmacology, Anhui Medical University, Key Laboratory of Anti-inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-inflammatory and Immune Medicine, Anhui Provincial Institute of Translational Medicine, Hefei, China
| | - Wei Wei
- Institute of Clinical Pharmacology, Anhui Medical University, Key Laboratory of Anti-inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-inflammatory and Immune Medicine, Anhui Provincial Institute of Translational Medicine, Hefei, China
| | - Yujing Wu
- Institute of Clinical Pharmacology, Anhui Medical University, Key Laboratory of Anti-inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-inflammatory and Immune Medicine, Anhui Provincial Institute of Translational Medicine, Hefei, China
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155
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Wang S, Zhang A, Pan Y, Liu L, Niu S, Zhang F, Liu X. Association between COVID-19 and Male Fertility: Systematic Review and Meta-Analysis of Observational Studies. World J Mens Health 2023; 41:311-329. [PMID: 36326165 PMCID: PMC10042646 DOI: 10.5534/wjmh.220091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 07/29/2022] [Accepted: 08/03/2022] [Indexed: 11/06/2022] Open
Abstract
PURPOSE Whether COVID-19 reduces male fertility remains requires further investigation. This meta-analysis and systematic review evaluated the impact of COVID-19 on male fertility. MATERIALS AND METHODS The literature in PubMed, Embase, MEDLINE, Web of Science, and Cochrane Library up to January 01, 2022 was systematically searched, and a meta-analysis was conducted to investigate the effect of COVID-19 on male fertility. Totally 17 studies with a total of 1,627 patients and 1,535 control subjects were included in our meta-analysis. RESULTS Regarding sperm quality, COVID-19 decreased the total sperm count (p=0.012), sperm concentration (p=0.001), total motility (p=0.001), progressive sperm motility (p=0.048), and viability (p=0.031). Subgroup analyses showed that different control group populations did not change the results. It was found that during the illness stage of COVID-19, semen volume decreased, and during the recovery stage of COVID-19, sperm concentration and total motility decreased <90 days. We found that sperm concentration and total motility decreased during recovery for ≥90 days. Fever because of COVID-19 significantly reduced sperm concentration and progressive sperm motility, and COVID-19 without fever ≥90 days, the sperm total motility and progressive sperm motility decreased. Regarding disease severity, the moderate type of COVID-19 significantly reduced sperm total motility, but not the mild type. Regarding sex hormones, COVID-19 increased prolactin and estradiol. Subgroup analyses showed that during the illness stage, COVID-19 decreased testosterone (T) levels and increased luteinizing hormone levels. A potential publication bias may have existed in our meta-analysis. CONCLUSIONS COVID-19 in men significantly reduced sperm quality and caused sex hormone disruption. COVID-19 had long-term effects on sperm quality, especially on sperm concentration and total motility. It is critical to conduct larger multicenter studies to determine the consequences of COVID-19 on male fertility.
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Affiliation(s)
- Shangren Wang
- Department of Urology, Tianjin Medical University General Hospital, Tianjin, China
| | - Aiqiao Zhang
- Department of Neonatology, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Department of Neonatology, National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, China
| | - Yang Pan
- Department of Urology, Tianjin Medical University General Hospital, Tianjin, China
| | - Li Liu
- Department of Urology, Tianjin Medical University General Hospital, Tianjin, China
| | - Shuai Niu
- Department of Urology, Tianjin Medical University General Hospital, Tianjin, China
| | - Fujun Zhang
- Department of Neonatology, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Department of Neonatology, National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, China
| | - Xiaoqiang Liu
- Department of Urology, Tianjin Medical University General Hospital, Tianjin, China.
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156
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Zhan Y, Jiao J, Jing W, Feng X, Tai B, Hu D, Lin HC, Wang B, Wang C, Zheng S, Liu X, Rong W, Wang W, Wang X, Si Y, Meng H. Association between periodontitis and hypertension: cross-sectional survey from the Fourth National Oral Health Survey of China (2015-2016). BMJ Open 2023; 13:e068724. [PMID: 36972967 PMCID: PMC10069577 DOI: 10.1136/bmjopen-2022-068724] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/29/2023] Open
Abstract
OBJECTIVES To evaluate the association between periodontitis severity and hypertension based on Chinese epidemiological data. DESIGN This cross-sectional survey enrolled adults from the Fourth National Oral Health Survey of China (2015-2016). SETTING The data were obtained from the Fourth National Oral Health Survey of China (2015-2016). PARTICIPANTS The study included individuals aged 35-44 years (n=4409), 55-64 years (n=4568) and 65-74 years (n=4218). PRIMARY AND SECONDARY OUTCOME MEASURES Periodontal status, defined on the basis of the 2017 classification scheme, and periodontal parameters (eg, bleeding on probing (BOP)) were compared between individuals with hypertension and individuals with normotension. Smoothed scatterplots were constructed to demonstrate the associations of periodontal parameters and periodontal status with hypertension. RESULTS Severe periodontitis (stages III and IV) was present in 41.4% of individuals with hypertension and 28.0% of individuals with normotension, respectively (p<0.001). The prevalence of severe periodontitis was higher in individuals with hypertension than that in individuals with normotension among participants aged 35-44 years (18.0% vs 10.1%, p<0.001) and 55-64 years (40.2% vs 36.7%, p=0.035), but not in participants aged 65-74 years (46.4% vs 45.1%, p=0.429). Therefore, the difference in periodontal status between individuals with hypertension and individuals with normotension decreased with age. There were higher prevalences of BOP, probing depth (PD) ≥4 mm and PD ≥6 mm in individuals with hypertension than in individuals with normotension (52.1% vs 49.2%, 19.6% vs 14.7% and 1.8% vs 1.1%, respectively). Periodontitis severity and the proportion of teeth with PD ≥4 or ≥6 mm were positively associated with hypertension. CONCLUSION Periodontitis is associated with hypertension in Chinese adults. Hypertension prevalence increased with periodontitis severity, particularly among young participants. Accordingly, it is necessary to improve the education, awareness of periodontal treatment and preventive management among individuals at risk of hypertension, particularly in the younger population.
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Affiliation(s)
- Yalin Zhan
- First Clinical Division & Department of Periodontology, Peking University School and Hospital of Stomatology & National Center for Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Beijing, People's Republic of China
| | - Jian Jiao
- First Clinical Division & Department of Periodontology, Peking University School and Hospital of Stomatology & National Center for Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Beijing, People's Republic of China
| | - Wudi Jing
- Department of Periodontology, Peking University School and Hospital of Stomatology & National Center for Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Beijing, People's Republic of China
| | - Xiping Feng
- Department of Preventive Dentistry, Shanghai Jiao Tong University School of Medicine Affiliated Ninth People's Hospital, Shanghai, People's Republic of China
| | - Baojun Tai
- School & Hospital of Stomatology, Wuhan University, Wuhan, Hubei, People's Republic of China
| | - Deyu Hu
- West China School of Stomatology, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Huan-Cai Lin
- Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-Sen University, Guangzhou, Guangdong, People's Republic of China
| | - Bo Wang
- Chinese Stomatological Association, Beijing, People's Republic of China
| | - Chunxiao Wang
- Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Shuguo Zheng
- Department of Preventive Dentistry, Peking University School and Hospital of Stomatology & National Center for Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Beijing, People's Republic of China
| | - Xuenan Liu
- Department of Preventive Dentistry, Peking University School and Hospital of Stomatology & National Center for Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Beijing, People's Republic of China
| | - Wensheng Rong
- Department of Preventive Dentistry, Peking University School and Hospital of Stomatology & National Center for Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Beijing, People's Republic of China
| | - Weijian Wang
- Department of Preventive Dentistry, Peking University School and Hospital of Stomatology & National Center for Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Beijing, People's Republic of China
| | - Xing Wang
- Chinese Stomatological Association, Beijing, People's Republic of China
| | - Yan Si
- Department of Preventive Dentistry, Peking University School and Hospital of Stomatology & National Center for Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Beijing, People's Republic of China
| | - Huanxin Meng
- Department of Periodontology, Peking University School and Hospital of Stomatology & National Center for Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Beijing, People's Republic of China
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157
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Li L, Jiang D, Zhang Q, Liu H, Xu F, Guo C, Qin Z, Wang H, Feng J, Liu Y, Chen W, Zhang X, Bai L, Tian S, Tan S, Xu C, Song Q, Liu Y, Zhong Y, Chen T, Zhou P, Zhao JY, Hou Y, Ding C. Integrative proteogenomic characterization of early esophageal cancer. Nat Commun 2023; 14:1666. [PMID: 36966136 PMCID: PMC10039899 DOI: 10.1038/s41467-023-37440-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 03/16/2023] [Indexed: 03/27/2023] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) is malignant while the carcinogenesis is still unclear. Here, we perform a comprehensive multi-omics analysis of 786 trace-tumor-samples from 154 ESCC patients, covering 9 histopathological stages and 3 phases. Proteogenomics elucidates cancer-driving waves in ESCC progression, and reveals the molecular characterization of alcohol drinking habit associated signatures. We discover chromosome 3q gain functions in the transmit from nontumor to intraepithelial neoplasia phases, and find TP53 mutation enhances DNA replication in intraepithelial neoplasia phase. The mutations of AKAP9 and MCAF1 upregulate glycolysis and Wnt signaling, respectively, in advanced-stage ESCC phase. Six major tracks related to different clinical features during ESCC progression are identified, which is validated by an independent cohort with another 256 samples. Hyperphosphorylated phosphoglycerate kinase 1 (PGK1, S203) is considered as a drug target in ESCC progression. This study provides insight into the understanding of ESCC molecular mechanism and the development of therapeutic targets.
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Affiliation(s)
- Lingling Li
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Human Phenome Institute, Zhongshan Hospital, Fudan University, Shanghai, 200433, China
| | - Dongxian Jiang
- Department of Pathology, Zhongshan Hospital Fudan University, Shanghai, 200032, China
| | - Qiao Zhang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Human Phenome Institute, Zhongshan Hospital, Fudan University, Shanghai, 200433, China
| | - Hui Liu
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Human Phenome Institute, Zhongshan Hospital, Fudan University, Shanghai, 200433, China
| | - Fujiang Xu
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, China
| | - Chunmei Guo
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Human Phenome Institute, Zhongshan Hospital, Fudan University, Shanghai, 200433, China
| | - Zhaoyu Qin
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Human Phenome Institute, Zhongshan Hospital, Fudan University, Shanghai, 200433, China
| | - Haixing Wang
- Department of Pathology, Zhongshan Hospital Fudan University, Shanghai, 200032, China
| | - Jinwen Feng
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Human Phenome Institute, Zhongshan Hospital, Fudan University, Shanghai, 200433, China
| | - Yang Liu
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Human Phenome Institute, Zhongshan Hospital, Fudan University, Shanghai, 200433, China
| | - Weijie Chen
- Department of Pathology, Zhongshan Hospital Fudan University, Shanghai, 200032, China
| | - Xue Zhang
- Department of Pathology, Zhongshan Hospital Fudan University, Shanghai, 200032, China
| | - Lin Bai
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Human Phenome Institute, Zhongshan Hospital, Fudan University, Shanghai, 200433, China
| | - Sha Tian
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Human Phenome Institute, Zhongshan Hospital, Fudan University, Shanghai, 200433, China
| | - Subei Tan
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Human Phenome Institute, Zhongshan Hospital, Fudan University, Shanghai, 200433, China
| | - Chen Xu
- Department of Pathology, Zhongshan Hospital Fudan University, Shanghai, 200032, China
| | - Qi Song
- Department of Pathology, Zhongshan Hospital Fudan University, Shanghai, 200032, China
| | - Yalan Liu
- Department of Pathology, Zhongshan Hospital Fudan University, Shanghai, 200032, China
| | - Yunshi Zhong
- Department of Pathology, Zhongshan Hospital Fudan University, Shanghai, 200032, China
| | - Tianyin Chen
- Department of Pathology, Zhongshan Hospital Fudan University, Shanghai, 200032, China
| | - Pinghong Zhou
- Endoscopy Center and Endoscopy Research Institute, Zhongshan Hospital Fudan University, Shanghai, 200032, China.
| | - Jian-Yuan Zhao
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Human Phenome Institute, Zhongshan Hospital, Fudan University, Shanghai, 200433, China.
- Institute for Development and Regenerative Cardiovascular Medicine, MOE-Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China.
- Department of Anatomy and Neuroscience Research Institute , School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, China.
| | - Yingyong Hou
- Department of Pathology, Zhongshan Hospital Fudan University, Shanghai, 200032, China.
| | - Chen Ding
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Human Phenome Institute, Zhongshan Hospital, Fudan University, Shanghai, 200433, China.
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158
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Silva-junior AL, Oliveira LDS, Belezia NCT, Tarragô AM, Costa AGD, Malheiro A. Immune Dynamics Involved in Acute and Convalescent COVID-19 Patients. Immuno 2023; 3:86-111. [DOI: 10.3390/immuno3010007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023] Open
Abstract
COVID-19 is a viral disease that has caused millions of deaths around the world since 2020. Many strategies have been developed to manage patients in critical conditions; however, comprehension of the immune system is a key factor in viral clearance, tissue repairment, and adaptive immunity stimulus. Participation of immunity has been identified as a major factor, along with biomarkers, prediction of clinical outcomes, and antibody production after infection. Immune cells have been proposed not only as a hallmark of severity, but also as a predictor of clinical outcomes, while dynamics of inflammatory molecules can also induce worse consequences for acute patients. For convalescent patients, mild disease was related to higher antibody production, although the factors related to the specific antibodies based on a diversity of antigens were not clear. COVID-19 was explored over time; however, the study of immunological predictors of outcomes is still lacking discussion, especially in convalescent patients. Here, we propose a review using previously published studies to identify immunological markers of COVID-19 outcomes and their relation to antibody production to further contribute to the clinical and laboratorial management of patients.
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159
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Eiger DS, Smith JS, Shi T, Stepniewski TM, Tsai CF, Honeycutt C, Boldizsar N, Gardner J, Nicora CD, Moghieb AM, Kawakami K, Choi I, Zheng K, Warman A, Alagesan P, Knape NM, Huang O, Silverman JD, Smith RD, Inoue A, Selent J, Jacobs JM, Rajagopal S. Phosphorylation barcodes direct biased chemokine signaling at CXCR3. bioRxiv 2023:2023.03.14.532634. [PMID: 36993369 PMCID: PMC10055163 DOI: 10.1101/2023.03.14.532634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
G protein-coupled receptor (GPCR) biased agonism, the activation of some signaling pathways over others, is thought to largely be due to differential receptor phosphorylation, or "phosphorylation barcodes." At chemokine receptors, ligands act as "biased agonists" with complex signaling profiles, which contributes to the limited success in pharmacologically targeting these receptors. Here, mass spectrometry-based global phosphoproteomics revealed that CXCR3 chemokines generate different phosphorylation barcodes associated with differential transducer activation. Chemokine stimulation resulted in distinct changes throughout the kinome in global phosphoproteomic studies. Mutation of CXCR3 phosphosites altered β-arrestin conformation in cellular assays and was confirmed by molecular dynamics simulations. T cells expressing phosphorylation-deficient CXCR3 mutants resulted in agonist- and receptor-specific chemotactic profiles. Our results demonstrate that CXCR3 chemokines are non-redundant and act as biased agonists through differential encoding of phosphorylation barcodes and lead to distinct physiological processes.
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Affiliation(s)
- Dylan S. Eiger
- Department of Biochemistry, Duke University, Durham, NC, 27710, USA
| | - Jeffrey S. Smith
- Department of Dermatology, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Dermatology, Brigham and Women’s Hospital, Boston, MA, 02115, USA
- Department of Dermatology, Beth Israel Deaconess Medical Center, Boston, MA, 02215, USA
- Dermatology Program, Boston Children’s Hospital, Boston, MA, 02115, USA
- Harvard Medical School, Boston, MA, 02115, USA
| | - Tujin Shi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Tomasz Maciej Stepniewski
- Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences of Pompeu Fabra University (UPF)-Hospital del Mar Medical Research Institute (IMIM), Barcelona, 08003, Spain
| | - Chia-Feng Tsai
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | | | | | - Julia Gardner
- Trinity College, Duke University, Durham, NC, 27710, USA
| | - Carrie D. Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | | | - Kouki Kawakami
- Department of Pharmaceutical Sciences, Tohoku University, Sendai, 980-8577, Japan
| | - Issac Choi
- Department of Medicine, Duke University, Durham, NC 27710 USA
| | - Kevin Zheng
- Trinity College, Duke University, Durham, NC, 27710, USA
| | - Anmol Warman
- Trinity College, Duke University, Durham, NC, 27710, USA
| | - Priya Alagesan
- Department of Biochemistry, Duke University, Durham, NC, 27710, USA
| | - Nicole M. Knape
- Department of Biochemistry, Duke University, Durham, NC, 27710, USA
| | - Ouwen Huang
- Department of Biomedical Engineering, Duke University, Durham, NC, 27710, USA
| | - Justin D. Silverman
- College of Information Sciences and Technology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Richard D. Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Asuka Inoue
- Department of Pharmaceutical Sciences, Tohoku University, Sendai, 980-8577, Japan
| | - Jana Selent
- Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences of Pompeu Fabra University (UPF)-Hospital del Mar Medical Research Institute (IMIM), Barcelona, 08003, Spain
| | - Jon M. Jacobs
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Sudarshan Rajagopal
- Department of Biochemistry, Duke University, Durham, NC, 27710, USA
- Department of Pharmaceutical Sciences, Tohoku University, Sendai, 980-8577, Japan
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160
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Bao S, Darvishi M, H Amin A, Al-Haideri MT, Patra I, Kashikova K, Ahmad I, Alsaikhan F, Al-Qaim ZH, Al-Gazally ME, Kiasari BA, Tavakoli-Far B, Sidikov AA, Mustafa YF, Akhavan-Sigari R. CXC chemokine receptor 4 (CXCR4) blockade in cancer treatment. J Cancer Res Clin Oncol 2023:10.1007/s00432-022-04444-w. [PMID: 36905421 DOI: 10.1007/s00432-022-04444-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 10/19/2022] [Indexed: 03/12/2023]
Abstract
CXC chemokine receptor type 4 (CXCR4) is a member of the G protein-coupled receptors (GPCRs) superfamily and is specific for CXC chemokine ligand 12 (CXCL12, also known as SDF-1), which makes CXCL12/CXCR4 axis. CXCR4 interacts with its ligand, triggering downstream signaling pathways that influence cell proliferation chemotaxis, migration, and gene expression. The interaction also regulates physiological processes, including hematopoiesis, organogenesis, and tissue repair. Multiple evidence revealed that CXCL12/CXCR4 axis is implicated in several pathways involved in carcinogenesis and plays a key role in tumor growth, survival, angiogenesis, metastasis, and therapeutic resistance. Several CXCR4-targeting compounds have been discovered and used for preclinical and clinical cancer therapy, most of which have shown promising anti-tumor activity. In this review, we summarized the physiological signaling of the CXCL12/CXCR4 axis and described the role of this axis in tumor progression, and focused on the potential therapeutic options and strategies to block CXCR4.
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Affiliation(s)
- Shunshun Bao
- The First Clinical Medical College, Xuzhou Medical University, 221000, Xuzhou, China
| | - Mohammad Darvishi
- Infectious Diseases and Tropical Medicine Research Center (IDTMRC), Department of Aerospace and Subaquatic Medicine, AJA University of Medicinal Sciences, Tehran, Iran
| | - Ali H Amin
- Deanship of Scientific Research, Umm Al-Qura University, 21955, Makkah, Saudi Arabia.,Zoology Department, Faculty of Science, Mansoura University, 35516, Mansoura, Egypt
| | - Maysoon T Al-Haideri
- Department of Physiotherapy, Cihan University-Erbil, Erbil, Kurdistan Region, Iraq
| | - Indrajit Patra
- An Independent Researcher, National Institute of Technology Durgapur, Durgapur, West Bengal, India
| | | | - Irfan Ahmad
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Fahad Alsaikhan
- College of Pharmacy, Prince Sattam Bin Abdulaziz University, Alkharj, Saudi Arabia
| | | | | | - Bahman Abedi Kiasari
- Virology Department, Faculty of Veterinary Medicine, The University of Tehran, Tehran, Iran.
| | - Bahareh Tavakoli-Far
- Dietary Supplements and Probiotic Research Center, Alborz University of Medical Sciences, Karaj, Iran. .,Department of Physiology and Pharmacology, Faculty of Medicine, Alborz University of Medical Sciences, Karaj, Iran.
| | - Akmal A Sidikov
- Rector, Ferghana Medical Institute of Public Health, Ferghana, Uzbekistan
| | - Yasser Fakri Mustafa
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Mosul, Mosul, 41001, Iraq
| | - Reza Akhavan-Sigari
- Department of Neurosurgery, University Medical Center Tuebingen, Tübingen, Germany.,Department of Health Care Management and Clinical Research, Collegium Humanum Warsaw Management University, Warsaw, Poland
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161
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Chatterjee S, Nalla LV, Sharma M, Sharma N, Singh AA, Malim FM, Ghatage M, Mukarram M, Pawar A, Parihar N, Arya N, Khairnar A. Association of COVID-19 with Comorbidities: An Update. ACS Pharmacol Transl Sci 2023; 6:334-354. [PMID: 36923110 PMCID: PMC10000013 DOI: 10.1021/acsptsci.2c00181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Indexed: 03/03/2023]
Abstract
Coronavirus disease (COVID-19) is caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) which was identified in Wuhan, China in December 2019 and jeopardized human lives. It spreads at an unprecedented rate worldwide, with serious and still-unfolding health conditions and economic ramifications. Based on the clinical investigations, the severity of COVID-19 appears to be highly variable, ranging from mild to severe infections including the death of an infected individual. To add to this, patients with comorbid conditions such as age or concomitant illnesses are significant predictors of the disease's severity and progression. SARS-CoV-2 enters inside the host cells through ACE2 (angiotensin converting enzyme2) receptor expression; therefore, comorbidities associated with higher ACE2 expression may enhance the virus entry and the severity of COVID-19 infection. It has already been recognized that age-related comorbidities such as Parkinson's disease, cancer, diabetes, and cardiovascular diseases may lead to life-threatening illnesses in COVID-19-infected patients. COVID-19 infection results in the excessive release of cytokines, called "cytokine storm", which causes the worsening of comorbid disease conditions. Different mechanisms of COVID-19 infections leading to intensive care unit (ICU) admissions or deaths have been hypothesized. This review provides insights into the relationship between various comorbidities and COVID-19 infection. We further discuss the potential pathophysiological correlation between COVID-19 disease and comorbidities with the medical interventions for comorbid patients. Toward the end, different therapeutic options have been discussed for COVID-19-infected comorbid patients.
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Affiliation(s)
- Sayan Chatterjee
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gujarat 382355, India
| | - Lakshmi Vineela Nalla
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gujarat 382355, India.,Department of Pharmacy, Koneru Lakshmaiah Education Foundation, Vaddeswaram, Andhra Pradesh 522302, India
| | - Monika Sharma
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gujarat 382355, India
| | - Nishant Sharma
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gujarat 382355, India
| | - Aditya A Singh
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gujarat 382355, India
| | - Fehmina Mushtaque Malim
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gujarat 382355, India
| | - Manasi Ghatage
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gujarat 382355, India
| | - Mohd Mukarram
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gujarat 382355, India
| | - Abhijeet Pawar
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gujarat 382355, India
| | - Nidhi Parihar
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gujarat 382355, India
| | - Neha Arya
- Department of Translational Medicine, All India Institute of Medical Sciences (AIIMS), Bhopal, Bhopal 462020, India
| | - Amit Khairnar
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gujarat 382355, India.,International Clinical Research Center, St. Anne's University Hospital Brno, Brno 602 00, Czech Republic.,ICRC-FNUSA Brno 656 91, Czech Republic.,Department of Physiology, Faculty of Medicine, Masaryk University, Kamenice 753/5, 62500 Brno, Czechia
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162
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Sousa A, Dugourd A, Memon D, Petursson B, Petsalaki E, Saez-Rodriguez J, Beltrao P. Pan-Cancer landscape of protein activities identifies drivers of signalling dysregulation and patient survival. Mol Syst Biol 2023; 19:e10631. [PMID: 36688815 PMCID: PMC9996241 DOI: 10.15252/msb.202110631] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 01/06/2023] [Accepted: 01/09/2023] [Indexed: 01/24/2023] Open
Abstract
Genetic alterations in cancer cells trigger oncogenic transformation, a process largely mediated by the dysregulation of kinase and transcription factor (TF) activities. While the mutational profiles of thousands of tumours have been extensively characterised, the measurements of protein activities have been technically limited until recently. We compiled public data of matched genomics and (phospho)proteomics measurements for 1,110 tumours and 77 cell lines that we used to estimate activity changes in 218 kinases and 292 TFs. Co-regulation of kinase and TF activities reflects previously known regulatory relationships and allows us to dissect genetic drivers of signalling changes in cancer. We find that loss-of-function mutations are not often associated with the dysregulation of downstream targets, suggesting frequent compensatory mechanisms. Finally, we identified the activities most differentially regulated in cancer subtypes and showed how these can be linked to differences in patient survival. Our results provide broad insights into the dysregulation of protein activities in cancer and their contribution to disease severity.
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Affiliation(s)
- Abel Sousa
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK.,Instituto de Investigação e Inovação em Saúde da Universidade do Porto (i3s), Porto, Portugal.,Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal.,Graduate Program in Areas of Basic and Applied Biology (GABBA), Abel Salazar Biomedical Sciences Institute, University of Porto, Porto, Portugal
| | - Aurelien Dugourd
- Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg University, Heidelberg, Germany.,Faculty of Medicine, Institute of Experimental Medicine and Systems Biology, RWTH Aachen University, Aachen, Germany
| | - Danish Memon
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Borgthor Petursson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Evangelia Petsalaki
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Julio Saez-Rodriguez
- Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg University, Heidelberg, Germany
| | - Pedro Beltrao
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK.,Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
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163
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Gargiulo E, Giordano M, Niemann CU, Moussay E, Paggetti J, Morande PE. The protective role of the microenvironment in hairy cell leukemia treatment: Facts and perspectives. Front Oncol 2023; 13:1122699. [PMID: 36968995 PMCID: PMC10031020 DOI: 10.3389/fonc.2023.1122699] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 02/22/2023] [Indexed: 03/11/2023] Open
Abstract
Hairy cell leukemia (HCL) is an incurable, rare lymphoproliferative hematological malignancy of mature B cAlthough first line therapy with purine analogues leads to positive results, almost half of HCL patients relapse after 5-10 years, and standard treatment may not be an option due to intolerance or refractoriness. Proliferation and survival of HCL cells is regulated by surrounding accessory cells and soluble signals present in the tumor microenvironment, which actively contributes to disease progression. In vitro studies show that different therapeutic approaches tested in HCL impact the tumor microenvironment, and that this milieu offers a protection affecting treatment efficacy. Herein we explore the effects of the tumor microenvironment to different approved and experimental therapeutic options for HCL. Dissecting the complex interactions between leukemia cells and their milieu will be essential to develop new targeted therapies for HCL patients.
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Affiliation(s)
- Ernesto Gargiulo
- Tumor Stroma Interactions – Department of Cancer Research, Luxembourg Institute of HealthLuxembourg, Luxembourg
- Chronic Lymphocytic Leukemia Laboratory, Department of Hematology, Rigshospitalet, Copenhagen, Denmark
- PERSIMUNE, Department of Infectious Diseases, Rigshospitalet, Copenhagen, Denmark
| | - Mirta Giordano
- Instituto de Medicina Experimental (IMEX)-CONICET, Academia Nacional de Medicina, Buenos Aires, Argentina
| | - Carsten U. Niemann
- Chronic Lymphocytic Leukemia Laboratory, Department of Hematology, Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Etienne Moussay
- Tumor Stroma Interactions – Department of Cancer Research, Luxembourg Institute of HealthLuxembourg, Luxembourg
- *Correspondence: Pablo Elías Morande, ; ; Etienne Moussay, ; Jérôme Paggetti,
| | - Jérôme Paggetti
- Tumor Stroma Interactions – Department of Cancer Research, Luxembourg Institute of HealthLuxembourg, Luxembourg
- *Correspondence: Pablo Elías Morande, ; ; Etienne Moussay, ; Jérôme Paggetti,
| | - Pablo Elías Morande
- Tumor Stroma Interactions – Department of Cancer Research, Luxembourg Institute of HealthLuxembourg, Luxembourg
- Instituto de Medicina Experimental (IMEX)-CONICET, Academia Nacional de Medicina, Buenos Aires, Argentina
- *Correspondence: Pablo Elías Morande, ; ; Etienne Moussay, ; Jérôme Paggetti,
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164
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Crews LA, Ma W, Ladel L, Pham J, Balaian L, Steel SK, Mondala PK, Diep RH, Wu CN, Mason CN, van der Werf I, Oliver I, Reynoso E, Pineda G, Whisenant TC, Wentworth P, La Clair JJ, Jiang Q, Burkart MD, Jamieson CHM. Reversal of malignant ADAR1 splice isoform switching with Rebecsinib. Cell Stem Cell 2023; 30:250-263.e6. [PMID: 36803553 PMCID: PMC10134781 DOI: 10.1016/j.stem.2023.01.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 11/15/2022] [Accepted: 01/20/2023] [Indexed: 02/18/2023]
Abstract
Adenosine deaminase acting on RNA1 (ADAR1) preserves genomic integrity by preventing retroviral integration and retrotransposition during stress responses. However, inflammatory-microenvironment-induced ADAR1p110 to p150 splice isoform switching drives cancer stem cell (CSC) generation and therapeutic resistance in 20 malignancies. Previously, predicting and preventing ADAR1p150-mediated malignant RNA editing represented a significant challenge. Thus, we developed lentiviral ADAR1 and splicing reporters for non-invasive detection of splicing-mediated ADAR1 adenosine-to-inosine (A-to-I) RNA editing activation; a quantitative ADAR1p150 intracellular flow cytometric assay; a selective small-molecule inhibitor of splicing-mediated ADAR1 activation, Rebecsinib, which inhibits leukemia stem cell (LSC) self-renewal and prolongs humanized LSC mouse model survival at doses that spare normal hematopoietic stem and progenitor cells (HSPCs); and pre-IND studies showing favorable Rebecsinib toxicokinetic and pharmacodynamic (TK/PD) properties. Together, these results lay the foundation for developing Rebecsinib as a clinical ADAR1p150 antagonist aimed at obviating malignant microenvironment-driven LSC generation.
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Affiliation(s)
- Leslie A Crews
- Department of Medicine, Division of Regenerative Medicine, Sanford Stem Cell Institute, University of California, San Diego, La Jolla, CA 92037, USA; Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Wenxue Ma
- Department of Medicine, Division of Regenerative Medicine, Sanford Stem Cell Institute, University of California, San Diego, La Jolla, CA 92037, USA
| | - Luisa Ladel
- Department of Medicine, Division of Regenerative Medicine, Sanford Stem Cell Institute, University of California, San Diego, La Jolla, CA 92037, USA
| | - Jessica Pham
- Department of Medicine, Division of Regenerative Medicine, Sanford Stem Cell Institute, University of California, San Diego, La Jolla, CA 92037, USA
| | - Larisa Balaian
- Department of Medicine, Division of Regenerative Medicine, Sanford Stem Cell Institute, University of California, San Diego, La Jolla, CA 92037, USA; Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - S Kathleen Steel
- Department of Medicine, Division of Regenerative Medicine, Sanford Stem Cell Institute, University of California, San Diego, La Jolla, CA 92037, USA
| | - Phoebe K Mondala
- Department of Medicine, Division of Regenerative Medicine, Sanford Stem Cell Institute, University of California, San Diego, La Jolla, CA 92037, USA
| | - Raymond H Diep
- Department of Medicine, Division of Regenerative Medicine, Sanford Stem Cell Institute, University of California, San Diego, La Jolla, CA 92037, USA
| | - Christina N Wu
- Department of Medicine, Division of Regenerative Medicine, Sanford Stem Cell Institute, University of California, San Diego, La Jolla, CA 92037, USA
| | - Cayla N Mason
- Department of Medicine, Division of Regenerative Medicine, Sanford Stem Cell Institute, University of California, San Diego, La Jolla, CA 92037, USA
| | - Inge van der Werf
- Department of Medicine, Division of Regenerative Medicine, Sanford Stem Cell Institute, University of California, San Diego, La Jolla, CA 92037, USA
| | - Isabelle Oliver
- Department of Medicine, Division of Regenerative Medicine, Sanford Stem Cell Institute, University of California, San Diego, La Jolla, CA 92037, USA
| | - Eduardo Reynoso
- Department of Medicine, Division of Regenerative Medicine, Sanford Stem Cell Institute, University of California, San Diego, La Jolla, CA 92037, USA
| | - Gabriel Pineda
- Department of Medicine, Division of Regenerative Medicine, Sanford Stem Cell Institute, University of California, San Diego, La Jolla, CA 92037, USA
| | - Thomas C Whisenant
- Center for Computational Biology & Bioinformatics (CCBB), Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Peggy Wentworth
- Department of Medicine, Division of Regenerative Medicine, Sanford Stem Cell Institute, University of California, San Diego, La Jolla, CA 92037, USA
| | - James J La Clair
- Departments of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Qingfei Jiang
- Department of Medicine, Division of Regenerative Medicine, Sanford Stem Cell Institute, University of California, San Diego, La Jolla, CA 92037, USA
| | - Michael D Burkart
- Departments of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Catriona H M Jamieson
- Department of Medicine, Division of Regenerative Medicine, Sanford Stem Cell Institute, University of California, San Diego, La Jolla, CA 92037, USA; Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA.
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165
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Nunez Lopez YO, Iliuk A, Casu A, Parikh A, Smith JS, Corbin K, Lupu D, Pratley RE. Extracellular vesicle proteomics and phosphoproteomics identify pathways for increased risk in patients hospitalized with COVID-19 and type 2 diabetes mellitus. Diabetes Res Clin Pract 2023; 197:110565. [PMID: 36736734 PMCID: PMC9890887 DOI: 10.1016/j.diabres.2023.110565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 01/22/2023] [Accepted: 01/30/2023] [Indexed: 02/04/2023]
Abstract
Recent studies suggest that extracellular vesicles (EVs) play a role in the pathogenesis of SARS-CoV-2 infection and the severity of COVID-19. However, their role in the interaction between COVID-19 and type 2 diabetes (T2D) has not been addressed. Here, we characterized the circulating EV proteomic and phosphoproteomic landscape in patients with and without T2D hospitalized with COVID-19 or non-COVID-19 acute respiratory illness (RSP). We detected differentially expressed protein and phosphoprotein signatures that effectively characterized the study groups. The trio of immunomodulatory and coagulation proteins C1QA, C1QB, and C1QC appeared to be a central cluster in both the COVID-19 and T2D functional networks. PKCβ appeared to be retained in cells by being diverted from EV pathways and contribute to the COVID-19 and T2D interaction via a PKC/BTK/TEC axis. EV-shuttled CASP3 and ROCK1 appeared to be coregulated and likely contribute to disease interactions in patients with COVID-19 and T2D. Predicted activation of AMPK, MAPK, and SYK appeared to also play important roles driving disease interaction. These results suggest that activated cellular kinases (i.e., PKC, AMPK, MAPK, and SYK) and multiple EV-shuttled kinases (i.e., PKCβ, BTK, TEC, MAP2K2, and ROCK1) may play key roles in severe COVID-19, particularly in patients with comorbid diabetes.
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Affiliation(s)
- Yury O Nunez Lopez
- Translational Research Institute, AdventHealth Orlando, Orlando, FL 32804, United States
| | - Anton Iliuk
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, United States; Tymora Analytical Operations, West Lafayette, IN 47906, United States.
| | - Anna Casu
- Translational Research Institute, AdventHealth Orlando, Orlando, FL 32804, United States
| | - Amay Parikh
- Division of Critical Care, AdventHealth Medical Group, AdventHealth Orlando, Orlando, FL 32804, United States
| | - Joshua S Smith
- Translational Research Institute, AdventHealth Orlando, Orlando, FL 32804, United States
| | - Karen Corbin
- Translational Research Institute, AdventHealth Orlando, Orlando, FL 32804, United States
| | - Daniel Lupu
- Translational Research Institute, AdventHealth Orlando, Orlando, FL 32804, United States
| | - Richard E Pratley
- Translational Research Institute, AdventHealth Orlando, Orlando, FL 32804, United States.
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166
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Abolhasani S, Hejazian SS, Karpisheh V, Khodakarami A, Mohammadi H, Gholizadeh Navashenaq J, Hojjat-Farsangi M, Jadidi-Niaragh F. The role of SF3B1 and NOTCH1 in the pathogenesis of leukemia. IUBMB Life 2023; 75:257-278. [PMID: 35848163 DOI: 10.1002/iub.2660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 06/18/2022] [Indexed: 11/09/2022]
Abstract
The discovery of new genes/pathways improves our knowledge of cancer pathogenesis and presents novel potential therapeutic options. For instance, splicing factor 3b subunit 1 (SF3B1) and NOTCH1 genetic alterations have been identified at a high frequency in hematological malignancies, such as leukemia, and may be related to the prognosis of involved patients because they change the nature of malignancies in different ways like mediating therapeutic resistance; therefore, studying these gene/pathways is essential. This review aims to discuss SF3B1 and NOTCH1 roles in the pathogenesis of various types of leukemia and the therapeutic potential of targeting these genes or their mutations to provide a foundation for leukemia treatment.
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Affiliation(s)
- Shiva Abolhasani
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Vahid Karpisheh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Atefeh Khodakarami
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hamed Mohammadi
- Non-communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran
| | | | - Mohammad Hojjat-Farsangi
- Bioclinicum, Department of Oncology-Pathology, Karolinska Institute, Stockholm, Sweden.,The Persian Gulf Marine Biotechnology Medicine Research Center, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Farhad Jadidi-Niaragh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.,Research Center for Integrative Medicine in Aging, Aging Research Institute, Tabriz University of Medical Sciences, Tabriz, Iran
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167
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Shen Z, Letra A, Silva RM. MicroRNAs Markedly Expressed in Apical Periodontitis Cooperatively Regulate Cytokines and Growth Factors Promoting an Anti-inflammatory Response. J Endod 2023; 49:286-293. [PMID: 36627081 DOI: 10.1016/j.joen.2022.12.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/29/2022] [Accepted: 12/30/2022] [Indexed: 01/08/2023]
Abstract
INTRODUCTION MicroRNAs have been shown to play a role in the pathogenesis of apical periodontitis. Upregulation of miR-10a-5p and downregulation of miR-891a-5p were previously reported in apical periodontitis samples. This study aims to perform a functional characterization of miR-10a-5p, investigating its capacity to regulate the expression of inflammatory cytokines and growth factors, as well as a possible co-regulation mechanism with miR-891a-5p in the development of apical periodontitis. METHODS miR-10a-5p mimics/controls and miR-891a-5p inhibitors/controls were introduced to human K-562 cells in the presence or absence of lipopolysaccharide. Total RNA was extracted from cell lysates, and target genes were examined via quantitative reverse transcription-polymerase chain reaction. Cell lysates were also subjected to proteomics analysis. Furthermore, mimics of miR-10a-5p and inhibitors of miR-891a-5p were co-transfected into K-562 cells. RNA sequencing and quantitative reverse transcription-polymerase chain reaction were carried out to examine their target genes. RESULTS Overexpression of miR-10a-5p led to downregulation of tumor necrosis factor-alpha and interleukin-1 beta mRNA and upregulation of transforming growth factor-beta 1 (TGFB1) mRNA expression, whereas interleukin 3 and TGF-β1 proteins were upregulated. Simultaneous overexpression of miR-10a-5p and inhibition of miR-891a-5p further increased TGFB1 mRNA transcript levels. RNA sequencing revealed that genes co-regulated by miR-10a-5p and miR-891a-5p may be involved in apical periodontitis-related pathways such as tumor necrosis factor, transient receptor potential, and vascular endothelial growth factor signaling pathways. CONCLUSIONS miR-10a-5p may modulate the expression of multiple inflammatory cytokines and growth factors such as tumor necrosis factor-alpha, IL-1β, interleukin 3, and TGF-β1. In addition, miR-10a-5p and miR-891a-5p cooperatively regulate TGFB1 gene expression, and the gene network of this co-regulation is integrated with many pathways in apical periodontitis.
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Affiliation(s)
- Zhen Shen
- Department of Endodontics, University of Texas Health Science Center at Houston, School of Dentistry at Houston, Houston, Texas
| | - Ariadne Letra
- Department of Oral and Craniofacial Sciences, University of Pittsburgh, School of Dental Medicine, Pittsburgh, Pennsylvania; Department of Endodontics, University of Pittsburgh, School of Dental Medicine, Pittsburgh, Pennsylvania
| | - Renato M Silva
- Department of Endodontics, University of Pittsburgh, School of Dental Medicine, Pittsburgh, Pennsylvania.
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168
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Zhang YQ, Li X, Shi Y, Chen T, Xu Z, Wang P, Yu M, Chen W, Li B, Jing Z, Jiang H, Fu L, Gao W, Jiang Y, Du X, Gong Z, Zhu W, Yang H, Xu HY. ETCM v2.0: An update with comprehensive resource and rich annotations for traditional chinese medicine. Acta Pharm Sin B 2023. [DOI: 10.1016/j.apsb.2023.03.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023] Open
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169
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Xu Y, Wang Y, Höti N, Clark DJ, Chen SY, Zhang H. The next "sweet" spot for pancreatic ductal adenocarcinoma: Glycoprotein for early detection. Mass Spectrom Rev 2023; 42:822-843. [PMID: 34766650 PMCID: PMC9095761 DOI: 10.1002/mas.21748] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 10/07/2021] [Accepted: 10/24/2021] [Indexed: 05/02/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is the most common neoplastic disease of the pancreas, accounting for more than 90% of all pancreatic malignancies. As a highly lethal malignancy, PDAC is the fourth leading cause of cancer-related deaths worldwide with a 5-year overall survival of less than 8%. The efficacy and outcome of PDAC treatment largely depend on the stage of disease at the time of diagnosis. Surgical resection followed by adjuvant chemotherapy remains the only possibly curative therapy, yet 80%-90% of PDAC patients present with nonresectable PDAC stages at the time of clinical presentation. Despite our advancing knowledge of PDAC, the prognosis remains strikingly poor, which is primarily due to the difficulty of diagnosing PDAC at the early stages. Recent advances in glycoproteomics and glycomics based on mass spectrometry have shown that aberrations in protein glycosylation plays a critical role in carcinogenesis, tumor progression, metastasis, chemoresistance, and immuno-response of PDAC and other types of cancers. A growing interest has thus been placed upon protein glycosylation as a potential early detection biomarker for PDAC. We herein take stock of the advancements in the early detection of PDAC that were carried out with mass spectrometry, with special focus on protein glycosylation.
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Affiliation(s)
- Yuanwei Xu
- Department of Pathology, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Yuefan Wang
- Department of Pathology, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Naseruddin Höti
- Department of Pathology, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - David J Clark
- Department of Pathology, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Shao-Yung Chen
- Department of Pathology, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Hui Zhang
- Department of Pathology, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA
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170
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Yang J, Bi L, Wang C, Wang G, Gou Y, Dong L, Wang M, Luo H, Wang K, Wang Y, Huang Y, Cai H, Xiao Z. ESCCdb: A Comprehensive Database and Key Regulator Exploring Platform Based on Cross Dataset Comparisons for Esophageal Squamous Cell Carcinoma. Comput Struct Biotechnol J 2023. [PMID: 36968016 PMCID: PMC10036886 DOI: 10.1016/j.csbj.2023.03.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 03/15/2023] [Accepted: 03/16/2023] [Indexed: 03/19/2023] Open
Abstract
Esophageal cancer is the seventh most prevalent and the sixth most lethal cancer. Esophageal squamous cell carcinoma (ESCC) is one of the major esophageal cancer subtypes that accounts for 87 % of the total cases. However, its molecular mechanism remains unclear. Here, we present an integrated database for ESCC called ESCCdb, which includes a total of 56 datasets and published studies from the GEO, Xena or SRA databases and related publications. It helps users to explore a particular gene with multiple graphical and interactive views with one click. The results comprise expression changes across 20 datasets, copy number alterations in 11 datasets, somatic mutations from 12 papers, related drugs derived from DGIdb, related pathways, and gene correlations. ESCCdb enables directly cross-dataset comparison of a gene's mutations, expressions and copy number changes in multiple datasets. This allows users to easily assess the alterations in ESCC. Furthermore, survival analysis, drug-gene relationships, and results from whole-genome CRISPR/Cas9 screening can help users determine the clinical relevance, derive functional inferences, and identify potential drugs. Notably, ESCCdb also enables the exploration of the correlation structure and identification of potential key regulators for a process. Finally, we identified 789 consistently differential expressed genes; we summarized recurrently mutated genes and genes affected by significant copy number alterations. These genes may be stable biomarkers or important players during ESCC development. ESCCdb fills the gap between massive omics data and users' needs for integrated analysis and can promote basic and clinical ESCC research. The database is freely accessible at http://cailab.labshare.cn/ESCCdb.
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171
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Firpo MA, Boucher KM, Bleicher J, Khanderao GD, Rosati A, Poruk KE, Kamal S, Marzullo L, De Marco M, Falco A, Genovese A, Adler JM, De Laurenzi V, Adler DG, Affolter KE, Garrido-Laguna I, Scaife CL, Turco MC, Mulvihill SJ. Multianalyte Serum Biomarker Panel for Early Detection of Pancreatic Adenocarcinoma. JCO Clin Cancer Inform 2023; 7:e2200160. [PMID: 36913644 PMCID: PMC10530881 DOI: 10.1200/cci.22.00160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 01/10/2023] [Accepted: 02/03/2023] [Indexed: 03/14/2023] Open
Abstract
PURPOSE We determined whether a large, multianalyte panel of circulating biomarkers can improve detection of early-stage pancreatic ductal adenocarcinoma (PDAC). MATERIALS AND METHODS We defined a biologically relevant subspace of blood analytes on the basis of previous identification in premalignant lesions or early-stage PDAC and evaluated each in pilot studies. The 31 analytes that met minimum diagnostic accuracy were measured in serum of 837 subjects (461 healthy, 194 benign pancreatic disease, and 182 early-stage PDAC). We used machine learning to develop classification algorithms using the relationship between subjects on the basis of their changes across the predictors. Model performance was subsequently evaluated in an independent validation data set from 186 additional subjects. RESULTS A classification model was trained on 669 subjects (358 healthy, 159 benign, and 152 early-stage PDAC). Model evaluation on a hold-out test set of 168 subjects (103 healthy, 35 benign, and 30 early-stage PDAC) yielded an area under the receiver operating characteristic curve (AUC) of 0.920 for classification of PDAC from non-PDAC (benign and healthy controls) and an AUC of 0.944 for PDAC versus healthy controls. The algorithm was then validated in 146 subsequent cases presenting with pancreatic disease (73 benign pancreatic disease and 73 early- and late-stage PDAC cases) and 40 healthy control subjects. The validation set yielded an AUC of 0.919 for classification of PDAC from non-PDAC and an AUC of 0.925 for PDAC versus healthy controls. CONCLUSION Individually weak serum biomarkers can be combined into a strong classification algorithm to develop a blood test to identify patients who may benefit from further testing.
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Affiliation(s)
- Matthew A. Firpo
- Department of Surgery, School of Medicine, University of Utah, Salt Lake City, UT
| | - Kenneth M. Boucher
- Department of Oncological Sciences, School of Medicine, University of Utah, Salt Lake City, UT
| | - Josh Bleicher
- Department of Surgery, School of Medicine, University of Utah, Salt Lake City, UT
| | - Gayatri D. Khanderao
- Department of Surgery, School of Medicine, University of Utah, Salt Lake City, UT
| | - Alessandra Rosati
- BIOUNIVERSA s.r.l., Baronissi, Italy
- Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana” University of Salerno, Baronissi, Italy
| | - Katherine E. Poruk
- Department of Surgery, School of Medicine, University of Utah, Salt Lake City, UT
| | - Sama Kamal
- Department of Surgery, School of Medicine, University of Utah, Salt Lake City, UT
| | - Liberato Marzullo
- BIOUNIVERSA s.r.l., Baronissi, Italy
- Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana” University of Salerno, Baronissi, Italy
| | - Margot De Marco
- BIOUNIVERSA s.r.l., Baronissi, Italy
- Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana” University of Salerno, Baronissi, Italy
| | - Antonia Falco
- BIOUNIVERSA s.r.l., Baronissi, Italy
- Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana” University of Salerno, Baronissi, Italy
| | - Armando Genovese
- University Hospital “San Giovanni di Dio e Ruggi D'Aragona,” Salerno, Italy
| | - Jessica M. Adler
- Department of Surgery, School of Medicine, University of Utah, Salt Lake City, UT
| | - Vincenzo De Laurenzi
- BIOUNIVERSA s.r.l., Baronissi, Italy
- Department of Medicine and Biotechnology, University G d'Annunzio and CeSI-MeT, Chieti, Italy
| | - Douglas G. Adler
- Department of Internal Medicine, School of Medicine, University of Utah, Salt Lake City, UT
| | - Kajsa E. Affolter
- Department of Pathology, School of Medicine, University of Utah, Salt Lake City, UT
| | - Ignacio Garrido-Laguna
- Department of Oncological Sciences, School of Medicine, University of Utah, Salt Lake City, UT
| | - Courtney L. Scaife
- Department of Surgery, School of Medicine, University of Utah, Salt Lake City, UT
| | - M. Caterina Turco
- BIOUNIVERSA s.r.l., Baronissi, Italy
- Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana” University of Salerno, Baronissi, Italy
| | - Sean J. Mulvihill
- Department of Surgery, School of Medicine, University of Utah, Salt Lake City, UT
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Ghasemi M, Rahgozar M, Kavousi K. Complex Disease Genes Identification Using a Heterogeneous Network Embedding Approach. IEEE/ACM Trans Comput Biol Bioinform 2023; 20:875-882. [PMID: 35594221 DOI: 10.1109/tcbb.2022.3175598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Finding the causal relation between a gene and a disease using experimental approaches is a time-consuming and expensive task. However, computational approaches are cost-efficient methods for identifying candidate genes. This article proposes a new heterogeneous biological network embedding approach, named NetEM, to identify disease-associated genes. To evaluate NetEM, we examine six complex diseases, including peroxisomal disorders, sarcoma, grave's disease, lysosomal storage diseases, blood coagulation disorders, and cardiomyopathy hypertrophic. Our experiments indicate that NetEM outperforms three well-known state-of-the-art algorithms: Cardigan, DIAMOnD and GeneWanderer, in identifying disease genes. We examine TCGA data of Invasive Lobular Breast Cancer and CPTAC data of human glioblastoma as other case studies to evaluate NetEM using real data. This evaluation also indicates the validity of the method. The source codes of NetEM and data are available in the supplementary of this article.
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173
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Szegvari G, Dora D, Lohinai Z. Effective Reversal of Macrophage Polarization by Inhibitory Combinations Predicted by a Boolean Protein–Protein Interaction Model. Biology 2023; 12:biology12030376. [PMID: 36979068 PMCID: PMC10045914 DOI: 10.3390/biology12030376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 02/17/2023] [Accepted: 02/22/2023] [Indexed: 03/03/2023]
Abstract
Background: The function and polarization of macrophages has a significant impact on the outcome of many diseases. Targeting tumor-associated macrophages (TAMs) is among the greatest challenges to solve because of the low in vitro reproducibility of the heterogeneous tumor microenvironment (TME). To create a more comprehensive model and to understand the inner workings of the macrophage and its dependence on extracellular signals driving polarization, we propose an in silico approach. Methods: A Boolean control network was built based on systematic manual curation of the scientific literature to model the early response events of macrophages by connecting extracellular signals (input) with gene transcription (output). The network consists of 106 nodes, classified as 9 input, 75 inner and 22 output nodes, that are connected by 217 edges. The direction and polarity of edges were manually verified and only included in the model if the literature plainly supported these parameters. Single or combinatory inhibitions were simulated mimicking therapeutic interventions, and output patterns were analyzed to interpret changes in polarization and cell function. Results: We show that inhibiting a single target is inadequate to modify an established polarization, and that in combination therapy, inhibiting numerous targets with individually small effects is frequently required. Our findings show the importance of JAK1, JAK3 and STAT6, and to a lesser extent STK4, Sp1 and Tyk2, in establishing an M1-like pro-inflammatory polarization, and NFAT5 in creating an anti-inflammatory M2-like phenotype. Conclusions: Here, we demonstrate a protein–protein interaction (PPI) network modeling the intracellular signalization driving macrophage polarization, offering the possibility of therapeutic repolarization and demonstrating evidence for multi-target methods.
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Affiliation(s)
- Gabor Szegvari
- Translational Medicine Institute, Semmelweis University, 1094 Budapest, Hungary
| | - David Dora
- Department of Anatomy, Histology and Embryology, Semmelweis University, 1094 Budapest, Hungary
- Correspondence: (D.D.); (Z.L.); Tel.: +36-1-2156920 (D.D.)
| | - Zoltan Lohinai
- Translational Medicine Institute, Semmelweis University, 1094 Budapest, Hungary
- Pulmonary Hospital Torokbalint, 2045 Torokbalint, Hungary
- Correspondence: (D.D.); (Z.L.); Tel.: +36-1-2156920 (D.D.)
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174
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Guo XX, An S, Bao F, Xu TR. Challenges and Perspectives in Target Identification and Mechanism Illustration for Chinese Medicine. Chin J Integr Med 2023. [PMID: 36809500 DOI: 10.1007/s11655-023-3629-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/11/2023] [Indexed: 02/23/2023]
Abstract
Chinese medicine (CM) is an important resource for human life understanding and discovery of drugs. However, due to the unclear pharmacological mechanism caused by unclear target, research and international promotion of many active components have made little progress in the past decades of years. CM is mainly composed of multi-ingredients with multi-targets. The identification of targets of multiple active components and the weight analysis of multiple targets in a specific pathological environment, that is, the determination of the most important target is the main obstacle to the mechanism clarification and thus hinders its internationalization. In this review, the main approach to target identification and network pharmacology were summarized. And BIBm (Bayesian inference modeling), a powerful method for drug target identification and key pathway determination was introduced. We aim to provide a new scientific basis and ideas for the development and international promotion of new drugs based on CM.
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175
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Ishibashi Y, Mochizuki S, Horiuchi K, Tsujimoto H, Kouzu K, Kishi Y, Okada Y, Ueno H. Periostin derived from cancer-associated fibroblasts promotes esophageal squamous cell carcinoma progression via ADAM17 activation. Biochim Biophys Acta Mol Basis Dis 2023; 1869:166669. [PMID: 36813090 DOI: 10.1016/j.bbadis.2023.166669] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 02/12/2023] [Accepted: 02/13/2023] [Indexed: 02/24/2023]
Abstract
Periostin (POSTN) is a matricellular protein that was originally identified in osteoblasts. Past studies have shown that POSTN is also preferentially expressed in cancer-associated fibroblasts (CAFs) in various types of cancer. We previously demonstrated that the increased expression of POSTN in stromal tissues is associated with an unfavorable clinical outcome in esophageal squamous cell carcinoma (ESCC) patients. In this study, we aimed to elucidate the role of POSNT in ESCC progression and its underlying molecular mechanism. We found that POSTN is predominantly produced by CAFs in ESCC tissues, and that CAFs-cultured media significantly promoted the migration, invasion, proliferation, and colony formation of ESCC cell lines in a POSTN-dependent manner. In ESCC cells, POSTN increased the phosphorylation of ERK1/2 and stimulated the expression and activity of a disintegrin and metalloproteinase 17 (ADAM17), which is critically involved in tumorigenesis and tumor progression. The effects of POSTN on ESCC cells were suppressed by interfering with the binding of POSTN to integrin αvβ3 or αvβ5 using neutralizing antibody against POSTN. Taken together, our data show that CAFs-derived POSTN stimulates ADAM17 activity through activation of the integrin αvβ3 or αvβ5-ERK1/2 pathway and thereby contributes to the progression of ESCC.
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Affiliation(s)
- Yusuke Ishibashi
- Department of Surgery, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Satsuki Mochizuki
- Department of Surgery, National Defense Medical College, Tokorozawa, Saitama, Japan.
| | - Keisuke Horiuchi
- Department of Orthopedic Surgery, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Hironori Tsujimoto
- Department of Surgery, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Keita Kouzu
- Department of Surgery, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Yoji Kishi
- Department of Orthopedic Surgery, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Yasunori Okada
- Department of Pathophysiology for Locomotive and Neoplastic Diseases, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Hideki Ueno
- Department of Surgery, National Defense Medical College, Tokorozawa, Saitama, Japan
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Zhang ZF. EXOC3L1: A Novel Prognostic Biomarker Correlated with Immune Infiltration in Esophageal Squamous Cell Carcinoma. Med Sci Monit 2023; 29:e938512. [PMID: 36852560 PMCID: PMC9942429 DOI: 10.12659/msm.938512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Exocyst complex component 3-like 1 (EXOC3L1) is ubiquitously present in multiple organs. However, its role in esophageal squamous cell carcinoma (ESCC) remains unknown. The aim of this study was to explore the relationship between EXOC3L1 and ESCC. MATERIAL AND METHODS A total of 652 normal samples and 82 ESCC samples obtained from the University of California Santa Cruz (UCSC) Xena were applied to detect the expression difference of EXOC3L1. GSE53625 with 179 paired samples and GSE161533 with 28 paired samples were used for validation. The correlation between clinicopathological features and EXOC3L1 expression was calculated. Kaplan-Meier method was employed to assess the prognostic value of EXOC3L1 in ESCC. Univariate and multivariate Cox regression analyses were carried out to screen the factors contributing to the prognosis of ESCC. In addition, functional enrichment analysis, protein-protein interaction (PPI) network analysis, and immune infiltration analysis were conducted to identify the significantly involved functions of EXOC3L1. RESULTS EXOC3L1 was significantly overexpressed in ESCC compared to normal samples. High expression of EXOC3L1 was associated with worse prognosis, and univariate and multivariate Cox regression analysis demonstrated that EXOC3L1 was an independent prognostic predictor of ESCC. Functional enrichment analysis and immune infiltration analysis disclosed that the expression of EXOC3L1 was correlated with the abundance of several types of immune cells. CONCLUSIONS EXOC3L1 plays a crucial role in the prognosis of ESCC, and it may serve as a reliable biomarker for predicting the survival and a potential therapeutic target for ESCC.
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Affiliation(s)
- Zhan-Fei Zhang
- Department of Cardiothoracic Surgery, Zhongshan People’s Hospital, Zhongshan, Guangdong, PR China,Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, Guangdong, PR China
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177
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Yuan L, Tang Y, Yin L, Lin X, Luo Z, Wang S, Li J, Liang P, Jiang B. The role of Transmembrane Protein 16A (TMEM16A) in pulmonary hypertension. Cardiovasc Pathol 2023; 65:107525. [PMID: 36781068 DOI: 10.1016/j.carpath.2023.107525] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 02/04/2023] [Accepted: 02/06/2023] [Indexed: 02/13/2023] Open
Abstract
Transmembrane protein 16A (TMEM16A), a member of the TMEM16 family, is the molecular basis of Ca2+-activated chloride channels (CaCCs) and is involved in a variety of physiological and pathological processes. Previous studies have focused more on respiratory-related diseases and tumors. However, recent studies have identified an important role for TMEM16A in cardiovascular diseases, especially in pulmonary hypertension. TMEM16A is expressed in both pulmonary artery smooth muscle cells and pulmonary artery endothelial cells and is involved in the development of pulmonary hypertension. This paper presents the structure and function of TMEM16A, the pathogenesis of pulmonary hypertension, and highlights the role and mechanism of TMEM16A in pulmonary hypertension, summarizing the controversies in this field and taking into account hypertension and portal hypertension, which have similar pathogenesis. It is hoped that the unique role of TMEM16A in pulmonary hypertension will be illustrated and provide ideas for research in this area.
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Affiliation(s)
- Ludong Yuan
- Department of Pathophysiology, Sepsis Translational Medicine Key Laboratory of Hunan Province, Xiangya School of Medicine, Central South University, Changsha, Hunan, China; National Medicine Functional Experimental Teaching Center, Central South University, Changsha, Hunan China
| | - Yuting Tang
- Department of Pathophysiology, Sepsis Translational Medicine Key Laboratory of Hunan Province, Xiangya School of Medicine, Central South University, Changsha, Hunan, China; National Medicine Functional Experimental Teaching Center, Central South University, Changsha, Hunan China
| | - Leijing Yin
- Department of Pathophysiology, Sepsis Translational Medicine Key Laboratory of Hunan Province, Xiangya School of Medicine, Central South University, Changsha, Hunan, China; National Medicine Functional Experimental Teaching Center, Central South University, Changsha, Hunan China
| | - Xiaofang Lin
- Department of Pathophysiology, Sepsis Translational Medicine Key Laboratory of Hunan Province, Xiangya School of Medicine, Central South University, Changsha, Hunan, China; National Medicine Functional Experimental Teaching Center, Central South University, Changsha, Hunan China
| | - Zhengyang Luo
- Department of Pathophysiology, Sepsis Translational Medicine Key Laboratory of Hunan Province, Xiangya School of Medicine, Central South University, Changsha, Hunan, China; National Medicine Functional Experimental Teaching Center, Central South University, Changsha, Hunan China
| | - Shuxin Wang
- Department of Pathophysiology, Sepsis Translational Medicine Key Laboratory of Hunan Province, Xiangya School of Medicine, Central South University, Changsha, Hunan, China; National Medicine Functional Experimental Teaching Center, Central South University, Changsha, Hunan China
| | - Jing Li
- Department of Pathophysiology, Sepsis Translational Medicine Key Laboratory of Hunan Province, Xiangya School of Medicine, Central South University, Changsha, Hunan, China; National Medicine Functional Experimental Teaching Center, Central South University, Changsha, Hunan China
| | - Pengfei Liang
- Department of Burns and Plastic Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Bimei Jiang
- Department of Pathophysiology, Sepsis Translational Medicine Key Laboratory of Hunan Province, Xiangya School of Medicine, Central South University, Changsha, Hunan, China; National Medicine Functional Experimental Teaching Center, Central South University, Changsha, Hunan China.
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Al Sharie AH, Al Zu'bi YO, El-Elimat T, Al-Kammash K, Abu Lil A, Isawi IH, Al Sharie S, Abu Mousa BM, Al Malkawi AA, Alali FQ. ANO4 Expression Is a Potential Prognostic Biomarker in Non-Metastasized Clear Cell Renal Cell Carcinoma. J Pers Med 2023; 13. [PMID: 36836529 DOI: 10.3390/jpm13020295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 01/28/2023] [Accepted: 02/02/2023] [Indexed: 02/10/2023] Open
Abstract
Background: Over the past decade, transcriptome profiling has elucidated many pivotal pathways involved in oncogenesis. However, a detailed comprehensive map of tumorigenesis remains an enigma to solve. Propelled research has been devoted to investigating the molecular drivers of clear cell renal cell carcinoma (ccRCC). To add another piece to the puzzle, we evaluated the role of anoctamin 4 (ANO4) expression as a potential prognostic biomarker in non-metastasized ccRCC. Methods: A total of 422 ccRCC patients with the corresponding ANO4 expression and clinicopathological data were obtained from The Cancer Genome Atlas Program (TCGA). Differential expression across several clinicopathological variables was performed. The Kaplan-Meier method was used to assess the impact of ANO4 expression on the overall survival (OS), progression-free interval (PFI), disease-free interval (DFI), and disease-specific survival (DSS). Univariate and multivariate Cox logistic regression analyses were conducted to identify independent factors modulating the aforementioned outcomes. Gene set enrichment analysis (GSEA) was used to discern a set of molecular mechanisms involved in the prognostic signature. Tumor immune microenvironment was estimated using xCell. Results: ANO4 expression was upregulated in tumor samples compared to normal kidney tissue. Albeit the latter finding, low ANO4 expression is associated with advanced clinicopathological variables such as tumor grade, stage, and pT. In addition, low ANO4 expression is linked to shorter OS, PFI, and DSS. Multivariate Cox logistic regression analysis identified ANO4 expression as an independent prognostic variable in OS (HR: 1.686, 95% CI: 1.120-2.540, p = 0.012), PFI (HR: 1.727, 95% CI: 1.103-2.704, p = 0.017), and DSS (HR: 2.688, 95% CI: 1.465-4.934, p = 0.001). GSEA identified the following pathways to be enriched within the low ANO4 expression group: epithelial-mesenchymal transition, G2-M checkpoint, E2F targets, estrogen response, apical junction, glycolysis, hypoxia, coagulation, KRAS, complement, p53, myogenesis, and TNF-α signaling via NF-κB pathways. ANO4 expression correlates significantly with monocyte (ρ = -0.1429, p = 0.0033) and mast cell (ρ = 0.1598, p = 0.001) infiltration. Conclusions: In the presented work, low ANO4 expression is portrayed as a potential poor prognostic factor in non-metastasized ccRCC. Further experimental studies should be directed to shed new light on the exact molecular mechanisms involved.
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Jiang K, Yin X, Zhang Q, Yin J, Tang Q, Xu M, Wu L, Shen Y, Zhou Z, Yu H, Yan S. STC2 activates PRMT5 to induce radioresistance through DNA damage repair and ferroptosis pathways in esophageal squamous cell carcinoma. Redox Biol 2023; 60:102626. [PMID: 36764215 PMCID: PMC9929488 DOI: 10.1016/j.redox.2023.102626] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 02/01/2023] [Accepted: 02/01/2023] [Indexed: 02/05/2023] Open
Abstract
Radioresistance is the major reason for the failure of radiotherapy in esophageal squamous cell carcinoma (ESCC). Previous evidence indicated that stanniocalcin 2 (STC2) participates in various biological processes of malignant tumors. However, researches on its effect on radioresistance in cancers are limited. In this study, STC2 was screened out by RNA-sequencing and bioinformatics analyses as a potential prognosis predictor of ESCC radiosensitivity and then was determined to facilitate radioresistance. We found that STC2 expression is increased in ESCC tissues compared to adjacent normal tissues, and a higher level of STC2 is associated with poor prognosis. Also, STC2 mRNA and protein expression levels were higher in radioresistant cells than in their parental cells. Further investigation revealed that STC2 could interact with protein methyltransferase 5 (PRMT5) and activate PRMT5, thus leading to the increased expression of symmetric dimethylation of histone H4 on Arg 3 (H4R3me2s). Mechanistically, STC2 can promote DDR through the homologous recombination and non-homologous end joining pathways by activating PRMT5. Meanwhile, STC2 can participate in SLC7A11-mediated ferroptosis in a PRMT5-dependent manner. Finally, these results were validated through in vivo experiments. These findings uncovered that STC2 might be an attractive therapeutic target to overcome ESCC radioresistance.
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Affiliation(s)
- Kan Jiang
- Department of Radiation Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China; Zhejiang University Cancer Center, Zhejiang, 310003, Hangzhou, China
| | - Xin Yin
- Department of Radiation Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China; Zhejiang University Cancer Center, Zhejiang, 310003, Hangzhou, China
| | - Qingyi Zhang
- Department of Thoracic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jie Yin
- Department of Colorectal Medicine, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Qiuying Tang
- Department of Radiation Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China; Zhejiang University Cancer Center, Zhejiang, 310003, Hangzhou, China
| | - Mengyou Xu
- Peking University Cancer Hospital & Institute, Beijing, China
| | - Lingyun Wu
- Department of Radiation Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China; Zhejiang University Cancer Center, Zhejiang, 310003, Hangzhou, China
| | - Yifan Shen
- Department of Orthopedic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ziyang Zhou
- Department of Radiation Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China; Zhejiang University Cancer Center, Zhejiang, 310003, Hangzhou, China
| | - Hao Yu
- Department of Radiation Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China; Zhejiang University Cancer Center, Zhejiang, 310003, Hangzhou, China
| | - Senxiang Yan
- Department of Radiation Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China; Zhejiang University Cancer Center, Zhejiang, 310003, Hangzhou, China.
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Uddin SMN, Haque M, Barek MA, Chowdhury MNU, Das A, Uddin MG, Islam MS. Analysis of serum calcium, sodium, potassium, zinc, and iron in patients with pre-eclampsia in Bangladesh: A case-control study. Health Sci Rep 2023; 6:e1097. [PMID: 36761032 PMCID: PMC9895321 DOI: 10.1002/hsr2.1097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 01/05/2023] [Accepted: 01/23/2023] [Indexed: 02/05/2023] Open
Abstract
Background and Aims Pre-eclampsia is a particular type of pregnancy condition. Although the primary etiology of pre-eclampsia is unclear, it hypothesizes that the alteration of trace elements and macro-minerals may play a crucial function in the pathogenesis of Pre-eclampsia. Therefore, our research sought to ascertain the serum level of trace elements (zinc, iron) and macro-minerals (sodium, calcium, potassium) and their possible association with pre-eclampsia. Methods The present study was conducted with 74 pre-eclampsia pregnant women (case) and 118 pregnant women having normal blood pressure (controls). Atomic Absorption Spectroscopy determined the serum level of trace components and electrolytes. Results The researchers discovered notable differences in maternal age, gestational period, body mass index, systolic and diastolic blood pressure, hemoglobin, and creatinine level. Results of serum analysis revealed that calcium (52.06 ± 3.71 mg/L vs. 65.93 ± 2.57 mg/L, p < 0.05) and potassium (63.44 ± 5.33 mg/L vs. 102.54 ± 4.25 mg/L, p < 0.001) concentrations were substantially lower in the patient group than in control. Serum zinc (0.34 ± 0.02 mg/L vs. 0.52 ± 0.02 mg/L, p < 0.001) and iron (0.38 ± 0.03 mg/L vs. 0.46 ± 0.02 mg/L, p < 0.05) concentration were also considerably decreased in pre-eclampsia participants compared with a pregnant normotensive group. Pearson's correlation research results in the patient group revealed a connection between trace elements or macro minerals. In addition, the systolic blood pressure was positively correlated with sodium (r = 0.392, p < 0.01) and negatively correlated with potassium (r = -0.257, p < 0.05) in the control group. Conclusions This study concludes that calcium, potassium, iron, and zinc levels were lower, whereas sodium levels were higher in Bangladeshi pre-eclampsia patients compared to controls. These findings with Pearson's correlation and the inter-element relationship between the patient and a control subject results can act as critical indication factors for patients with pre-eclampsia in Bangladesh and, as a result, may require a higher intake of calcium, potassium, iron, and zinc for effective therapeutic intervention and reduce the intake of sodium.
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Affiliation(s)
- S. M. Naim Uddin
- Department of PharmacyUniversity of ChittagongChittagongBangladesh
| | - Mahmodul Haque
- Department of PharmacyNoakhali Science and Technology UniversityNoakhaliBangladesh
| | - Md Abdul Barek
- Department of PharmacyNoakhali Science and Technology UniversityNoakhaliBangladesh
| | | | - Abhijit Das
- Department of PharmacyNoakhali Science and Technology UniversityNoakhaliBangladesh
| | - Md. Giash Uddin
- Department of PharmacyUniversity of ChittagongChittagongBangladesh
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Nithya C, Kiran M, Nagarajaram HA. Dissection of hubs and bottlenecks in a protein-protein interaction network. Comput Biol Chem 2023; 102:107802. [PMID: 36603332 DOI: 10.1016/j.compbiolchem.2022.107802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 11/20/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022]
Abstract
Analysis of degree centrality in conjunction with betweenness centrality of proteins in a human protein-protein interaction network revealed three categories of centrally important proteins: a) proteins with high degree and betweenness (hub-bottlenecks denoted as MX), b) proteins with high betweenness and low degree (non-hub-bottlenecks/pure bottlenecks denoted as PB) and c) proteins with high degree and low betweenness (hub-non-bottlenecks/pure hubs denoted as PH). When subjected to a detailed statistical analysis of their molecular-level properties, the proteins belonging to each of these categories were found to be associated with distinct canonical molecular properties, i.e., "molecular markers". The MX proteins are a) conformationally versatile, mainly comprising of essential proteins, b) the targets for interactions by the proteins of viral and bacterial pathogens, c) evolutionally constrained, involved in multiple pathways, enriched with disease genes and d) involved in the functions such as protein stabilization, phosphorylation, and mRNA slicing processes. PB proteins are a) enriched with extracellular and cancer-related proteins, b) enriched with the approved drug targets and c) involved in cell-cell signaling processes. Finally, PH are a) structurally versatile, b) enriched with essential proteins primarily involved in housekeeping processes (transcription and replication). The fact that the proteins belonging to these three categories form three distinct sets in terms of their molecular properties reveals the existence of trichotomy among hubs and bottlenecks, and this knowledge is of paramount importance while prioritizing protein targets for further studies such as drug design and disease association studies based on their network centrality values.
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Affiliation(s)
- Chandramohan Nithya
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana 500046, India
| | - Manjari Kiran
- Department of Systems and Computational Biology, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana 500046, India
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Selvaraj C, Panwar U, Ramalingam KR, Vijayakumar R, Singh SK. Exploring the macromolecules for secretory pathway in cancer disease. Adv Protein Chem Struct Biol 2023; 133:55-83. [PMID: 36707206 DOI: 10.1016/bs.apcsb.2022.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Secretory proteins play an important role in the tumor microenvironment and are widely distributed throughout tumor tissues. Tumor cells secrete a protein that mediates communication between tumor cells and stromal cells, thereby controlling tumor growth and affecting the success of cancer treatments in the clinic. The cancer secretome is produced by various secretory pathways and has a wide range of applications in oncoproteomics. Secretory proteins are involved in cancer development and tumor cell migration, and thus serve as biomarkers or effective therapeutic targets for a variety of cancers. Several proteomic strategies have recently been used for the analysis of cancer secretomes in order to gain a better understanding and elaborate interpretation. For instance, the development of exosome proteomics, degradomics, and tumor-host cell interaction provide clear information regarding the mechanism of cancer pathobiology. In this chapter, we emphasize the recent advances in secretory protein and the challenges in the field of secretome analysis and their clinical applications.
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Affiliation(s)
- Chandrabose Selvaraj
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, Tamil Nadu, India.
| | - Umesh Panwar
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Karthik Raja Ramalingam
- Department of Biotechnology, Division of Research and Innovation, Saveetha School of Engineering, SIMATS, Chennai, Tamil Nadu, India
| | - Rajendran Vijayakumar
- Department of Biology, College of Science in Zulfi, Majmaah University, Majmaah, Saudi Arabia
| | - Sanjeev Kumar Singh
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, Tamil Nadu, India.
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Li G, Zhang P, Sun W, Xu J, Hu L, Zhang W. GA-ENs: A novel drug-target interactions prediction method by incorporating prior Knowledge Graph into dual Wasserstein Generative Adversarial Network with gradient penalty. Appl Soft Comput 2023. [DOI: 10.1016/j.asoc.2023.110151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
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184
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Zheng S, Lin N, Wu Q, He H, Yang C. Prognostic model construction and validation of esophageal cancer cellular senescence-related genes and correlation with immune infiltration. Front Surg 2023; 10:1090700. [PMID: 36761024 PMCID: PMC9905418 DOI: 10.3389/fsurg.2023.1090700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 01/06/2023] [Indexed: 01/26/2023] Open
Abstract
Introduction Cellular senescence is a cellular response to stress, including the activation of oncogenes, and is characterized by irreversible proliferation arrest. Restricted studies have provided a relationship between cellular senescence and immunotherapy for esophageal cancer. Methods In the present study, we obtained clinical sample of colon cancer from the TCGA database and cellular senescence-related genes from MSigDB and Genecard datasets. Cellular senescence-related prognostic genes were identified by WGCNA, COX, and lasso regression analysis, and a cellular senescence-related risk score (CSRS) was calculated. We constructed a prognostic model based on CSRS. Validation was performed with an independent cohort that GSE53625. Three scoring systems for immuno-infiltration analysis were performed, namely ssGSEA analysis, ESTIMATE scores and TIDE scores. Result Five cellular senescence-related genes, including H3C1, IGFBP1, MT1E, SOX5 and CDHR4 and used to calculate risk score. Multivariate regression analysis using cox regression model showed that cellular senescence-related risk scores (HR=2.440, 95% CI=1.154-5.159, p=0.019) and pathological stage (HR=2.423, 95% CI=1.119-5.249, p=0.025) were associated with overall survival (OS). The nomogram model predicts better clinical benefit than the American Joint Committee on Cancer (AJCC) staging for prognosis of patients with esophageal cancer with a five-year AUC of 0.946. Patients with high CSRS had a poor prognosis (HR=2.93, 95%CI=1.74-4.94, p<0.001). We observed differences in the distribution of CSRS in different pathological staging and therefore performed a subgroup survival analysis finding that assessment of prognosis by CSRS independent of pathological staging. Comprehensive immune infiltration analysis and functional enrichment analysis suggested that patients with high CSRS may develop immunotherapy resistance through mechanisms of deacetylation and methylation. Discussion In summary, our study suggested that CSRS is a prognostic risk factor for esophageal cancer. Patients with high CSRS may have worse immunotherapy outcomes.
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Affiliation(s)
- Shiyao Zheng
- College of Clinical Medicine for Oncology, Fujian Medical University, Fuzhou, China,Department of Gastrointestinal Surgical Oncology, Fujian Provincial Cancer Hospital, Fuzhou, China
| | - Nan Lin
- Fuzong Clinical Medical College of Fujian Medical University, Fujian Medical University, Fuzhou, China
| | - Qing Wu
- Department of Oncology, Molecular Oncology Research Institute, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Hongxin He
- College of Clinical Medicine for Oncology, Fujian Medical University, Fuzhou, China,Department of Gastrointestinal Surgical Oncology, Fujian Provincial Cancer Hospital, Fuzhou, China
| | - Chunkang Yang
- College of Clinical Medicine for Oncology, Fujian Medical University, Fuzhou, China,Department of Gastrointestinal Surgical Oncology, Fujian Provincial Cancer Hospital, Fuzhou, China,Correspondence: Chunkang Yang
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Li M, Cai X, Xu S, Ji H. Metapath-aggregated heterogeneous graph neural network for drug-target interaction prediction. Brief Bioinform 2023; 24:6966534. [PMID: 36592060 DOI: 10.1093/bib/bbac578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 11/03/2022] [Accepted: 11/26/2022] [Indexed: 01/03/2023] Open
Abstract
Drug-target interaction (DTI) prediction is an essential step in drug repositioning. A few graph neural network (GNN)-based methods have been proposed for DTI prediction using heterogeneous biological data. However, existing GNN-based methods only aggregate information from directly connected nodes restricted in a drug-related or a target-related network and are incapable of capturing high-order dependencies in the biological heterogeneous graph. In this paper, we propose a metapath-aggregated heterogeneous graph neural network (MHGNN) to capture complex structures and rich semantics in the biological heterogeneous graph for DTI prediction. Specifically, MHGNN enhances heterogeneous graph structure learning and high-order semantics learning by modeling high-order relations via metapaths. Additionally, MHGNN enriches high-order correlations between drug-target pairs (DTPs) by constructing a DTP correlation graph with DTPs as nodes. We conduct extensive experiments on three biological heterogeneous datasets. MHGNN favorably surpasses 17 state-of-the-art methods over 6 evaluation metrics, which verifies its efficacy for DTI prediction. The code is available at https://github.com/Zora-LM/MHGNN-DTI.
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Affiliation(s)
- Mei Li
- Tianjin Key Laboratory of Network and Data Security Technology, China.,College of Computer Science, Nankai University, 300350, Tianjin, China
| | - Xiangrui Cai
- Tianjin Key Laboratory of Network and Data Security Technology, China.,College of Computer Science, Nankai University, 300350, Tianjin, China
| | - Sihan Xu
- Tianjin Key Laboratory of Network and Data Security Technology, China.,College of Cyber Science, Nankai University, 300350, Tianjin, China
| | - Hua Ji
- Tianjin Key Laboratory of Network and Data Security Technology, China.,College of Computer Science, Nankai University, 300350, Tianjin, China
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186
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Zhou Q, Lei C, Cui F, Chen H, Cao X. Circ-ATIC regulates esophageal squamous cell carcinoma growth and metastasis through miR-1294/PBX3 pathway. Heliyon 2023; 9:e12916. [PMID: 36699282 PMCID: PMC9868444 DOI: 10.1016/j.heliyon.2023.e12916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 01/08/2023] [Accepted: 01/09/2023] [Indexed: 01/12/2023] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) is a digestive tract malignancy associated with poor clinical outcome. Growing evidence have elucidated that circular RNAs (circRNAs) play important roles in the pathological process of ESCC. However, the detailed mechanisms how circRNAs modulate the development of ESCC remain largely unknown. Our study aimed to decipher the role and mechanism of circ-ATIC (also termed as circRNA_0058063) in regulating the progression of ESCC. We found that circ-ATIC and its host gene ATIC were significantly increased in ESCC tissues and cells compared with the adjacent noncancerous tissues or normal esophagus epithelial cell. Circ-ATIC knockdown substantially reduced proliferation and the number of invaded ESCC cells and retarded EMT process, reflecting by the decreased N-cadherin and elevated E-cadherin. However, the level of host gene ATIC was not changed under circ-ATIC suppression. It was predicted that circ-ATIC could bind to miR-1294 and serve as a sponge RNA. The luciferase reporter assay and RNA immunoprecipitation (RIP) assay confirmed their relations. MiR-1294 was decreased in ESCC tissues and cells, which was reversely correlated with circ-ATIC level. Furthermore, PBX3 was predicted and proved to be a downstream direct target of miR-1294. PBX3 mRNA and protein were obviously upregulated in ESCC tumor tissues and cells. PBX3 overexpression could reverse the suppressive roles of miR-1294 mimics on ESCC proliferation and invasion. In an xenograft nude mice model, stable transfection of sh-circ-ATIC significantly retarded the growth of tumor and suppressed VEGF and Ki67. Collectively, circ-ATIC promoted ESCC proliferation and invasion by regulating miR-1294/PBX3 axis.
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Affiliation(s)
- Qian Zhou
- Department of Cardiothoracic Surgery, Jingzhou Central Hospital (Jingzhou Hospital Affiliated to Yangtze University), Jingzhou, 434000, Hubei, PR China
| | - Chengang Lei
- Department of Cardiothoracic Surgery, Jingzhou Central Hospital (Jingzhou Hospital Affiliated to Yangtze University), Jingzhou, 434000, Hubei, PR China
| | - Fenghe Cui
- Department of Cardiothoracic Surgery, Jingzhou Central Hospital (Jingzhou Hospital Affiliated to Yangtze University), Jingzhou, 434000, Hubei, PR China
| | - Hao Chen
- Department of Cardiothoracic Surgery, Sinopharm Dongfeng General Hospital, Hubei University of Medicine, Shiyan, 442008, Hubei, PR China
| | - Xianzhao Cao
- Department of Cardiothoracic Surgery, Sinopharm Dongfeng General Hospital, Hubei University of Medicine, Shiyan, 442008, Hubei, PR China,Corresponding author. Department of Cardiothoracic Surgery, Sinopharm Dongfeng General Hospital, Hubei University of Medicine, No. 16 Daling Road, Zhangwan District, Shiyan, 442008, Hubei, PR China.
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187
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Hong H, Chen X, Wang H, Gu X, Yuan Y, Zhang Z. Global profiling of protein lysine lactylation and potential target modified protein analysis in hepatocellular carcinoma. Proteomics 2023; 23:e2200432. [PMID: 36625413 DOI: 10.1002/pmic.202200432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 12/23/2022] [Accepted: 01/04/2023] [Indexed: 01/11/2023]
Abstract
Hepatocellular carcinoma (HCC), the most common type of primary liver cancer, often metastasizes to the lungs. The implications of lysine lactylation (Kla), a recently identified histone post-translational modification (PTM), in the pathology of HCC remain unclear. Here, we report the first proteomic survey of this specific modification in HCC (with no metastasis during 3 years of follow-up), normal liver tissues, and lung metastasis samples of HCC. Of the 2045 modification sites detected on 960 proteins, 1438 sites on 772 proteins contained quantitative information. Subsequently, we analyzed the differentially modified proteins among the different groups. Differentially lactylated proteins were found to be involved in several biological processes, including-but not limited to-amino acid metabolism, ribosomal protein synthesis, and fatty acid metabolism. In addition, we identified numerous highly valuable lactate-modified proteins from the literature. Among them, we verified the lactate modification levels of the following two tumor-related proteins and obtained similar results: USP14 and ABCF1. These two modified proteins will be further investigated in our future studies. This paper is the first report on the lactylome of HCC and it provides a reliable foundation for further research on Kla in HCC.
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Affiliation(s)
- Han Hong
- Department of General Surgery, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China
| | - Xi Chen
- Department of Hepatobiliary Surgery of the Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, Jiangsu Province, China
| | - Honggang Wang
- Department of Gastrointestinal Surgery of the Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, Jiangsu Province, China
| | - Xiangqian Gu
- Department of Hepatobiliary Surgery of the Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, Jiangsu Province, China
| | - Yin Yuan
- Department of Hepatobiliary Surgery of the Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, Jiangsu Province, China
| | - Zixiang Zhang
- Department of General Surgery, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China
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Punetha A, Kotiya D. Advancements in Oncoproteomics Technologies: Treading toward Translation into Clinical Practice. Proteomes 2023; 11:2. [PMID: 36648960 PMCID: PMC9844371 DOI: 10.3390/proteomes11010002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 01/03/2023] [Accepted: 01/04/2023] [Indexed: 01/12/2023] Open
Abstract
Proteomics continues to forge significant strides in the discovery of essential biological processes, uncovering valuable information on the identity, global protein abundance, protein modifications, proteoform levels, and signal transduction pathways. Cancer is a complicated and heterogeneous disease, and the onset and progression involve multiple dysregulated proteoforms and their downstream signaling pathways. These are modulated by various factors such as molecular, genetic, tissue, cellular, ethnic/racial, socioeconomic status, environmental, and demographic differences that vary with time. The knowledge of cancer has improved the treatment and clinical management; however, the survival rates have not increased significantly, and cancer remains a major cause of mortality. Oncoproteomics studies help to develop and validate proteomics technologies for routine application in clinical laboratories for (1) diagnostic and prognostic categorization of cancer, (2) real-time monitoring of treatment, (3) assessing drug efficacy and toxicity, (4) therapeutic modulations based on the changes with prognosis and drug resistance, and (5) personalized medication. Investigation of tumor-specific proteomic profiles in conjunction with healthy controls provides crucial information in mechanistic studies on tumorigenesis, metastasis, and drug resistance. This review provides an overview of proteomics technologies that assist the discovery of novel drug targets, biomarkers for early detection, surveillance, prognosis, drug monitoring, and tailoring therapy to the cancer patient. The information gained from such technologies has drastically improved cancer research. We further provide exemplars from recent oncoproteomics applications in the discovery of biomarkers in various cancers, drug discovery, and clinical treatment. Overall, the future of oncoproteomics holds enormous potential for translating technologies from the bench to the bedside.
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Affiliation(s)
- Ankita Punetha
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Rutgers University, 225 Warren St., Newark, NJ 07103, USA
| | - Deepak Kotiya
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, 900 South Limestone St., Lexington, KY 40536, USA
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Shang J, Zhu X, Sun Y, Li F, Kong X, Liu JX. DM-MOGA: a multi-objective optimization genetic algorithm for identifying disease modules of non-small cell lung cancer. BMC Bioinformatics 2023; 24:13. [PMID: 36624376 PMCID: PMC9830734 DOI: 10.1186/s12859-023-05136-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Constructing molecular interaction networks from microarray data and then identifying disease module biomarkers can provide insight into the underlying pathogenic mechanisms of non-small cell lung cancer. A promising approach for identifying disease modules in the network is community detection. RESULTS In order to identify disease modules from gene co-expression networks, a community detection method is proposed based on multi-objective optimization genetic algorithm with decomposition. The method is named DM-MOGA and possesses two highlights. First, the boundary correction strategy is designed for the modules obtained in the process of local module detection and pre-simplification. Second, during the evolution, we introduce Davies-Bouldin index and clustering coefficient as fitness functions which are improved and migrated to weighted networks. In order to identify modules that are more relevant to diseases, the above strategies are designed to consider the network topology of genes and the strength of connections with other genes at the same time. Experimental results of different gene expression datasets of non-small cell lung cancer demonstrate that the core modules obtained by DM-MOGA are more effective than those obtained by several other advanced module identification methods. CONCLUSIONS The proposed method identifies disease-relevant modules by optimizing two novel fitness functions to simultaneously consider the local topology of each gene and its connection strength with other genes. The association of the identified core modules with lung cancer has been confirmed by pathway and gene ontology enrichment analysis.
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Affiliation(s)
- Junliang Shang
- grid.412638.a0000 0001 0227 8151School of Computer Science, Qufu Normal University, Rizhao, 276826 China
| | - Xuhui Zhu
- grid.412638.a0000 0001 0227 8151School of Computer Science, Qufu Normal University, Rizhao, 276826 China
| | - Yan Sun
- grid.412638.a0000 0001 0227 8151School of Computer Science, Qufu Normal University, Rizhao, 276826 China
| | - Feng Li
- grid.412638.a0000 0001 0227 8151School of Computer Science, Qufu Normal University, Rizhao, 276826 China
| | - Xiangzhen Kong
- grid.412638.a0000 0001 0227 8151School of Computer Science, Qufu Normal University, Rizhao, 276826 China
| | - Jin-Xing Liu
- grid.412638.a0000 0001 0227 8151School of Computer Science, Qufu Normal University, Rizhao, 276826 China
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190
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Zhang Y, Zhang Y, Song C, Zhao X, Ai B, Wang Y, Zhou L, Zhu J, Feng C, Xu L, Wang Q, Sun H, Fang Q, Xu X, Li E, Li C. CRdb: a comprehensive resource for deciphering chromatin regulators in human. Nucleic Acids Res 2023; 51:D88-D100. [PMID: 36318256 PMCID: PMC9825595 DOI: 10.1093/nar/gkac960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 10/04/2022] [Accepted: 10/12/2022] [Indexed: 11/05/2022] Open
Abstract
Chromatin regulators (CRs) regulate epigenetic patterns on a partial or global scale, playing a critical role in affecting multi-target gene expression. As chromatin immunoprecipitation sequencing (ChIP-seq) data associated with CRs are rapidly accumulating, a comprehensive resource of CRs needs to be built urgently for collecting, integrating, and processing these data, which can provide abundant annotated information on CR upstream and downstream regulatory analyses as well as CR-related analysis functions. This study established an integrative CR resource, named CRdb (http://cr.liclab.net/crdb/), with the aim of curating a large number of available resources for CRs and providing extensive annotations and analyses of CRs to help biological researchers clarify the regulation mechanism and function of CRs. The CRdb database comprised a total of 647 CRs and 2,591 ChIP-seq samples from more than 300 human tissues and cell types. These samples have been manually curated from NCBI GEO/SRA and ENCODE. Importantly, CRdb provided the abundant and detailed genetic annotations in CR-binding regions based on ChIP-seq. Furthermore, CRdb supported various functional annotations and upstream regulatory information on CRs. In particular, it embedded four types of CR regulatory analyses: CR gene set enrichment, CR-binding genomic region annotation, CR-TF co-occupancy analysis, and CR regulatory axis analysis. CRdb is a useful and powerful resource that can help in exploring the potential functions of CRs and their regulatory mechanism in diseases and biological processes.
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Affiliation(s)
- Yimeng Zhang
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou 515041, China
| | | | | | - Xilong Zhao
- School of Medical Informatics, Daqing Campus, Harbin Medical University.Daqing 163319, China
| | - Bo Ai
- School of Medical Informatics, Daqing Campus, Harbin Medical University.Daqing 163319, China
| | - Yuezhu Wang
- School of Medical Informatics, Daqing Campus, Harbin Medical University.Daqing 163319, China
| | - Liwei Zhou
- School of Medical Informatics, Daqing Campus, Harbin Medical University.Daqing 163319, China
| | - Jiang Zhu
- School of Medical Informatics, Daqing Campus, Harbin Medical University.Daqing 163319, China
| | - Chenchen Feng
- School of Medical Informatics, Daqing Campus, Harbin Medical University.Daqing 163319, China
| | - Liyan Xu
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou 515041, China
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Institute of Oncologic Pathology, Cancer Research Center, Shantou University Medical College, Shantou 515041, China
| | - Qiuyu Wang
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- School of Computer, University of South China, Hengyang, Hunan 421001, China
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- Hunan Provincial Base for Scientific and Technological Innovation Cooperation, University of South China, Hengyang, Hunan 421001, China
- The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Hong Sun
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou 515041, China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, China
| | - Qiaoli Fang
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- School of Computer, University of South China, Hengyang, Hunan 421001, China
| | - Xiaozheng Xu
- School of Medical Informatics, Daqing Campus, Harbin Medical University.Daqing 163319, China
| | - Enmin Li
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou 515041, China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, China
| | - Chunquan Li
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- School of Computer, University of South China, Hengyang, Hunan 421001, China
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- Hunan Provincial Base for Scientific and Technological Innovation Cooperation, University of South China, Hengyang, Hunan 421001, China
- The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South
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191
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Altay G, Zapardiel-Gonzalo J, Peters B. RNA-seq preprocessing and sample size considerations for gene network inference. bioRxiv 2023:2023.01.02.522518. [PMID: 36711979 PMCID: PMC9881880 DOI: 10.1101/2023.01.02.522518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Background Gene network inference (GNI) methods have the potential to reveal functional relationships between different genes and their products. Most GNI algorithms have been developed for microarray gene expression datasets and their application to RNA-seq data is relatively recent. As the characteristics of RNA-seq data are different from microarray data, it is an unanswered question what preprocessing methods for RNA-seq data should be applied prior to GNI to attain optimal performance, or what the required sample size for RNA-seq data is to obtain reliable GNI estimates. Results We ran 9144 analysis of 7 different RNA-seq datasets to evaluate 300 different preprocessing combinations that include data transformations, normalizations and association estimators. We found that there was no single best performing preprocessing combination but that there were several good ones. The performance varied widely over various datasets, which emphasized the importance of choosing an appropriate preprocessing configuration before GNI. Two preprocessing combinations appeared promising in general: First, Log-2 TPM (transcript per million) with Variance-stabilizing transformation (VST) and Pearson Correlation Coefficient (PCC) association estimator. Second, raw RNA-seq count data with PCC. Along with these two, we also identified 18 other good preprocessing combinations. Any of these algorithms might perform best in different datasets. Therefore, the GNI performances of these approaches should be measured on any new dataset to select the best performing one for it. In terms of the required biological sample size of RNA-seq data, we found that between 30 to 85 samples were required to generate reliable GNI estimates. Conclusions This study provides practical recommendations on default choices for data preprocessing prior to GNI analysis of RNA-seq data to obtain optimal performance results.
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Affiliation(s)
- Gökmen Altay
- La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | | | - Bjoern Peters
- La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
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192
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Testa U, Castelli G, Pelosi E. The Molecular Characterization of Genetic Abnormalities in Esophageal Squamous Cell Carcinoma May Foster the Development of Targeted Therapies. Curr Oncol 2023; 30:610-640. [PMID: 36661697 PMCID: PMC9858483 DOI: 10.3390/curroncol30010048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/24/2022] [Accepted: 12/29/2022] [Indexed: 01/06/2023] Open
Abstract
Esophageal cancer is among the most common tumors in the world and is associated with poor outcomes, with a 5-year survival rate of about 10-20%. Two main histological subtypes are observed: esophageal squamous cell carcinoma (ESCC), more frequent among Asian populations, and esophageal adenocarcinoma (EAC), the predominant type in Western populations. The development of molecular analysis techniques has led to the definition of the molecular alterations observed in ESCC, consistently differing from those observed in EAC. The genetic alterations observed are complex and heterogeneous and involve gene mutations, gene deletions and gene amplifications. However, despite the consistent progress in the definition of the molecular basis of ESCC, precision oncology for these patients is still virtually absent. The recent identification of molecular subtypes of ESCC with clinical relevance may foster the development of new therapeutic strategies. It is estimated that about 40% of the genetic alterations observed in ESCC are actionable. Furthermore, the recent introduction of solid tumor immunotherapy with immune checkpoint inhibitors (ICIs) showed that a minority of ESCC patients are responsive, and the administration of ICIs, in combination with standard chemotherapy, significantly improves overall survival over chemotherapy in ESCC patients with advanced disease.
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Affiliation(s)
- Ugo Testa
- Department of Oncology, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
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Alotaibi A, Gadekar VP, Gundla PS, Mandarthi S, Ravi S, Mallya D, Tungekar A, Lavanya BV, Bhagavath AK, Cordero MW, Pitkaniemi J, Seetharam RN, Bepari A, Hebbar P. A comprehensive analysis of mRNA expression profiles of Esophageal Squamous Cell Carcinoma reveals downregulation of Desmoglein 1 and crucial genomic targets. Cancer Biomark 2023; 38:465-487. [PMID: 38073377 DOI: 10.3233/cbm-230145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2023]
Abstract
AIM Esophageal Squamous Cell Carcinoma (ESCC) is a histological subtype of esophageal cancer that begins in the squamous cells in the esophagus. In only 19% of the ESCC-diagnosed patients, a five-year survival rate has been seen. This necessitates the identification of high-confidence biomarkers for early diagnosis, prognosis, and potential therapeutic targets for the mitigation of ESCC. METHOD We performed a meta-analysis of 10 mRNA datasets and identified consistently perturbed genes across the studies. Then, integrated with ESCC ATLAS to segregate 'core' genes to identify consequences of primary gene perturbation events leading to gene-gene interactions and dysregulated molecular signaling pathways. Further, by integrating with toxicogenomics data, inferences were drawn for gene interaction with environmental exposures, trace elements, chemical carcinogens, and drug chemicals. We also deduce the clinical outcomes of candidate genes based on survival analysis using the ESCC related dataset in The Cancer Genome Atlas. RESULT We identified 237 known and 18 novel perturbed candidate genes. Desmoglein 1 (DSG1) is one such gene that we found significantly downregulated (Fold Change =-1.89, p-value = 8.2e-06) in ESCC across six different datasets. Further, we identified 31 'core' genes (that either harbor genetic variants or are regulated by epigenetic modifications) and found regulating key biological pathways via adjoining genes in gene-gene interaction networks. Functional enrichment analysis showed dysregulated biological processes and pathways including "Extracellular matrix", "Collagen trimmer" and "HPV infection" are significantly overrepresented in our candidate genes. Based on the toxicogenomic inferences from Comparative Toxicogenomics Database we report the key genes that interacted with risk factors such as tobacco smoking, zinc, nitroso benzylmethylamine, and drug chemicals such as cisplatin, Fluorouracil, and Mitomycin in relation to ESCC. We also point to the STC2 gene that shows a high risk for mortality in ESCC patients. CONCLUSION We identified novel perturbed genes in relation to ESCC and explored their interaction network. DSG1 is one such gene, its association with microbiota and a clinical presentation seen commonly with ESCC hints that it is a good candidate for early diagnostic marker. Besides, in this study we highlight candidate genes and their molecular connections to risk factors, biological pathways, drug chemicals, and the survival probability of ESCC patients.
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Affiliation(s)
- Amal Alotaibi
- Basic Science Department, College of Medicine, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
- Basic Science Department, College of Medicine, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Veerendra P Gadekar
- Mbiomics LLC, Lewes DE, USA
- Basic Science Department, College of Medicine, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | | | | | | | | | | | | | - Ashok Kumar Bhagavath
- Department of Cellular and Molecular Biology, University of Texas Health Science Center, Tyler, Texas, TX, USA
| | - MaryAnne Wong Cordero
- Basic Science Department, College of Medicine, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Janne Pitkaniemi
- Finnish Cancer Registry, Helsinki, Finland
- Department of Public Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Raviraja N Seetharam
- Manipal Center for Biotherapeutics Research, Manipal Academy of Higher Education, Manipal, India
| | - Asmatanzeem Bepari
- Basic Science Department, College of Medicine, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Prashantha Hebbar
- Mbiomics LLC, Lewes DE, USA
- Manipal Center for Biotherapeutics Research, Manipal Academy of Higher Education, Manipal, India
- Meta Biosciences Pvt Ltd., Manipal - GOK Bioincubator, Advanced Research Center, Manipal, India
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194
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Zheng X, Li F, Zhao H, Tang Y, Xue K, Zhang X, Liang W, Zhao R, Lv X, Song X, Zhang C, Xu Y, Zhang Y. A novel method to identify and characterize personalized functional driver lncRNAs in cancer samples. Comput Struct Biotechnol J 2023; 21:2471-2482. [PMID: 37077174 PMCID: PMC10106482 DOI: 10.1016/j.csbj.2023.03.041] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 03/17/2023] [Accepted: 03/23/2023] [Indexed: 04/21/2023] Open
Abstract
Cancer is a highly heterogeneous disease, and different individuals of the same cancer type can display different therapeutic effects and prognosis. Genetic variation of long non-coding RNA is the key factor driving tumor development, and plays an important role in genetic and biological heterogeneity. Therefore, it is of great significance to identify lncRNA as a driving factor in the non-coding region and explain its function in tumors for revealing the pathogenesis of cancer. In this study, we developed an integrated method to identify Personalized Functional Driver lncRNAs (PFD-lncRNAs) by integrating the DNA copy number data, gene expression data, and the biological subpathways information. Then, we applied the method to identify 2695 PFD-lncRNAs in 5334 samples across 19 cancer types. We performed an analysis of the association between PFD-lncRNAs and drug sensitivity, which provides medication guidance in disease therapy and drug discovery in the individual. Our research is of great significance for elucidating the biological roles of lncRNA genetic variation in cancer, revealing the related mechanism of cancer, and providing novel insights for individualized medicine.
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195
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Park E, Lee C, Park J, Liu J, Hong J, Shin DY, Byun JM, Yun H, Koh Y, Yoon SS. Mitigating the BFL1-mediated antiapoptotic pathway in diffuse large B cell lymphoma by inhibiting HDACs. Leuk Lymphoma 2023; 64:205-216. [PMID: 36331521 DOI: 10.1080/10428194.2022.2140282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Endogenous BFL1 expression renders diffuse large B-cell lymphoma (DLBCL) cells insensitive to B-cell lymphoma 2 (BCL2) and/or MCL1 inhibitors. Considering the difficulties in developing a direct BFL1 inhibitor, we intended to inhibit histone deacetylase (HDAC) to mitigate the biological role of BFL1 by modulating WT1 and NOXA. Cells expressing high BFL1 exhibited enhanced sensitivity to pan-HDAC inhibitor compared to low BFL1 expressing cells, mainly attributable to the difference in the amount of apoptosis. HDAC inhibitors decreased BFL1 and WT1 expressions while increasing NOXA levels. The BFL1 knockdown experiment demonstrated that HDAC inhibitor's sensitivity depends on the BFL1 expression in DLBCL cells. Furthermore, we found that the specific HDAC class was expected to play a critical role in BFL1 inhibition by comparing the effects of several HDAC inhibitors. Thus, our study provides a rationale for using HDAC inhibitors to induce apoptosis in DLBCL patients using BFL1 as a predictive biomarker.
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Affiliation(s)
- Eunchae Park
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea.,Center for Medical Innovation, Seoul National University Hospital, Seoul, Republic of Korea
| | - Chansub Lee
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea.,Center for Medical Innovation, Seoul National University Hospital, Seoul, Republic of Korea
| | - Jihyun Park
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea.,Center for Medical Innovation, Seoul National University Hospital, Seoul, Republic of Korea
| | - Jun Liu
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea.,Center for Medical Innovation, Seoul National University Hospital, Seoul, Republic of Korea
| | - Junshik Hong
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea.,Center for Medical Innovation, Seoul National University Hospital, Seoul, Republic of Korea.,Department of Internal Medicine, Division of Hematology and Medical Oncology, Seoul National University Hospital, Seoul, Republic of Korea
| | - Dong-Yeop Shin
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea.,Center for Medical Innovation, Seoul National University Hospital, Seoul, Republic of Korea.,Department of Internal Medicine, Division of Hematology and Medical Oncology, Seoul National University Hospital, Seoul, Republic of Korea
| | - Ja Min Byun
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea.,Center for Medical Innovation, Seoul National University Hospital, Seoul, Republic of Korea.,Department of Internal Medicine, Division of Hematology and Medical Oncology, Seoul National University Hospital, Seoul, Republic of Korea
| | - Hongseok Yun
- Center for Medical Innovation, Seoul National University Hospital, Seoul, Republic of Korea.,Department of Internal Medicine, Division of Hematology and Medical Oncology, Seoul National University Hospital, Seoul, Republic of Korea.,Center for Precision Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Youngil Koh
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea.,Center for Medical Innovation, Seoul National University Hospital, Seoul, Republic of Korea.,Department of Internal Medicine, Division of Hematology and Medical Oncology, Seoul National University Hospital, Seoul, Republic of Korea
| | - Sung-Soo Yoon
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea.,Center for Medical Innovation, Seoul National University Hospital, Seoul, Republic of Korea.,Department of Internal Medicine, Division of Hematology and Medical Oncology, Seoul National University Hospital, Seoul, Republic of Korea
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196
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Huang P, Yan L, Li Z, Zhao S, Feng Y, Zeng J, Chen L, Huang A, Chen Y, Lei S, Huang X, Deng Y, Xie D, Guan H, Peng W, Yu L, Chen B. Potential shared gene signatures and molecular mechanisms between atherosclerosis and depression: Evidence from transcriptome data. Comput Biol Med 2023; 152:106450. [PMID: 36565484 DOI: 10.1016/j.compbiomed.2022.106450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/09/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND Atherosclerosis and depression contribute to each other; however, mechanisms linking them at the genetic level remain unexplored. This study aimed to identify shared gene signatures and related pathways between these comorbidities. METHODS Atherosclerosis-related datasets were downloaded from the Gene Expression Omnibus database. Differential and weighted gene co-expression network analyses were employed to identify atherosclerosis-related genes. Depression-related genes were downloaded from the DisGeNET database, and the overlaps between atherosclerosis-related genes and depression-related genes were characterized as crosstalk genes. The functional enrichment analysis and protein-protein interaction network were performed in these gene sets. Subsequently, the Boruta algorithm and Recursive Feature Elimination algorithm were performed to identify feature-selection genes. A support vector machine was constructed to measure the accuracy of calculations, and two external validation sets were included to verify the results. RESULTS Based on two atherosclerosis-related datasets (GSE28829 and GSE43292), 165 genes were determined as atherosclerosis-related genes. Meanwhile, 1478 depression-related genes were obtained. After intersecting, 24 crosstalk genes were identified, and two pathways, "lipid and atherosclerosis" and "tryptophan metabolism," were revealed as mutual pathways according to the enrichment analysis results. Through the protein-protein interaction network, Molecular Complex Detection plugin, and cytoHubba plugin, PTPRC and MMP9 were identified as the hub gene. Moreover, SLC22A3, CASP1, AMPD3, and PIK3CG were recognized as feature-selection genes. Based on two external validation sets, CASP1 and MMP9 were finally determined as the critical crosstalk genes. CONCLUSIONS "Lipid and atherosclerosis" and "tryptophan metabolism" were possibly the pathways of atherosclerosis secondary to depression and depression due to atherosclerosis, respectively. CASP1 and MMP9 were revealed as the most pivotal candidates linking atherosclerosis and depression by mediating these two pathways. Further experimentation is needed to confirm these conclusions.
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Affiliation(s)
- Peiying Huang
- The Second Clinical Medical School of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Li Yan
- Department of Neurosurgery of Shenyang Second Hospital of Traditional Chinese Medicine, Shenyang, China
| | - Zhishang Li
- Emergency Department of Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou, China
| | - Shuai Zhao
- Emergency Department of Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou, China
| | - Yuchao Feng
- Guangdong Provincial Key Laboratory of Research on Emergency in Traditional Chinese Medicine, Clinical Research Team of Prevention and Treatment of Cardiac Emergencies with Traditional Chinese Medicine, Guangzhou, China
| | - Jing Zeng
- Emergency Department of Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou, China
| | - Li Chen
- Emergency Department of Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou, China
| | - Afang Huang
- Departments of Laboratory Medicine of Foshan Forth People's Hospital, Foshan, China
| | - Yan Chen
- Emergency Department of Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou, China
| | - Sisi Lei
- The Second Clinical Medical School of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xiaoyan Huang
- Emergency Department of Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou, China
| | - Yi Deng
- Emergency Department of Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou, China
| | - Dan Xie
- The Second Clinical Medical School of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Hansu Guan
- The Third Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Weihang Peng
- The Second Clinical Medical School of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Liyuan Yu
- The Second Clinical Medical School of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Bojun Chen
- The Second Clinical Medical School of Guangzhou University of Chinese Medicine, Guangzhou, China; Emergency Department of Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou, China; Guangdong Provincial Key Laboratory of Research on Emergency in Traditional Chinese Medicine, Clinical Research Team of Prevention and Treatment of Cardiac Emergencies with Traditional Chinese Medicine, Guangzhou, China.
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197
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Stabenau KA, Samuels TL, Lam TK, Mathison AJ, Wells C, Altman KW, Battle MA, Johnston N. Pepsinogen/Proton Pump Co-Expression in Barrett's Esophageal Cells Induces Cancer-Associated Changes. Laryngoscope 2023; 133:59-69. [PMID: 35315085 DOI: 10.1002/lary.30109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 02/27/2022] [Accepted: 03/04/2022] [Indexed: 02/02/2023]
Abstract
EDUCATIONAL OBJECTIVE At the conclusion of this presentation, participants should better understand the carcinogenic potential of pepsin and proton pump expression in Barrett's esophagus. OBJECTIVE Barrett's esophagus (BE) is a well-known risk factor for esophageal adenocarcinoma (EAC). Gastric H+ /K+ ATPase proton pump and pepsin expression has been demonstrated in some cases of BE; however, the contribution of local pepsin and proton pump expression to carcinogenesis is unknown. In this study, RNA sequencing was used to examine global transcriptomic changes in a BE cell line ectopically expressing pepsinogen and/or gastric H+ /K+ ATPase proton pumps. STUDY DESIGN In vitro translational. METHODS BAR-T, a human BE cell line devoid of expression of pepsinogen or proton pumps, was transduced by lentivirus-encoding pepsinogen (PGA5) and/or gastric proton pump subunits (ATP4A, ATP4B). Changes relative to the parental line were assessed by RNA sequencing. RESULTS Top canonical pathways associated with protein-coding genes differentially expressed in pepsinogen and/or proton pump expressing BAR-T cells included those involved in the tumor microenvironment and epithelial-mesenchymal transition. Top upstream regulators of coding transcripts included TGFB1 and ERBB2, which are associated with the pathogenesis and prognosis of BE and EAC. Top upstream regulators of noncoding transcripts included p300-CBP, I-BET-151, and CD93, which have previously described associations with EAC or carcinogenesis. The top associated disease of both coding and noncoding transcripts was cancer. CONCLUSIONS These data support the carcinogenic potential of pepsin and proton pump expression in BE and reveal molecular pathways affected by their expression. Further study is warranted to investigate the role of these pathways in carcinogenesis associated with BE. LEVEL OF EVIDENCE NA Laryngoscope, 133:59-69, 2023.
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Affiliation(s)
- Kaleigh A Stabenau
- Department of Otolaryngology and Communication Sciences, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Tina L Samuels
- Department of Otolaryngology and Communication Sciences, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Tina K Lam
- Department of Otolaryngology and Communication Sciences, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Angela J Mathison
- Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Clive Wells
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Kenneth W Altman
- Department of Otolaryngology, Geisinger Health System, Danville, California, USA
| | - Michele A Battle
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Nikki Johnston
- Department of Otolaryngology and Communication Sciences, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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Vora DS, Kalakoti Y, Sundar D. Computational Methods and Deep Learning for Elucidating Protein Interaction Networks. Methods Mol Biol 2023; 2553:285-323. [PMID: 36227550 DOI: 10.1007/978-1-0716-2617-7_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Protein interactions play a critical role in all biological processes, but experimental identification of protein interactions is a time- and resource-intensive process. The advances in next-generation sequencing and multi-omics technologies have greatly benefited large-scale predictions of protein interactions using machine learning methods. A wide range of tools have been developed to predict protein-protein, protein-nucleic acid, and protein-drug interactions. Here, we discuss the applications, methods, and challenges faced when employing the various prediction methods. We also briefly describe ways to overcome the challenges and prospective future developments in the field of protein interaction biology.
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Affiliation(s)
- Dhvani Sandip Vora
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India
| | - Yogesh Kalakoti
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India
| | - Durai Sundar
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India.
- School of Artificial Intelligence, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India.
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199
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Paulussen FM, Grossmann TN. Peptide-based covalent inhibitors of protein-protein interactions. J Pept Sci 2023; 29:e3457. [PMID: 36239115 PMCID: PMC10077911 DOI: 10.1002/psc.3457] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/10/2022] [Accepted: 10/11/2022] [Indexed: 12/13/2022]
Abstract
Protein-protein interactions (PPI) are involved in all cellular processes and many represent attractive therapeutic targets. However, the frequently rather flat and large interaction areas render the identification of small molecular PPI inhibitors very challenging. As an alternative, peptide interaction motifs derived from a PPI interface can serve as starting points for the development of inhibitors. However, certain proteins remain challenging targets when applying inhibitors with a competitive mode of action. For that reason, peptide-based ligands with an irreversible binding mode have gained attention in recent years. This review summarizes examples of covalent inhibitors that employ peptidic binders and have been tested in a biological context.
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Affiliation(s)
- Felix M Paulussen
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Department of Molecular Microbiology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Tom N Grossmann
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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200
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Tripathi G, Tripathi A, Johnson J, Kashyap MK. Role of RNA Splicing in Regulation of Cancer Stem Cell. Curr Stem Cell Res Ther 2023; 18:3-6. [PMID: 34875992 DOI: 10.2174/1574888x16666211207103628] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 09/16/2021] [Accepted: 10/01/2021] [Indexed: 02/07/2023]
Affiliation(s)
- Greesham Tripathi
- Amity Stem Cell Institute, Amity Medical School, Amity University Haryana, Panchgaon (Manesar), Haryana 122413, India
| | - Avantika Tripathi
- Amity Stem Cell Institute, Amity Medical School, Amity University Haryana, Panchgaon (Manesar), Haryana 122413, India
| | - Joel Johnson
- Amity Stem Cell Institute, Amity Medical School, Amity University Haryana, Panchgaon (Manesar), Haryana 122413, India
| | - Manoj Kumar Kashyap
- Amity Stem Cell Institute, Amity Medical School, Amity University Haryana, Panchgaon (Manesar), Haryana 122413, India
- Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Bajhol, Solan, Himachal Pradesh 173229, India
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