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Sommariva M, Dolci M, Triulzi T, Ambrogi F, Dugo M, De Cecco L, Le Noci V, Bernardo G, Anselmi M, Montanari E, Pupa SM, Signorini L, Gagliano N, Sfondrini L, Delbue S, Tagliabue E. Impact of in vitro SARS-CoV-2 infection on breast cancer cells. Sci Rep 2024; 14:13134. [PMID: 38849411 PMCID: PMC11161491 DOI: 10.1038/s41598-024-63804-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 06/03/2024] [Indexed: 06/09/2024] Open
Abstract
The pandemic of coronavirus disease 19 (COVID-19), caused by severe respiratory syndrome coronavirus 2 (SARS-CoV-2), had severe repercussions for breast cancer patients. Increasing evidence indicates that SARS-CoV-2 infection may directly impact breast cancer biology, but the effects of SARS-CoV-2 on breast tumor cells are still unknown. Here, we analyzed the molecular events occurring in the MCF7, MDA-MB-231 and HCC1937 breast cancer cell lines, representative of the luminal A, basal B/claudin-low and basal A subtypes, respectively, upon SARS-CoV-2 infection. Viral replication was monitored over time, and gene expression profiling was conducted. We found that MCF7 cells were the most permissive to viral replication. Treatment of MCF7 cells with Tamoxifen reduced the SARS-CoV-2 replication rate, suggesting an involvement of the estrogen receptor in sustaining virus replication in malignant cells. Interestingly, a metagene signature based on genes upregulated by SARS-CoV-2 infection in all three cell lines distinguished a subgroup of premenopausal luminal A breast cancer patients with a poor prognosis. As SARS-CoV-2 still spreads among the population, it is essential to understand the impact of SARS-CoV-2 infection on breast cancer, particularly in premenopausal patients diagnosed with the luminal A subtype, and to assess the long-term impact of COVID-19 on breast cancer outcomes.
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Affiliation(s)
- Michele Sommariva
- Dipartimento di Scienze Biomediche per la Salute, Università degli Studi di Milano, Via Mangiagalli 31, 20133, Milan, Italy.
- Microambiente e Biomarcatori dei Tumori Solidi, Dipartimento di Oncologia Sperimentale, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Via Amadeo 42, 20133, Milan, Italy.
| | - Maria Dolci
- Dipartimento di Scienze Biomediche, Chirurgiche ed Odontoiatriche, Università degli Studi di Milano, Via Pascal 36, 20133, Milan, Italy
| | - Tiziana Triulzi
- Microambiente e Biomarcatori dei Tumori Solidi, Dipartimento di Oncologia Sperimentale, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Via Amadeo 42, 20133, Milan, Italy
| | - Federico Ambrogi
- Dipartimento di Scienze Cliniche e di Comunità, Università degli Studi di Milano, Via Celoria 22, 20133, Milan, Italy
| | - Matteo Dugo
- Department of Medical Oncology, IRCCS Ospedale San Raffaele, Via Olgettina 60, 20132, Milan, Italy
| | - Loris De Cecco
- Integrated Biology of Rare Tumors, Dipartimento di Oncologia Sperimentale, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Via Amadeo 42, 20133, Milan, Italy
| | - Valentino Le Noci
- Dipartimento di Scienze Biomediche per la Salute, Università degli Studi di Milano, Via Mangiagalli 31, 20133, Milan, Italy
| | - Giancarla Bernardo
- Dipartimento di Scienze Biomediche per la Salute, Università degli Studi di Milano, Via Mangiagalli 31, 20133, Milan, Italy
| | - Martina Anselmi
- Dipartimento di Scienze Biomediche per la Salute, Università degli Studi di Milano, Via Mangiagalli 31, 20133, Milan, Italy
| | - Elena Montanari
- Dipartimento di Scienze Biomediche per la Salute, Università degli Studi di Milano, Via Mangiagalli 31, 20133, Milan, Italy
| | - Serenella M Pupa
- Microambiente e Biomarcatori dei Tumori Solidi, Dipartimento di Oncologia Sperimentale, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Via Amadeo 42, 20133, Milan, Italy
| | - Lucia Signorini
- Dipartimento di Scienze Biomediche, Chirurgiche ed Odontoiatriche, Università degli Studi di Milano, Via Pascal 36, 20133, Milan, Italy
| | - Nicoletta Gagliano
- Dipartimento di Scienze Biomediche per la Salute, Università degli Studi di Milano, Via Mangiagalli 31, 20133, Milan, Italy
| | - Lucia Sfondrini
- Dipartimento di Scienze Biomediche per la Salute, Università degli Studi di Milano, Via Mangiagalli 31, 20133, Milan, Italy
- Microambiente e Biomarcatori dei Tumori Solidi, Dipartimento di Oncologia Sperimentale, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Via Amadeo 42, 20133, Milan, Italy
| | - Serena Delbue
- Dipartimento di Scienze Biomediche, Chirurgiche ed Odontoiatriche, Università degli Studi di Milano, Via Pascal 36, 20133, Milan, Italy
| | - Elda Tagliabue
- Microambiente e Biomarcatori dei Tumori Solidi, Dipartimento di Oncologia Sperimentale, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Via Amadeo 42, 20133, Milan, Italy
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Farah CS, Shearston K, Turner EC, Vacher M, Fox SA. Global gene expression profile of proliferative verrucous leukoplakia and its underlying biological disease mechanisms. Oral Oncol 2024; 151:106737. [PMID: 38408418 DOI: 10.1016/j.oraloncology.2024.106737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 02/21/2024] [Indexed: 02/28/2024]
Abstract
BACKGROUND Proliferative verrucous leukoplakia (PVL) is a rare and enigmatic oral potentially malignant disorder which almost invariably results in oral squamous cell carcinoma (OSCC). The aims of this project were to use transcriptome profiling to characterise PVL gene expression patterns for biomarker identification and gain insight into the molecular aetiopathogenesis of PVL. METHODS Forty-three oral cavity mucosal biopsies from 32 patients with oral lesions clinically compatible with either PVL or non-PVL conventional oral leukoplakia (OLK) underwent transcriptome profiling by RNA sequencing. Data was analysed by hierarchical clustering, differential gene expression, functional enrichment and network analysis, sparse partial least squares discriminant analysis sPLS-DA, and immune cell phenotypic estimation. RESULTS We found 464 genes significantly differentially expressed at least 2-fold between PVL and non-PVL OLK (193 up and 271 down). HOX genes, including HOXA1 and HOXB7, keratin-associated proteins (KRTAPs) and olfactory receptor G proteins (OR) were significantly upregulated in PVL. Other upregulated genes in PVL included FOS, WNT16 and IFNA1. Pathway analysis showed that there was a significant downregulation of connective tissue signalling in PVL. Classifying multivariate models based upon 22 genes discriminated PVL from non-PVL OLK. Bioinformatic profiling showed that immune cell profiles in PVL and OLK were similar except that fibroblast markers were reduced in PVL. CONCLUSION These results demonstrate that PVL and conventional OLK are molecularly distinct with upregulation of many cancer-associated genes. They provide insight into the pathogenesis of PVL and show that biomarker based molecular diagnostics is feasible to discriminate and inform diagnosis and management.
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Affiliation(s)
- Camile S Farah
- Australian Centre for Oral Oncology Research & Education, Nedlands, WA, Australia; Central Queensland University, Rockhampton, Queensland, Australia; Genomics for Life, Milton, QLD, Australia.
| | - Kate Shearston
- Australian Centre for Oral Oncology Research & Education, Nedlands, WA, Australia; UWA Dental School, University of Western Australia, Nedlands, WA, Australia.
| | - Emma C Turner
- UWA Dental School, University of Western Australia, Nedlands, WA, Australia; Special Needs Dental Unit, Royal Darwin Hospital, Tiwi, NT, Australia
| | - Michael Vacher
- The Australian eHealth Research Centre, CSIRO Health and Biosecurity, Kensington, WA, Australia.
| | - Simon A Fox
- Australian Centre for Oral Oncology Research & Education, Nedlands, WA, Australia; UWA Dental School, University of Western Australia, Nedlands, WA, Australia.
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Wu C, Xu M, Dong J, Cui W, Yuan S. The structure and function of olfactory receptors. Trends Pharmacol Sci 2024; 45:268-280. [PMID: 38296675 DOI: 10.1016/j.tips.2024.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 01/08/2024] [Accepted: 01/09/2024] [Indexed: 02/02/2024]
Abstract
Olfactory receptors (ORs) form the most important chemosensory receptor family responsible for our sense of smell in the nasal olfactory epithelium. This receptor family belongs to the class A G protein-coupled receptors (GPCRs). Recent research has indicated that ORs are involved in many nonolfactory physiological processes in extranasal tissue, such as the brain, pancreas, and testes, and implies the possible role of their dysregulation in various diseases. The recently released structures of OR51E2 and consensus OR52 have also unveiled the uniqueness of ORs from other class A GPCR members. In this review, we discuss these recent developments and computational modeling efforts toward understanding the structural properties of unresolved ORs, which could guide potential future OR-targeted drug discovery.
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Affiliation(s)
- Chenyang Wu
- The AlphaMol-SIAT Joint Laboratory, Shenzhen 518055, China; The Research Center for Computer-aided Drug Discovery, The Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Marc Xu
- The AlphaMol-SIAT Joint Laboratory, Shenzhen 518055, China; The Research Center for Computer-aided Drug Discovery, The Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Junlin Dong
- The AlphaMol-SIAT Joint Laboratory, Shenzhen 518055, China; The Research Center for Computer-aided Drug Discovery, The Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenqiang Cui
- The AlphaMol-SIAT Joint Laboratory, Shenzhen 518055, China
| | - Shuguang Yuan
- The AlphaMol-SIAT Joint Laboratory, Shenzhen 518055, China; AlphaMol Science Ltd, Shenzhen 518055, China.
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Zhu Z, Zhou Q, Sun Y, Lai F, Wang Z, Hao Z, Li G. MethMarkerDB: a comprehensive cancer DNA methylation biomarker database. Nucleic Acids Res 2024; 52:D1380-D1392. [PMID: 37889076 PMCID: PMC10767949 DOI: 10.1093/nar/gkad923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/21/2023] [Accepted: 10/10/2023] [Indexed: 10/28/2023] Open
Abstract
DNA methylation plays a crucial role in tumorigenesis and tumor progression, sparking substantial interest in the clinical applications of cancer DNA methylation biomarkers. Cancer-related whole-genome bisulfite sequencing (WGBS) data offers a promising approach to precisely identify these biomarkers with differentially methylated regions (DMRs). However, currently there is no dedicated resource for cancer DNA methylation biomarkers with WGBS data. Here, we developed a comprehensive cancer DNA methylation biomarker database (MethMarkerDB, https://methmarkerdb.hzau.edu.cn/), which integrated 658 WGBS datasets, incorporating 724 curated DNA methylation biomarker genes from 1425 PubMed published articles. Based on WGBS data, we documented 5.4 million DMRs from 13 common types of cancer as candidate DNA methylation biomarkers. We provided search and annotation functions for these DMRs with different resources, such as enhancers and SNPs, and developed diagnostic and prognostic models for further biomarker evaluation. With the database, we not only identified known DNA methylation biomarkers, but also identified 781 hypermethylated and 5245 hypomethylated pan-cancer DMRs, corresponding to 693 and 2172 genes, respectively. These novel potential pan-cancer DNA methylation biomarkers hold significant clinical translational value. We hope that MethMarkerDB will help identify novel cancer DNA methylation biomarkers and propel the clinical application of these biomarkers.
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Affiliation(s)
- Zhixian Zhu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, Key Laboratory of Smart Farming for Agricultural Animals, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiangwei Zhou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, Key Laboratory of Smart Farming for Agricultural Animals, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuanhui Sun
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, Key Laboratory of Smart Farming for Agricultural Animals, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Fuming Lai
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, Key Laboratory of Smart Farming for Agricultural Animals, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhenji Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, Key Laboratory of Smart Farming for Agricultural Animals, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhigang Hao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, Key Laboratory of Smart Farming for Agricultural Animals, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Guoliang Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, Key Laboratory of Smart Farming for Agricultural Animals, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
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Yarlagadda S, Giorgio TD. A guide to single-cell RNA sequencing analysis using web-based tools for non-bioinformatician. FEBS J 2023. [PMID: 38148322 DOI: 10.1111/febs.17036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 12/14/2023] [Indexed: 12/28/2023]
Abstract
Single-cell RNA sequencing (scRNA-seq) is a technique that has proven to be a powerful tool for a wide range of fields and research studies. However, scRNA-seq data analysis has been dominated by scientists highly trained in bioinformatics or those with extensive computational experience and understanding. Recently, this trend has begun to shift as more user-friendly web-based scRNA-seq analysis tools have been developed that require little computational experience to use. However, barriers persist for nonbioinformaticians in using this technique. Complex, unfamiliar language and scarce comprehensive literature guidance to provide a framework for understanding scRNA-seq analysis outputs are among the obstacles. This work introduces many popular web-based tools for scRNA-seq and provides a general overview of their user interfaces and features. Then, a comprehensive start-to-finish introductory scRNA-seq analysis pipeline is described in detail, which aims to enable researchers to carry out scRNA-seq analysis, regardless of computational experience. Companion video tutorials can be found at "EasyScRNAseqTutorials" on YouTube (https://www.youtube.com/@scrnaseqtutorials). However, as scRNA-seq continues to penetrate new fields and expand in importance, there remains a need for more literature to help overcome barriers to its use by explaining further the highly complex and advanced analyses that are introduced within this paper.
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Affiliation(s)
| | - Todd D Giorgio
- Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
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Vaganova AN, Maslennikova DD, Konstantinova VV, Kanov EV, Gainetdinov RR. The Expression of Trace Amine-Associated Receptors (TAARs) in Breast Cancer Is Coincident with the Expression of Neuroactive Ligand-Receptor Systems and Depends on Tumor Intrinsic Subtype. Biomolecules 2023; 13:1361. [PMID: 37759760 PMCID: PMC10526748 DOI: 10.3390/biom13091361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/31/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
Currently, the contribution of trace amine-associated receptors (TAARs) to breast cancer (BC) is recognized, but their associations with various pathological characteristics are not yet understood. There is accumulated transcriptomic data for BC tumors, which are represented in publicly accessible databases. We estimated TAARs' (including TAAR1, TAAR2, TAAR5, TAAR6, TAAR8, and TAAR9) associations with BC stage, grade, and molecular subtypes in these data and identified that the expression of all TAARs was associated with more unfavorable cancer subtypes, including basal-like and HER2-positive tumors. Also, the significant upregulation of all TAARs was demonstrated in circulating tumor cells compared to the metastatic lesions. Considering that co-expressed genes are more likely to be involved in the same biologic processes, we analyzed genes that are co-expressed with TAARs in BC. These gene sets were enriched with the genes of the olfactory transduction pathway and neuroactive ligand-receptor interaction participants. TAARs are co-expressed with G-protein-coupled receptors of monoamine neurotransmitters including dopamine, norepinephrine, and serotonin as well as with other neuroactive ligand-specific receptors. Since TAAR1 is able to modulate the activity of monoamine receptors that are involved in the regulation of BC growth, TAAR1 and potentially other TAARs may be regarded as prospective therapeutic targets for breast cancer.
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Affiliation(s)
- Anastasia N. Vaganova
- Institute of Translational Biomedicine, St. Petersburg State University, Universitetskaya nab. 7/9, 199034 St. Petersburg, Russia; (A.N.V.); (E.V.K.)
- St. Petersburg University Hospital, St. Petersburg State University, Universitetskaya nab. 7/9, 199034 St. Petersburg, Russia;
| | - Daria D. Maslennikova
- Faculty of Biology, St. Petersburg State University, Universitetskaya nab. 7/9, 199034 St. Petersburg, Russia;
| | - Valeria V. Konstantinova
- St. Petersburg University Hospital, St. Petersburg State University, Universitetskaya nab. 7/9, 199034 St. Petersburg, Russia;
| | - Evgeny V. Kanov
- Institute of Translational Biomedicine, St. Petersburg State University, Universitetskaya nab. 7/9, 199034 St. Petersburg, Russia; (A.N.V.); (E.V.K.)
- St. Petersburg University Hospital, St. Petersburg State University, Universitetskaya nab. 7/9, 199034 St. Petersburg, Russia;
| | - Raul R. Gainetdinov
- Institute of Translational Biomedicine, St. Petersburg State University, Universitetskaya nab. 7/9, 199034 St. Petersburg, Russia; (A.N.V.); (E.V.K.)
- St. Petersburg University Hospital, St. Petersburg State University, Universitetskaya nab. 7/9, 199034 St. Petersburg, Russia;
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Amgalan B, Day CP, Przytycka TM. Exploring tumor-normal cross-talk with TranNet: Role of the environment in tumor progression. PLoS Comput Biol 2023; 19:e1011472. [PMID: 37721939 PMCID: PMC10538798 DOI: 10.1371/journal.pcbi.1011472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/28/2023] [Accepted: 08/23/2023] [Indexed: 09/20/2023] Open
Abstract
There is a growing awareness that tumor-adjacent normal tissues used as control samples in cancer studies do not represent fully healthy tissues. Instead, they are intermediates between healthy tissues and tumors. The factors that contribute to the deviation of such control samples from healthy state include exposure to the tumor-promoting factors, tumor-related immune response, and other aspects of tumor microenvironment. Characterizing the relation between gene expression of tumor-adjacent control samples and tumors is fundamental for understanding roles of microenvironment in tumor initiation and progression, as well as for identification of diagnostic and prognostic biomarkers for cancers. To address the demand, we developed and validated TranNet, a computational approach that utilizes gene expression in matched control and tumor samples to study the relation between their gene expression profiles. TranNet infers a sparse weighted bipartite graph from gene expression profiles of matched control samples to tumors. The results allow us to identify predictors (potential regulators) of this transition. To our knowledge, TranNet is the first computational method to infer such dependencies. We applied TranNet to the data of several cancer types and their matched control samples from The Cancer Genome Atlas (TCGA). Many predictors identified by TranNet are genes associated with regulation by the tumor microenvironment as they are enriched in G-protein coupled receptor signaling, cell-to-cell communication, immune processes, and cell adhesion. Correspondingly, targets of inferred predictors are enriched in pathways related to tissue remodelling (including the epithelial-mesenchymal Transition (EMT)), immune response, and cell proliferation. This implies that the predictors are markers and potential stromal facilitators of tumor progression. Our results provide new insights into the relationships between tumor adjacent control sample, tumor and the tumor environment. Moreover, the set of predictors identified by TranNet will provide a valuable resource for future investigations.
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Affiliation(s)
- Bayarbaatar Amgalan
- National Center for Biotechnology Information/National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Chi-Ping Day
- Laboratory of Cancer Biology and Genetics/Center for Cancer Research/National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Teresa M. Przytycka
- National Center for Biotechnology Information/National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
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Sorokin M, Buzdin AA, Guryanova A, Efimov V, Suntsova MV, Zolotovskaia MA, Koroleva EV, Sekacheva MI, Tkachev VS, Garazha A, Kremenchutckaya K, Drobyshev A, Seryakov A, Gudkov A, Alekseenko IV, Rakitina O, Kostina MB, Vladimirova U, Moisseev A, Bulgin D, Radomskaya E, Shestakov V, Baklaushev VP, Prassolov V, Shegay PV, Li X, Poddubskaya EV, Gaifullin N. Large-scale assessment of pros and cons of autopsy-derived or tumor-matched tissues as the norms for gene expression analysis in cancers. Comput Struct Biotechnol J 2023; 21:3964-3986. [PMID: 37635765 PMCID: PMC10448432 DOI: 10.1016/j.csbj.2023.07.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 07/17/2023] [Accepted: 07/30/2023] [Indexed: 08/29/2023] Open
Abstract
Normal tissues are essential for studying disease-specific differential gene expression. However, healthy human controls are typically available only in postmortal/autopsy settings. In cancer research, fragments of pathologically normal tissue adjacent to tumor site are frequently used as the controls. However, it is largely underexplored how cancers can systematically influence gene expression of the neighboring tissues. Here we performed a comprehensive pan-cancer comparison of molecular profiles of solid tumor-adjacent and autopsy-derived "healthy" normal tissues. We found a number of systemic molecular differences related to activation of the immune cells, intracellular transport and autophagy, cellular respiration, telomerase activation, p38 signaling, cytoskeleton remodeling, and reorganization of the extracellular matrix. The tumor-adjacent tissues were deficient in apoptotic signaling and negative regulation of cell growth including G2/M cell cycle transition checkpoint. We also detected an extensive rearrangement of the chemical perception network. Molecular targets of 32 and 37 cancer drugs were over- or underexpressed, respectively, in the tumor-adjacent norms. These processes may be driven by molecular events that are correlated between the paired cancer and adjacent normal tissues, that mostly relate to inflammation and regulation of intracellular molecular pathways such as the p38, MAPK, Notch, and IGF1 signaling. However, using a model of macaque postmortal tissues we showed that for the 30 min - 24-hour time frame at 4ºC, an RNA degradation pattern in lung biosamples resulted in an artifact "differential" expression profile for 1140 genes, although no differences could be detected in liver. Thus, such concerns should be addressed in practice.
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Affiliation(s)
- Maksim Sorokin
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region 141701, Russia
- Omicsway Corp., Walnut, CA 91789, USA
- I.M. Sechenov First Moscow State Medical University, Moscow 119991, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Anton A. Buzdin
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region 141701, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
- World-Class Research Center "Digital biodesign and personalized healthcare", Sechenov First Moscow State Medical University, Moscow, Russia
- PathoBiology Group, European Organization for Research and Treatment of Cancer (EORTC), Brussels, Belgium
| | - Anastasia Guryanova
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region 141701, Russia
| | - Victor Efimov
- World-Class Research Center "Digital biodesign and personalized healthcare", Sechenov First Moscow State Medical University, Moscow, Russia
| | - Maria V. Suntsova
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region 141701, Russia
- I.M. Sechenov First Moscow State Medical University, Moscow 119991, Russia
| | - Marianna A. Zolotovskaia
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region 141701, Russia
- Omicsway Corp., Walnut, CA 91789, USA
| | - Elena V. Koroleva
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region 141701, Russia
| | - Marina I. Sekacheva
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region 141701, Russia
- I.M. Sechenov First Moscow State Medical University, Moscow 119991, Russia
| | - Victor S. Tkachev
- Omicsway Corp., Walnut, CA 91789, USA
- Oncobox Ltd., Moscow 121205, Russia
| | - Andrew Garazha
- Omicsway Corp., Walnut, CA 91789, USA
- Oncobox Ltd., Moscow 121205, Russia
| | | | - Aleksey Drobyshev
- I.M. Sechenov First Moscow State Medical University, Moscow 119991, Russia
| | | | - Alexander Gudkov
- I.M. Sechenov First Moscow State Medical University, Moscow 119991, Russia
| | - Irina V. Alekseenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", 2, Kurchatov Square, Moscow 123182, Russian
- FSBI "National Medical Research Center for Obstetrics, Gynecology and Perinatology named after Academician V.I. Kulakov" Ministry of Healthcare of the Russian Federation, Moscow 117198, Russia
| | - Olga Rakitina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Maria B. Kostina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Uliana Vladimirova
- I.M. Sechenov First Moscow State Medical University, Moscow 119991, Russia
- Oncobox Ltd., Moscow 121205, Russia
| | - Aleksey Moisseev
- I.M. Sechenov First Moscow State Medical University, Moscow 119991, Russia
| | - Dmitry Bulgin
- Research Institute of Medical Primatology, 177 Mira str., Veseloye, Sochi 354376, Russia
| | - Elena Radomskaya
- Research Institute of Medical Primatology, 177 Mira str., Veseloye, Sochi 354376, Russia
| | - Viktor Shestakov
- Research Institute of Medical Primatology, 177 Mira str., Veseloye, Sochi 354376, Russia
| | | | - Vladimir Prassolov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilova str., Moscow 119991, Russia
| | - Petr V. Shegay
- National Medical Research Radiological Center of the Ministry of Health of the Russian Federation, 249036 Obninsk, Russia
| | - Xinmin Li
- UCLA Technology Center for Genomics & Bioinformatics, Department of Pathology & Laboratory Medicine, 650 Charles E Young Dr., Los Angeles, CA 90095, USA
| | | | - Nurshat Gaifullin
- Department of Physiology and General Pathology, Faculty of Medicine, Lomonosov Moscow State University, Moscow 119991, Russia
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9
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Shamsoon K, Hiraki D, Yoshida K, Takabatake K, Takebe H, Yokozeki K, Horie N, Fujita N, Nasrun NE, Okui T, Nagatsuka H, Abiko Y, Hosoya A, Saito T, Shimo T. The Role of Hedgehog Signaling in the Melanoma Tumor Bone Microenvironment. Int J Mol Sci 2023; 24:ijms24108862. [PMID: 37240209 DOI: 10.3390/ijms24108862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 05/02/2023] [Accepted: 05/12/2023] [Indexed: 05/28/2023] Open
Abstract
A crucial regulator in melanoma progression and treatment resistance is tumor microenvironments, and Hedgehog (Hh) signals activated in a tumor bone microenvironment are a potential new therapeutic target. The mechanism of bone destruction by melanomas involving Hh/Gli signaling in such a tumor microenvironment is unknown. Here, we analyzed surgically resected oral malignant melanoma specimens and observed that Sonic Hedgehog, Gli1, and Gli2 were highly expressed in tumor cells, vasculatures, and osteoclasts. We established a tumor bone destruction mouse model by inoculating B16 cells into the bone marrow space of the right tibial metaphysis of 5-week-old female C57BL mice. An intraperitoneal administration of GANT61 (40 mg/kg), a small-molecule inhibitor of Gli1 and Gli2, resulted in significant inhibition of cortical bone destruction, TRAP-positive osteoclasts within the cortical bone, and endomucin-positive tumor vessels. The gene set enrichment analysis suggested that genes involved in apoptosis, angiogenesis, and the PD-L1 expression pathway in cancer were significantly altered by the GANT61 treatment. A flow cytometry analysis revealed that PD-L1 expression was significantly decreased in cells in which late apoptosis was induced by the GANT61 treatment. These results suggest that molecular targeting of Gli1 and Gli2 may release immunosuppression of the tumor bone microenvironment through normalization of abnormal angiogenesis and bone remodeling in advanced melanoma with jaw bone invasion.
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Affiliation(s)
- Karnoon Shamsoon
- Division of Reconstructive Surgery for Oral and Maxillofacial Region, Department of Human Biology and Pathophysiology, School of Dentistry, Health Sciences University of Hokkaido, Tobetsu 061-0293, Japan
- Division of Clinical Cariology and Endodontology, Department of Oral Rehabilitation, School of Dentistry, Health Sciences University of Hokkaido, Tobetsu 061-0293, Japan
| | - Daichi Hiraki
- Division of Reconstructive Surgery for Oral and Maxillofacial Region, Department of Human Biology and Pathophysiology, School of Dentistry, Health Sciences University of Hokkaido, Tobetsu 061-0293, Japan
| | - Koki Yoshida
- Division of Oral Medicine and Pathology, Department of Human Biology and Pathophysiology, School of Dentistry, Health Sciences University of Hokkaido, Tobetsu 061-0293, Japan
| | - Kiyofumi Takabatake
- Department of Oral Pathology and Medicine, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8525, Japan
| | - Hiroaki Takebe
- Division of Histology, Department of Oral Growth and Development, School of Dentistry, Health Sciences University of Hokkaido, Tobetsu 061-0293, Japan
| | - Kenji Yokozeki
- Division of Reconstructive Surgery for Oral and Maxillofacial Region, Department of Human Biology and Pathophysiology, School of Dentistry, Health Sciences University of Hokkaido, Tobetsu 061-0293, Japan
| | - Naohiro Horie
- Division of Reconstructive Surgery for Oral and Maxillofacial Region, Department of Human Biology and Pathophysiology, School of Dentistry, Health Sciences University of Hokkaido, Tobetsu 061-0293, Japan
| | - Naomasa Fujita
- Division of Dental Anesthesiology, Department of Human Biology and Pathophysiology, School of Dentistry, Health Sciences University of Hokkaido, Tobetsu 061-0293, Japan
| | - Nisrina Ekayani Nasrun
- Division of Reconstructive Surgery for Oral and Maxillofacial Region, Department of Human Biology and Pathophysiology, School of Dentistry, Health Sciences University of Hokkaido, Tobetsu 061-0293, Japan
| | - Tatsuo Okui
- Department of Oral and Maxillofacial Surgery, Faculty of Medicine, Shimane University, Izumo 693-8501, Japan
| | - Hitoshi Nagatsuka
- Department of Oral Pathology and Medicine, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8525, Japan
| | - Yoshihiro Abiko
- Division of Oral Medicine and Pathology, Department of Human Biology and Pathophysiology, School of Dentistry, Health Sciences University of Hokkaido, Tobetsu 061-0293, Japan
| | - Akihiro Hosoya
- Division of Histology, Department of Oral Growth and Development, School of Dentistry, Health Sciences University of Hokkaido, Tobetsu 061-0293, Japan
| | - Takashi Saito
- Division of Clinical Cariology and Endodontology, Department of Oral Rehabilitation, School of Dentistry, Health Sciences University of Hokkaido, Tobetsu 061-0293, Japan
| | - Tsuyoshi Shimo
- Division of Reconstructive Surgery for Oral and Maxillofacial Region, Department of Human Biology and Pathophysiology, School of Dentistry, Health Sciences University of Hokkaido, Tobetsu 061-0293, Japan
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Singh R, Meng H, Shen T, Lumahan LEV, Nguyen S, Shen H, Dasgupta S, Qin L, Karri D, Zhu B, Yang F, Coarfa C, O’Malley BW, Yi P. TRAF4-mediated nonproteolytic ubiquitination of androgen receptor promotes castration-resistant prostate cancer. Proc Natl Acad Sci U S A 2023; 120:e2218229120. [PMID: 37155905 PMCID: PMC10193960 DOI: 10.1073/pnas.2218229120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 03/24/2023] [Indexed: 05/10/2023] Open
Abstract
Castration-resistant prostate cancer (CRPC) poses a major clinical challenge with the androgen receptor (AR) remaining to be a critical oncogenic player. Several lines of evidence indicate that AR induces a distinct transcriptional program after androgen deprivation in CRPCs. However, the mechanism triggering AR binding to a distinct set of genomic loci in CRPC and how it promotes CRPC development remain unclear. We demonstrate here that atypical ubiquitination of AR mediated by an E3 ubiquitin ligase TRAF4 plays an important role in this process. TRAF4 is highly expressed in CRPCs and promotes CRPC development. It mediates K27-linked ubiquitination at the C-terminal tail of AR and increases its association with the pioneer factor FOXA1. Consequently, AR binds to a distinct set of genomic loci enriched with FOXA1- and HOXB13-binding motifs to drive different transcriptional programs including an olfactory transduction pathway. Through the surprising upregulation of olfactory receptor gene transcription, TRAF4 increases intracellular cAMP levels and boosts E2F transcription factor activity to promote cell proliferation under androgen deprivation conditions. Altogether, these findings reveal a posttranslational mechanism driving AR-regulated transcriptional reprogramming to provide survival advantages for prostate cancer cells under castration conditions.
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Affiliation(s)
- Ramesh Singh
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX77030
| | - Huan Meng
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX77030
| | - Tao Shen
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX77030
| | | | - Steven Nguyen
- Department of Biology and Biochemistry, Center for Nuclear Receptors and Cell Signaling, University of Houston, Houston, TX77204
| | - Hong Shen
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX77030
| | - Subhamoy Dasgupta
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX77030
| | - Li Qin
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX77030
| | - Dileep Karri
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX77030
| | - Bokai Zhu
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX77030
| | - Feng Yang
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX77030
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX77030
| | - Cristian Coarfa
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX77030
| | - Bert W. O’Malley
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX77030
| | - Ping Yi
- Department of Biology and Biochemistry, Center for Nuclear Receptors and Cell Signaling, University of Houston, Houston, TX77204
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11
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Doğan B, Ayar B, Pirim D. Investigation of putative roles of smoking-associated salivary microbiome alterations on carcinogenesis by integrative in silico analysis. Comput Biol Chem 2023; 102:107805. [PMID: 36587566 DOI: 10.1016/j.compbiolchem.2022.107805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 12/20/2022] [Accepted: 12/21/2022] [Indexed: 12/27/2022]
Abstract
Growing evidence suggests that cigarette smoking alters the salivary microbiome composition and affects the risk of various complex diseases including cancer. However, the potential role of the smoking-associated microbiome in cancer development remains unexplained. Here, the putative roles of smoking-related microbiome alterations in carcinogenesis were investigated by in silico analysis and suggested evidence can be further explored by experimental methodologies. The Disbiome database was used to extract smoking-associated microbial taxa in saliva and taxon set enrichment analysis (TSEA) was conducted to identify the gene sets associated with extracted microbial taxa. We further analyzed the expression profiles of identified genes by using RNA-sequencing data from TCGA and GTEx projects. Associations of the genes with smoking-related phenotypes in cancer datasets were analyzed to prioritize genes for their interplay between smoking-related microbiome and carcinogenesis. Thirty-eight microbial taxa associated with smoking were included in the TSEA and this revealed sixteen genes that were significantly associated with smoking-associated microbial taxa. All genes were found to be differentially expressed in at least one cancer dataset, yet the ELF3 and CTSH were the most common differentially expressed genes giving significant results for several cancer types. Moreover, C2CD3, CTSH, DSC3, ELF3, RHOT2, and WSB2 showed statistically significant associations with smoking-related phenotypes in cancer datasets. This study provides in silico evidence for the potential roles of the salivary microbiome on carcinogenesis. The results shed light on the importance of smoking cessation strategies for cancer management and interventions to stratify smokers for their risk of smoking-induced carcinogenesis.
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Affiliation(s)
- Berkcan Doğan
- Bursa Uludag University, Institute of Health Science, Department of Translational Medicine, 16059 Bursa, Turkey; Bursa Uludag University, Faculty of Medicine, Department of Medical Genetics, 16059 Bursa, Turkey
| | - Berna Ayar
- Bursa Uludag University, Department of Molecular Biology and Genetics, 16059 Bursa, Turkey; Istinye University, Institute of Health Science, Department of Molecular Oncology, 34010 Istanbul, Turkey
| | - Dilek Pirim
- Bursa Uludag University, Institute of Health Science, Department of Translational Medicine, 16059 Bursa, Turkey; Bursa Uludag University, Department of Molecular Biology and Genetics, 16059 Bursa, Turkey.
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12
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Zheng YZ, Li JY, Ning LW, Xie N. Predictive and Prognostic Value of TRIM58 Protein Expression in Patients with Breast Cancer Receiving Neoadjuvant Chemotherapy. BREAST CANCER (DOVE MEDICAL PRESS) 2022; 14:475-487. [PMID: 36578908 PMCID: PMC9790805 DOI: 10.2147/bctt.s387209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 11/30/2022] [Indexed: 12/24/2022]
Abstract
Introduction Tripartite motif-containing protein (TRIM) family members play crucial roles in carcinogenesis and chemotherapy resistance. In this study, we aimed to determine whether TRIM58 protein expression is related to patient responses to neoadjuvant therapy (NAT) and their survival outcome. Methods Immunohistochemistry was performed on female breast cancer samples from biopsies before NAT in Shenzhen Second People's Hospital. Univariate and multivariate logistic regression tests were used to analyze the association between TRIM58 protein expression and pathological complete response (pCR). The Cox proportional hazards model was used to calculate the adjusted hazard ratio (HR) with a 95% confidence interval (95% CI). The Kaplan-Meier plotter database was used to analyze the prognostic value of TRIM58. Results High TRIM58 expression was associated with small tumor size in all the patients (n = 58). Multivariate analysis suggested that low TRIM58 expression was an independent predictive factor for higher pCR (odds ratio = 0.06, 95% CI 0.005-0.741, P = 0.028). The Kaplan-Meier Plotter dataset suggested that the TRIM58 high-expression group showed a worse 5-year overall survival than the low-expression group (HR = 1.34, 95% CI 1.07-1.67, P = 0.01). Pathway analysis revealed the potential mechanisms of TRIM58 in chemoresistance. Discussion Our study suggests that TRIM58 is a promising biomarker for both neoadjuvant chemosensitivity and long-term clinical outcomes in breast cancer. It may also help to identify candidate responders and determine treatment strategies.
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Affiliation(s)
- Yi-Zi Zheng
- Department of Thyroid and Breast Surgery, Shenzhen Breast Tumor Research Center for Diagnosis and Treatment, the First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital, Shenzhen University, Shenzhen, Guangdong, People’s Republic of China
| | - Jia-Ying Li
- Hengyang Medical School, University of South China, Hengyang, Hunan, People’s Republic of China,Biobank, First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital, Shenzhen University, Shenzhen, Guangdong, People’s Republic of China
| | - Lv-Wen Ning
- Biobank, First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital, Shenzhen University, Shenzhen, Guangdong, People’s Republic of China
| | - Ni Xie
- Biobank, First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital, Shenzhen University, Shenzhen, Guangdong, People’s Republic of China,Correspondence: Ni Xie, Biobank, First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital, Shenzhen University, 3002 Sungang West Road, Shenzhen, 518035, Guangdong, People’s Republic of China, Tel +86-13501580802, Fax +86-0755-83003435, Email
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13
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Reply to: Target expression is a relevant factor in synthetic lethal screens. Commun Biol 2022; 5:836. [PMID: 35986082 PMCID: PMC9391391 DOI: 10.1038/s42003-022-03747-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 07/21/2022] [Indexed: 11/25/2022] Open
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14
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Target expression is a relevant factor in synthetic lethal screens. Commun Biol 2022; 5:835. [PMID: 35986164 PMCID: PMC9391323 DOI: 10.1038/s42003-022-03746-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 01/28/2022] [Indexed: 11/24/2022] Open
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15
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Significance of TP53 Mutational Status-Associated Signature in the Progression and Prognosis of Endometrial Carcinoma. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:1817339. [PMID: 35847579 PMCID: PMC9280614 DOI: 10.1155/2022/1817339] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 06/06/2022] [Accepted: 06/19/2022] [Indexed: 01/27/2023]
Abstract
Background. TP53 mutations are associated with poor outcome for patients with endometrial carcinoma (EC). However, to date, there have been no studies focused on the construction of TP53 mutational status-associated signature in EC. In this study, we aim to conduct a TP53 mutation-associated prognostic gene signature for EC. Methods. Hence, we explored the mutational landscape of TP53 in patients with EC based on the simple nucleotide variation data downloaded from The Cancer Genome Atlas (TCGA) database. Differential expression analysis and least absolute shrinkage and selection operator (LASSO)–Cox analysis was used to establish TP53 mutation-associated prognostic gene signature. The overall survival rate between the high-risk and low-risk groups was compared by the Kaplan–Meier (K-M) method. Results. We found that the TP53 mutation was associated with poor outcome, older age, lower BMI, and higher grade and stage of EC in patients. A TP53 mutational status-associated signature was established based on transcriptome profiling data. Moreover, the patients in TCGA database were categorized into high- and low-risk groups. Kaplan–Meier (K-M) analysis indicated that the patients in the high-risk group have poor survival outcome. Furthermore, receiver operating characteristic (ROC) curves confirmed the robust prognostic prediction efficiency of the TP53 mutational status-associated signature. Finally, the prognostic ability was successfully verified in the other two datasets from cBioPortal database as well as in 60 clinical specimens. Univariate (hazard ratio
,
,
) and multivariate (hazard ratio
,
,
) Cox regression analyses indicated that the TP53 mutational status-associated signature could be used as an independent prognostic factor for EC patients. Conclusion. In summary, our research constructed a powerful TP53 mutational status-associated signature that could be a potential novel prognostic biomarker and therapeutic target for EC.
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16
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Martin AL, Anadon CM, Biswas S, Mine JA, Handley KF, Payne KK, Mandal G, Chaurio RA, Powers JJ, Sprenger KB, Rigolizzo KE, Innamarato P, Harro CM, Mehta S, Perez BA, Wenham RM, Conejo-Garcia JR. Olfactory Receptor OR2H1 Is an Effective Target for CAR T Cells in Human Epithelial Tumors. Mol Cancer Ther 2022; 21:1184-1194. [PMID: 35499393 PMCID: PMC9256805 DOI: 10.1158/1535-7163.mct-21-0872] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 03/04/2022] [Accepted: 04/13/2022] [Indexed: 01/07/2023]
Abstract
Although chimeric antigen receptor (CAR)-expressing T cells have proven success in hematologic malignancies, their effectiveness in solid tumors has been largely unsuccessful thus far. We found that some olfactory receptors are expressed in a variety of solid tumors of different histologic subtypes, with a limited pattern of expression in normal tissues. Quantification of OR2H1 expression by qRT-PCR and Western blot analysis of 17 normal tissues, 82 ovarian cancers of various histologies, eight non-small cell lung cancers (NSCLCs), and 17 breast cancers demonstrated widespread OR2H1 expression in solid epithelial tumors with expression in normal human tissues limited to the testis. CAR T cells recognizing the extracellular domain of the olfactory receptor OR2H1 were generated with a targeting motif identified through the screening of a phage display library and demonstrated OR2H1-specific cytotoxic killing in vitro and in vivo, using tumor cells with spontaneous expression of variable OR2H1 levels. Importantly, recombinant OR2H1 IgG generated with the VH/VL sequences of the CAR construct specifically detected OR2H1 protein signal in 60 human lung cancers, 40 ovarian carcinomas, and 73 cholangiocarcinomas, at positivity rates comparable with mRNA expression and without OR2H1 staining in 58 normal tissues. CRISPR/Cas9-mediated ablation of OR2H1 confirmed targeting specificity of the CAR and the tumor-promoting role of OR2H1 in glucose metabolism. Therefore, T cells redirected against OR2H1-expressing tumor cells represent a promising therapy against a broad range of epithelial cancers, likely with an admissible toxicity profile.
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Affiliation(s)
- Alexandra L Martin
- Department of Clinical Science, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Carmen M Anadon
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Subir Biswas
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Jessica A Mine
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Katelyn F Handley
- Gynecologic Oncology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
- Division of Gynecologic Oncology, Department of Obstetrics & Gynecology, Morsani College of Medicine, University of South Florida, Tampa, Florida
| | - Kyle K Payne
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Gunjan Mandal
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Ricardo A Chaurio
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - John J Powers
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Kimberly B Sprenger
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Kristen E Rigolizzo
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Patrick Innamarato
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Carly M Harro
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Sumit Mehta
- Gynecologic Oncology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
- Division of Gynecologic Oncology, Department of Obstetrics & Gynecology, Morsani College of Medicine, University of South Florida, Tampa, Florida
| | - Bradford A Perez
- Radiation Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Robert M Wenham
- Gynecologic Oncology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Jose R Conejo-Garcia
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
- Gynecologic Oncology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
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17
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Nelligan NM, Bender MR, Feltus FA. Simulating the restoration of normal gene expression from different thyroid cancer stages using deep learning. BMC Cancer 2022; 22:612. [PMID: 35659616 PMCID: PMC9166476 DOI: 10.1186/s12885-022-09704-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 05/24/2022] [Indexed: 11/18/2022] Open
Abstract
Background Thyroid cancer (THCA) is the most common endocrine malignancy and incidence is increasing. There is an urgent need to better understand the molecular differences between THCA tumors at different pathologic stages so appropriate diagnostic, prognostic, and treatment strategies can be applied. Transcriptome State Perturbation Generator (TSPG) is a tool created to identify the changes in gene expression necessary to transform the transcriptional state of a source sample to mimic that of a target. Methods We used TSPG to perturb the bulk RNA expression data from various THCA tumor samples at progressive stages towards the transcriptional pattern of normal thyroid tissue. The perturbations produced were analyzed to determine if there are consistently up- or down-regulated genes or functions in certain stages of tumors. Results Some genes of particular interest were investigated further in previous research. SLC6A15 was found to be down-regulated in all stage 1–3 samples. This gene has previously been identified as a tumor suppressor. The up-regulation of PLA2G12B in all samples was notable because the protein encoded by this gene belongs to the PLA2 superfamily, which is involved in metabolism, a major function of the thyroid gland. REN was up-regulated in all stage 3 and 4 samples. The enzyme renin encoded by this gene, has a role in the renin-angiotensin system; this system regulates angiogenesis and may have a role in cancer development and progression. This is supported by the consistent up-regulation of REN only in later stage tumor samples. Functional enrichment analysis showed that olfactory receptor activities and similar terms were enriched for the up-regulated genes which supports previous research concluding that abundance and stimulation of olfactory receptors is linked to cancer. Conclusions TSPG can be a useful tool in exploring large gene expression datasets and extracting the meaningful differences between distinct classes of data. We identified genes that were characteristically perturbed in certain sample types, including only late-stage THCA tumors. Additionally, we provided evidence for potential transcriptional signatures of each stage of thyroid cancer. These are potentially relevant targets for future investigation into THCA tumorigenesis. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-09704-z.
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18
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Sakellakis M. Orphan receptors in prostate cancer. Prostate 2022; 82:1016-1024. [PMID: 35538397 DOI: 10.1002/pros.24370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/22/2022] [Accepted: 04/22/2022] [Indexed: 11/11/2022]
Abstract
BACKGROUND The identification of new cellular receptors has been increasing rapidly. A receptor is called "orphan" if an endogenous ligand has not been identified yet. METHODS Here we review receptors that contribute to prostate cancer and are considered orphan or partially orphan. This means that the full spectrum of their endogenous ligands remains unknown. RESULTS The orphan receptors are divided into two major families. The first group includes G protein-coupled receptors. Most are orphan olfactory receptors. OR51E1 inhibits cell proliferation and induces senescence in prostate cancer. OR51E2 inhibits prostate cancer growth, but promotes invasiveness and metastasis. GPR158, GPR110, and GPCR-X play significant roles in prostate cancer development and progression. However, GPR160 induces cell cycle arrest and apoptosis. The other major subset of orphan receptors are nuclear receptors. Receptor-related orphan receptor α (RORα) inhibits tumor growth, but RORγ stimulates androgen receptor signaling. PXR contributes to metabolic deactivation of androgens and inhibits cell proliferation. TLX has protumorigenic effects in prostate cancer, while its knockdown triggers cellular senescence and growth arrest. Estrogen-related receptor ERRγ can inhibit tumor growth but ERRα is protumorigenic. Dax1 and short heterodimeric partner are also inhibitory in prostate cancer. CONCLUSION There is a "zoo" of relatively underappreciated orphan receptors that play key roles in prostate cancer.
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Affiliation(s)
- Minas Sakellakis
- Fourth Oncology Department and Comprehensive Clinical Trials Center, Metropolitan Hospital, Athens, Greece
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19
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Aggarwal P, Hutcheson KA, Yu R, Wang J, Fuller CD, Garden AS, Goepfert RP, Rigert J, Mott FE, Lu C, Lai SY, Gunn GB, Chambers MS, Li G, Wu CC, Hanna EY, Sturgis EM, Shete S. Genetic susceptibility to patient-reported xerostomia among long-term oropharyngeal cancer survivors. Sci Rep 2022; 12:6662. [PMID: 35459784 PMCID: PMC9033773 DOI: 10.1038/s41598-022-10538-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 03/29/2022] [Indexed: 12/04/2022] Open
Abstract
Genetic susceptibility for xerostomia, a common sequela of radiotherapy and chemoradiotherapy for head and neck cancer, is unknown. Therefore, to identify genetic variants associated with moderate to severe xerostomia, we conducted a GWAS of 359 long-term oropharyngeal cancer (OPC) survivors using 579,956 autosomal SNPs. Patient-reported cancer treatment-related xerostomia was assessed using the MD Anderson Symptom Inventory. Patient response was dichotomized as moderate to severe or none to mild symptoms. In our study, 39.2% of OPC survivors reported moderate to severe xerostomia. Our GWAS identified eight SNPs suggestively associated with higher risk of moderate to severe xerostomia in six genomic regions (2p13.3, rs6546481, Minor Allele (MA) = A, ANTXR1, P = 4.3 × 10-7; 5p13.2-p13.1, rs16903936, MA = G, EGFLAM, P = 5.1 × 10-6; 4q21.1, rs10518156, MA = G, SHROOM3, P = 7.1 × 10-6; 19q13.42, rs11882068, MA = G, NLRP9, P = 1.7 × 10-5; 12q24.33, rs4760542, MA = G, GLT1D1, P = 1.8 × 10-5; and 3q27.3, rs11714564, MA = G, RTP1, P = 2.9 × 10-5. Seven SNPs were associated with lower risk of moderate to severe xerostomia, of which only one mapped to specific genomic region (15q21.3, rs4776140, MA = G, LOC105370826, a ncRNA class RNA gene, P = 1.5 × 10-5). Although our small exploratory study did not reach genome-wide statistical significance, our study provides, for the first time, preliminary evidence of genetic susceptibility to xerostomia. Further studies are needed to elucidate the role of genetic susceptibility to xerostomia.
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Affiliation(s)
- Puja Aggarwal
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Katherine A Hutcheson
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Robert Yu
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jian Wang
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Clifton D Fuller
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Adam S Garden
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ryan P Goepfert
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jillian Rigert
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Frank E Mott
- Department of Thoracic Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Charles Lu
- Department of Thoracic Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Stephen Y Lai
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - G Brandon Gunn
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mark S Chambers
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Guojun Li
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chih-Chieh Wu
- Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan, 701, Taiwan
| | - Ehab Y Hanna
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Erich M Sturgis
- Department of Otolaryngology-Head and Neck Surgery, Baylor College of Medicine, Houston, TX, USA
| | - Sanjay Shete
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Division of Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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Differential Expression and Bioinformatics Analysis of tRF/tiRNA in Endometriosis Patients. BIOMED RESEARCH INTERNATIONAL 2022; 2022:9911472. [PMID: 35281615 PMCID: PMC8913131 DOI: 10.1155/2022/9911472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 10/22/2021] [Accepted: 02/10/2022] [Indexed: 11/17/2022]
Abstract
Background. Endometriosis (EMs) is a benign chronic condition that tends to recur in women of childbearing age, with an incidence of approximately 10%. It is a multifactorial disease for which the pathogenesis is currently unclear. This study is aimed at investigating the expression and clinical significance of tRNA-derived small RNA (tsRNA), a novel noncoding small RNA with potential regulatory functions, in endometriosis. Methods. The tRF/tiRNA expression profiles in endometrial tissues from three pairs of endometriosis patients and controls were detected by tRF&tiRNA PCR microarray technology and then verified by quantitative real-time polymerase chain reaction (qPCR). The target genes and target sites of TRF396, tiRNA-5030-GlnTTG-3, TRF308, and TRF320 were predicted by miRanda, and the network diagram of their interaction with miRNA was drawn. The impact of tRNA-derived fragments on the pathogenesis of endometriosis was analyzed using the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). Results. Two upregulated and 19 downregulated tRNA-derived fragments were identified. The qRT-PCR results of 2 upregulated and 2 downregulated RNA-derived fragments were consistent with the RNA Seq data. The OR2B4 gene related to TRF396, the DGAT1 gene related to tiRNA-5030-GlnTTG-3, the KLF16 gene of TRF308, and the RNF213 gene of TRF320 had significant correlations. Gene Ontology and pathway analysis showed that the target genes of TRF396 and tiRNA-5030-GlnTTG-3 were mainly involved in the intrinsic components of the membrane and the overall composition of the membrane in cell components; molecular functions mainly involve olfactory conduction and G protein-coupled receptor activity. In the biological process, it was mainly involved in the detection of sensory stimuli. The target genes of TRF308 and TRF320 were mainly involved in the intracellular part; molecular functions are mainly related to DNA binding transcription factor activity and protein binding and mainly related to biological regulation of biological processes. Pathway analysis showed that the RAP1 signaling pathway and the AXON GUIDANCE signaling pathway may participate in the progression of endometriosis. Conclusion. The differential expression of tRF/tiRNA in endometriosis may be related to the pathogenesis of endometriosis. Furthermore, tRF/tiRNA may be a biomarker for the diagnosis and treatment of EMs in the future.
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Abstract
Odorant receptors (ORs), the largest subfamily of G protein-coupled receptors, detect odorants in the nose. In addition, ORs were recently shown to be expressed in many nonolfactory tissues and cells, indicating that these receptors have physiological and pathophysiological roles beyond olfaction. Many ORs are expressed by tumor cells and tissues, suggesting that they may be associated with cancer progression or may be cancer biomarkers. This review describes OR expression in various types of cancer and the association of these receptors with various types of signaling mechanisms. In addition, the clinical relevance and significance of the levels of OR expression were evaluated. Namely, levels of OR expression in cancer were analyzed based on RNA-sequencing data reported in the Cancer Genome Atlas; OR expression patterns were visualized using t-distributed stochastic neighbor embedding (t-SNE); and the associations between patient survival and levels of OR expression were analyzed. These analyses of the relationships between patient survival and expression patterns obtained from an open mRNA database in cancer patients indicate that ORs may be cancer biomarkers and therapeutic targets.
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Affiliation(s)
- Chan Chung
- Department of New Biology, DGIST, Daegu 42988, Korea
- New Biology Research Center (NBRC), DGIST, Daegu 42988, Korea
| | - Hee Jin Cho
- Department of Biomedical Convergence Science and Technology, Kyungpook National University, Daegu 41566, Korea
- Cell and Matrix Research Institute, Kyungpook National University, Daegu 41944, Korea
| | - ChaeEun Lee
- Department of New Biology, DGIST, Daegu 42988, Korea
- New Biology Research Center (NBRC), DGIST, Daegu 42988, Korea
| | - JaeHyung Koo
- Department of New Biology, DGIST, Daegu 42988, Korea
- New Biology Research Center (NBRC), DGIST, Daegu 42988, Korea
- Korea Brain Research Institute (KBRI), Daegu 41062, Korea
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22
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Cho HJ, Koo J. Odorant G protein-coupled receptors as potential therapeutic targets for adult diffuse gliomas: a systematic analysis and review. BMB Rep 2021. [PMID: 34847986 PMCID: PMC8728539 DOI: 10.5483/bmbrep.2021.54.12.165] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Odorant receptors (ORs) account for about 60% of all human G protein-coupled receptors (GPCRs). OR expression outside of the nose has functions distinct from odor perception, and may contribute to the pathogenesis of disorders including brain diseases and cancers. Glioma is the most common adult malignant brain tumor and requires novel therapeutic strategies to improve clinical outcomes. Here, we outlined the expression of brain ORs and investigated OR expression levels in glioma. Although most ORs were not ubiquitously expressed in gliomas, a subset of ORs displayed glioma subtype-specific expression. Moreover, through systematic survival analysis on OR genes, OR51E1 (mouse Olfr558) was identified as a potential biomarker of unfavorable overall survival, and OR2C1 (mouse Olfr15) was identified as a potential biomarker of favorable overall survival in isocitrate dehydrogenase (IDH) wild-type glioma. In addition to transcriptomic analysis, mutational profiles revealed that somatic mutations in OR genes were detected in > 60% of glioma samples. OR5D18 (mouse Olfr1155) was the most frequently mutated OR gene, and OR5AR1 (mouse Olfr1019) showed IDH wild-type-specific mutation. Based on this systematic analysis and review of the genomic and transcriptomic profiles of ORs in glioma, we suggest that ORs are potential biomarkers and therapeutic targets for glioma.
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Affiliation(s)
- Hee Jin Cho
- Department of Biomedical Convergence Science and Technology, Kyungpook National University, Daegu 41566, Korea
- Cell and Matrix Research Institute, Kyungpook National University, Daegu 41944, Korea
| | - JaeHyung Koo
- Department of New Biology, DGIST, Daegu 42988, Korea
- 4New Biology Research Center (NBRC), DGIST, Daegu 42988, 5Korea Brain Research Institute (KBRI), Daegu 41062, Korea
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Recurrent high-impact mutations at cognate structural positions in class A G protein-coupled receptors expressed in tumors. Proc Natl Acad Sci U S A 2021; 118:2113373118. [PMID: 34916293 PMCID: PMC8713800 DOI: 10.1073/pnas.2113373118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/01/2021] [Indexed: 12/23/2022] Open
Abstract
GPCRs and GPCR pathways are increasingly being implicated in human malignancies, placing them among the most promising cancer drug candidates. Our results reveal enrichment of highly impactful, recurrent GPCR mutations within cancers. We found that cognate mutations in selected class A GPCRs have deleterious effects on signaling function. The results also suggest that olfactory receptors, often considered inconsequential, display a nonrandom mutation pattern in tumors in which they are expressed. These findings support the idea that protein paralogs can act in parallel as members of an onco-group. G protein-coupled receptors (GPCRs) are the largest family of human proteins. They have a common structure and, signaling through a much smaller set of G proteins, arrestins, and effectors, activate downstream pathways that often modulate hallmark mechanisms of cancer. Because there are many more GPCRs than effectors, mutations in different receptors could perturb signaling similarly so as to favor a tumor. We hypothesized that somatic mutations in tumor samples may not be enriched within a single gene but rather that cognate mutations with similar effects on GPCR function are distributed across many receptors. To test this possibility, we systematically aggregated somatic cancer mutations across class A GPCRs and found a nonrandom distribution of positions with variant amino acid residues. Individual cancer types were enriched for highly impactful, recurrent mutations at selected cognate positions of known functional motifs. We also discovered that no single receptor drives this pattern, but rather multiple receptors contain amino acid substitutions at a few cognate positions. Phenotypic characterization suggests these mutations induce perturbation of G protein activation and/or β-arrestin recruitment. These data suggest that recurrent impactful oncogenic mutations perturb different GPCRs to subvert signaling and promote tumor growth or survival. The possibility that multiple different GPCRs could moonlight as drivers or enablers of a given cancer through mutations located at cognate positions across GPCR paralogs opens a window into cancer mechanisms and potential approaches to therapeutics.
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Li M, Schweiger MW, Ryan DJ, Nakano I, Carvalho LA, Tannous BA. Olfactory receptor 5B21 drives breast cancer metastasis. iScience 2021; 24:103519. [PMID: 34917897 PMCID: PMC8666352 DOI: 10.1016/j.isci.2021.103519] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 10/12/2021] [Accepted: 11/23/2021] [Indexed: 02/08/2023] Open
Abstract
Olfactory receptors (ORs), responsible for the sense of smell, play an essential role in various physiological processes outside the nasal epithelium, including cancer. In breast cancer, however, the expression and function of ORs remain understudied. We examined the significance of OR transcript abundance in primary and metastatic breast cancer to the brain, bone, and lung. Although 20 OR transcripts were differentially expressed in distant metastases, OR5B21 displayed an increased transcript abundance in all three metastatic sites compared with the primary tumor. Knockdown of OR5B21 significantly decreased the invasion and migration of breast cancer cells as well as metastasis to different organs especially the brain, whereas increasing of OR5B21 transcript abundance had the opposite effect. Mechanistically, OR5B21 expression was associated with epithelial to mesenchymal transition through the STAT3/NF-κB/CEBPβ signaling axis. We propose OR5B21 (and potentially other ORs) as a novel oncogene contributing to breast cancer metastasis and a potential target for adjuvant therapy.
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Affiliation(s)
- Mao Li
- Department of Neurosurgery, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
- Experimental Therapeutics and Molecular Imaging Laboratory, Department of Neurology, Neuro-Oncology Division, Massachusetts General Hospital, 149 13th Street, Charlestown, Boston, MA 02129, USA
- Neuroscience Program, Harvard Medical School, Boston, MA 02129, USA
| | - Markus W. Schweiger
- Experimental Therapeutics and Molecular Imaging Laboratory, Department of Neurology, Neuro-Oncology Division, Massachusetts General Hospital, 149 13th Street, Charlestown, Boston, MA 02129, USA
- Neuroscience Program, Harvard Medical School, Boston, MA 02129, USA
- Department of Neurosurgery, Cancer Center Amsterdam, Brain Tumor Center Amsterdam, Amsterdam UMC, Vrije Universiteit, 1081 HV Amsterdam, the Netherlands
| | - Daniel J. Ryan
- Experimental Therapeutics and Molecular Imaging Laboratory, Department of Neurology, Neuro-Oncology Division, Massachusetts General Hospital, 149 13th Street, Charlestown, Boston, MA 02129, USA
- Neuroscience Program, Harvard Medical School, Boston, MA 02129, USA
| | - Ichiro Nakano
- Department of Neurosurgery and Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Litia A. Carvalho
- Experimental Therapeutics and Molecular Imaging Laboratory, Department of Neurology, Neuro-Oncology Division, Massachusetts General Hospital, 149 13th Street, Charlestown, Boston, MA 02129, USA
- Neuroscience Program, Harvard Medical School, Boston, MA 02129, USA
| | - Bakhos A. Tannous
- Experimental Therapeutics and Molecular Imaging Laboratory, Department of Neurology, Neuro-Oncology Division, Massachusetts General Hospital, 149 13th Street, Charlestown, Boston, MA 02129, USA
- Neuroscience Program, Harvard Medical School, Boston, MA 02129, USA
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25
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Klauser AL, Hirschfeld M, Ritter A, Rücker G, Jäger M, Gundarova J, Weiss D, Juhasz-Böss I, Berner K, Erbes T, Asberger J. Anticarcinogenic Effects of Odorant Substances Citral, Citrathal R and Cyclovertal on Breast Cancer in vitro. BREAST CANCER: TARGETS AND THERAPY 2021; 13:659-673. [PMID: 34916844 PMCID: PMC8668161 DOI: 10.2147/bctt.s322619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 09/17/2021] [Indexed: 12/09/2022]
Abstract
Purpose In 2020, breast cancer still represents the most common type of cancer in women worldwide. Depending on the specific molecular subtype, clinical breast cancer management comprises surgery, radiotherapy, chemotherapy and targeted therapy. Furthermore, there are some therapeutic approaches from the field of complementary and alternative medicine. Current research focuses on the elucidation of new therapeutic targets for treatment development. Odorant substances affect apoptosis, proliferation and cell cycle in healthy and cancerous cells. Exact signalling pathways involved are not entirely clear. The present study aims to analyse their therapeutic potential in breast cancer. Methods This study focuses on the effect of commonly used odorant substances (citral, citrathal R, cyclovertal, para-cymol, hexylacetat, herbavert, dihydromyrcerol and limonen) on the breast cancer cell lines MDA-MB-231, T47-D and BT474. Methodologically, this study applied cell culturing, MTT assay for detection of IC50 of the odorant substance, RNA purification followed by qRT-PCR, protein isolation and Western Blot, as well as immunocytochemistry. Further, this study investigates the role of transient receptor potential channel V1 (TRPV1), involved in the mechanisms of action for some odorant substances. Therefore, capsazepine, a TRPV1 antagonist, was used. Results The odorant substances citral, citrathal R and cyclovertal have significant pro-apoptotic (p < 0.001), anti-proliferative (p < 0.001) and cell cycle-arresting effects measurable in RNA expression as well as in protein levels and immunocytochemical staining. The combination of citral and capsazepine no longer showed significant pro-apoptotic, antiproliferative, and cell cycle inhibitory effects compared to the compounds alone. This indicates that TRPV1 is necessary for the signal transduction of citral. Conclusion This present study reveals three odorant substances with effects on cell viability, indicating their potential use in breast cancer therapy. ![]()
Point your SmartPhone at the code above. If you have a QR code reader the video abstract will appear. Or use: https://youtu.be/-gpMvmx9sCU
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Affiliation(s)
| | - Marc Hirschfeld
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Department of Obstetrics and Gynecology, Medical Center – University of Freiburg, Freiburg, Germany
- Institute of Veterinary Medicine, University of Göttingen, Göttingen, Germany
| | - Andrea Ritter
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Department of Obstetrics and Gynecology, Medical Center – University of Freiburg, Freiburg, Germany
| | - Gerta Rücker
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Institute of Medical Biometry and Statistics, Medical Center – University of Freiburg, Freiburg, Germany
| | - Markus Jäger
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Department of Obstetrics and Gynecology, Medical Center – University of Freiburg, Freiburg, Germany
| | - Julia Gundarova
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Daniela Weiss
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Department of Obstetrics and Gynecology, Medical Center – University of Freiburg, Freiburg, Germany
| | - Ingolf Juhasz-Böss
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Department of Obstetrics and Gynecology, Medical Center – University of Freiburg, Freiburg, Germany
| | - Kai Berner
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Department of Obstetrics and Gynecology, Medical Center – University of Freiburg, Freiburg, Germany
| | - Thalia Erbes
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Department of Obstetrics and Gynecology, Medical Center – University of Freiburg, Freiburg, Germany
| | - Jasmin Asberger
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Department of Obstetrics and Gynecology, Medical Center – University of Freiburg, Freiburg, Germany
- Correspondence: Jasmin Asberger Department of Obstetrics and Gynecology, Faculty of Medicine and Medical Center – University of Freiburg, Hugstetterstr. 55, Freiburg, 79106, GermanyTel +49 761 270 30020Fax +49 761 270 30370 Email
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Yin H, Zheng X, Tang X, Zang Z, Li B, He S, Shen R, Yang H, Li S. Potential biomarkers and lncRNA-mRNA regulatory networks in invasive growth hormone-secreting pituitary adenomas. J Endocrinol Invest 2021; 44:1947-1959. [PMID: 33559847 DOI: 10.1007/s40618-021-01510-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 01/15/2021] [Indexed: 02/06/2023]
Abstract
PURPOSE Growth hormone-secreting pituitary adenomas (GH-PAs) are common subtypes of functional PAs. Invasive GH-PAs play a key role in restricting poor outcomes. The transcriptional changes in GH-PAs were evaluated. METHODS In this study, the transcriptome analysis of six different GH-PA samples was performed. The functional roles, co-regulatory network, and chromosome location of differentially expressed (DE) genes in invasive GH-PAs were explored. RESULTS Bioinformatic analysis revealed 101 DE mRNAs and 70 DE long non-coding RNAs (lncRNAs) between invasive and non-invasive GH-PAs. Functional enrichment analysis showed that epithelial cell differentiation and development pathways were suppressed in invasive GH-PAs, whereas the pathways of olfactory transduction, retinol metabolism, drug metabolism-cytochrome P450, and metabolism of xenobiotics by cytochrome P450 had an active trend. In the protein-protein interaction network, 11 main communities were characterized by cell- adhesion, -motility, and -cycle; transport process; phosphorus and hormone metabolic processes. The SGK1 gene was suggested to play a role in the invasiveness of GH-PAs. Furthermore, the up-regulated genes OR51B6, OR52E4, OR52E8, OR52E6, OR52N2, MAGEA6, MAGEC1, ST8SIA6-AS1, and the down-regulated genes GAD1-AS1 and SPINT1-AS1 were identified in the competing endogenous RNA network. The RT-qPCR results further supported the aberrant expression of those genes. Finally, the enrichment of DE genes in chromosome 11p15 and 12p13 regions were detected. CONCLUSION Our findings provide a new perspective for studies evaluating the underlying mechanism of invasive GH-PAs.
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Affiliation(s)
- H Yin
- Department of Neurosurgery, Xinqiao Hospital, The Army Medical University, Chongqing, China
| | - X Zheng
- Department of Neurosurgery, Xinqiao Hospital, The Army Medical University, Chongqing, China
| | - X Tang
- Department of Neurosurgery, Xinqiao Hospital, The Army Medical University, Chongqing, China
| | - Z Zang
- Department of Neurosurgery, Xinqiao Hospital, The Army Medical University, Chongqing, China
| | - B Li
- College of Life Sciences, Chongqing Normal University, Chongqing, China
| | - S He
- Department of Neurosurgery, Xinqiao Hospital, The Army Medical University, Chongqing, China
| | - R Shen
- Department of Endocrinology, Xinqiao Hospital, The Army Medical University, Chongqing, China
| | - H Yang
- Department of Neurosurgery, Xinqiao Hospital, The Army Medical University, Chongqing, China.
| | - S Li
- Department of Neurosurgery, Xinqiao Hospital, The Army Medical University, Chongqing, China.
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Nam GE, Zhang ZF, Rao J, Zhou H, Jung SY. Interactions Between Adiponectin-Pathway Polymorphisms and Obesity on Postmenopausal Breast Cancer Risk Among African American Women: The WHI SHARe Study. Front Oncol 2021; 11:698198. [PMID: 34367982 PMCID: PMC8335565 DOI: 10.3389/fonc.2021.698198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 07/02/2021] [Indexed: 11/23/2022] Open
Abstract
Background A decreased level of serum adiponectin is associated with obesity and an increased risk of breast cancer among postmenopausal women. Yet, the interplay between genetic variants associated with adiponectin phenotype, obesity, and breast cancer risk is unclear in African American (AA) women. Methods We examined 32 single-nucleotide polymorphisms (SNPs) previously identified in genome-wide association and replication studies of serum adiponectin levels using data from 7,991 AA postmenopausal women in the Women’s Health Initiative SNP Health Association Resource. Results Stratifying by obesity status, we identified 18 adiponectin-related SNPs that were associated with breast cancer risk. Among women with BMI ≥ 30 kg/m2, the minor TT genotype of FER rs10447248 had an elevated breast cancer risk. Interaction was observed between obesity and the CT genotype of ADIPOQ rs6773957 on the additive scale for breast cancer risk (relative excess risk due to interaction, 0.62; 95% CI, 0.32–0.92). The joint effect of BMI ≥ 30 kg/m2 and the TC genotype of OR8S1 rs11168618 was larger than the sum of the independent effects on breast cancer risk. Conclusions We demonstrated that obesity plays a significant role as an effect modifier in an increased effect of the SNPs on breast cancer risk using one of the most extensive data on postmenopausal AA women. Impact The results suggest the potential use of adiponectin genetic variants as obesity-associated biomarkers for informing AA women who are at greater risk for breast cancer and also for promoting behavioral interventions, such as weight control, to those with risk genotypes.
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Affiliation(s)
- Gina E Nam
- Department of Epidemiology, Fielding School of Public Health, University of California at Los Angeles (UCLA), Los Angeles, CA, United States
| | - Zuo-Feng Zhang
- Department of Epidemiology, Fielding School of Public Health, University of California at Los Angeles (UCLA), Los Angeles, CA, United States.,Center for Human Nutrition, Department of Medicine, UCLA David Geffen School of Medicine, University of California at Los Angeles (UCLA), Los Angeles, CA, United States
| | - Jianyu Rao
- Department of Epidemiology, Fielding School of Public Health, University of California at Los Angeles (UCLA), Los Angeles, CA, United States
| | - Hua Zhou
- Department of Biostatistics, Fielding School of Public Health, University of California at Los Angeles (UCLA), Los Angeles, CA, United States
| | - Su Yon Jung
- Translational Sciences Section, School of Nursing, University of California at Los Angeles (UCLA), Los Angeles, CA, United States.,Jonsson Comprehensive Cancer Center, University of California at Los Angeles (UCLA), Los Angeles, CA, United States
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Wang FL, Zhang XL, Yang M, Lin J, Yue YF, Li YD, Wang X, Shu Q, Jin HC. Prevalence and characteristics of mouse mammary tumor virus-like virus associated breast cancer in China. Infect Agent Cancer 2021; 16:47. [PMID: 34174934 PMCID: PMC8235620 DOI: 10.1186/s13027-021-00383-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 06/07/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Despite extensive molecular epidemiological studies, the prevalence and characteristics of Mouse Mammary Tumor Virus-Like Virus (MMTV-LV) in Chinese women breast cancer are still unclear. Besides, the prevalence of MMTV-LV in women breast cancer tissue varies in different countries and its dependent factors remain inconclusive. METHODS In the first part of the study, a case-control study was performed. 119 breast cancer samples (84 from Northern China and 35 from Southern China) and 50 breast fibroadenoma specimens were collected from Chinese women patients. MMTV-like env sequence and the homology to MMTV env gene were analysed by semi-nested polymerase chain reaction (PCR). We also explored the association of MMTV-LV prevalence with sample sources (Southern and Northern China) and patients' clinicopathological characteristics. To investigate the dependent factors of the prevalence of MMTV-LV in breast cancer worldwide, a meta-analysis was conducted in the second part of the study. RESULTS We found that the prevalence of MMTV-LV was much higher in breast cancer tissues (17.65%) than that in breast fibroadenoma specimens (4.00%) (P < 0.05). MMTV-LV prevalence in Chinese women breast cancer tissues was significantly different between Southern China (5.71%) and Northern China (22.62%) (P < 0.05). The prevalence of MMTV-LV also associates significantly with expression of HER2, but shows no significant correlation with other parameters. In the meta-analysis, we found that MMTV-LV prevalence in breast cancer tissue was dependent on the distribution of M. domesticus mouse (M. d), M. musculus mouse (M.m) and M.castaneus mouse (M.c) worldwide (P < 0.05). CONCLUSION The distribution of house mice may be a crucial environmental factor that explains the geographic differences in human breast cancer incidence. Our findings may provide a potential avenue of prevention, diagnosis and treatment for breast cancer.
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Affiliation(s)
- Fa-Liang Wang
- Department of Surgical Oncology, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Binsheng Road 3333, Hangzhou, 310052, China.
| | - Xiao-Li Zhang
- Electron Microscope Room, Medical School of Hebei North University, Zhangjiakou, China
| | - Ming Yang
- Department of Surgical Oncology, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Binsheng Road 3333, Hangzhou, 310052, China
| | - Jun Lin
- Department of Medical Oncology, the Second People's Hospital of Jande, Hangzhou, China
| | - Yong-Fang Yue
- Department of Obstetrics and Gynecology, the Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Ya-Dan Li
- Laboratory of Cancer Biology, Department of Medical Oncology, Key lab of Biotherapy in Zhejiang, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, East Qingchun Road 3, Hangzhou, 310000, China
| | - Xian Wang
- Laboratory of Cancer Biology, Department of Medical Oncology, Key lab of Biotherapy in Zhejiang, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, East Qingchun Road 3, Hangzhou, 310000, China
| | - Qiang Shu
- Department of Surgical Oncology, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Binsheng Road 3333, Hangzhou, 310052, China. .,Department of Cardiothoracic Surgery, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Binsheng Road 3333, Hangzhou, 310052, China.
| | - Hong-Chuan Jin
- Laboratory of Cancer Biology, Department of Medical Oncology, Key lab of Biotherapy in Zhejiang, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, East Qingchun Road 3, Hangzhou, 310000, China.
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Shibel R, Sarfstein R, Nagaraj K, Lapkina-Gendler L, Laron Z, Dixit M, Yakar S, Werner H. The Olfactory Receptor Gene Product, OR5H2, Modulates Endometrial Cancer Cells Proliferation via Interaction with the IGF1 Signaling Pathway. Cells 2021; 10:cells10061483. [PMID: 34204736 PMCID: PMC8231575 DOI: 10.3390/cells10061483] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 06/08/2021] [Accepted: 06/08/2021] [Indexed: 12/19/2022] Open
Abstract
Endometrial cancer is the most common gynecologic malignancy in Western countries. The insulin-like growth factor-1 (IGF1) axis has an important role in endometrial cancer biology and emerged as a promising therapeutic target in oncology. However, there is an urgent need to identify biomarkers that may help in patient stratification and prognosis. Laron syndrome (LS) is a type of dwarfism that results from the mutation of the growth hormone receptor (GHR) gene, leading to congenital IGF1 deficiency. While high circulating IGF1 is regarded as a risk factor in cancer, epidemiological studies have shown that LS patients are protected from cancer development. Recent genome-wide profilings conducted on LS-derived lymphoblastoid cells led to the identification of a series of genes whose over- or under-representation in this condition might be mechanistically linked to cancer protection. The olfactory receptor 5 subfamily H member 2 (OR5H2) was the top downregulated gene in LS, its expression level being 5.8-fold lower than in the control cells. In addition to their typical role in the olfactory epithelium, olfactory receptors (ORs) are expressed in multiple tissues and play non-classical roles in various pathologies, including cancer. The aim of our study was to investigate the regulation of OR5H2 gene expression by IGF1 in endometrial cancer. Data showed that IGF1 and insulin stimulate OR5H2 mRNA and the protein levels in uterine cancer cell lines expressing either a wild-type or a mutant p53. OR5H2 silencing led to IGF1R downregulation, with ensuing reductions in the downstream cytoplasmic mediators. In addition, OR5H2 knockdown reduced the proliferation rate and cell cycle progression. Analyses of olfr196 (the mouse orthologue of OR5H2) mRNA expression in animal models of GHR deficiency or GH overexpression corroborated the human data. In summary, OR5H2 emerged as a novel target for positive regulation by IGF1, with potential relevance in endometrial cancer.
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Affiliation(s)
- Rand Shibel
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel; (R.S.); (R.S.); (K.N.); (L.L.-G.)
| | - Rive Sarfstein
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel; (R.S.); (R.S.); (K.N.); (L.L.-G.)
| | - Karthik Nagaraj
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel; (R.S.); (R.S.); (K.N.); (L.L.-G.)
| | - Lena Lapkina-Gendler
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel; (R.S.); (R.S.); (K.N.); (L.L.-G.)
| | - Zvi Laron
- Endocrinology and Diabetes Research Unit, Schneider Children’s Medical Center, Petah Tikva 49292, Israel;
| | - Manisha Dixit
- David B. Kriser Dental Center, Department of Basic Science and Craniofacial Biology, New York University College of Dentistry, New York, NY 10010-4086, USA; (M.D.); (S.Y.)
| | - Shoshana Yakar
- David B. Kriser Dental Center, Department of Basic Science and Craniofacial Biology, New York University College of Dentistry, New York, NY 10010-4086, USA; (M.D.); (S.Y.)
| | - Haim Werner
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel; (R.S.); (R.S.); (K.N.); (L.L.-G.)
- Correspondence:
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30
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Zhou K, Arslanturk S, Craig DB, Heath E, Draghici S. Discovery of primary prostate cancer biomarkers using cross cancer learning. Sci Rep 2021; 11:10433. [PMID: 34001952 PMCID: PMC8128891 DOI: 10.1038/s41598-021-89789-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 04/30/2021] [Indexed: 02/03/2023] Open
Abstract
Prostate cancer (PCa), the second leading cause of cancer death in American men, is a relatively slow-growing malignancy with multiple early treatment options. Yet, a significant number of low-risk PCa patients are over-diagnosed and over-treated with significant and long-term quality of life effects. Further, there is ever increasing evidence of metastasis and higher mortality when hormone-sensitive or castration-resistant PCa tumors are treated indistinctively. Hence, the critical need is to discover clinically-relevant and actionable PCa biomarkers by better understanding the biology of PCa. In this paper, we have discovered novel biomarkers of PCa tumors through cross-cancer learning by leveraging the pathological and molecular similarities in the DNA repair pathways of ovarian, prostate, and breast cancer tumors. Cross-cancer disease learning enriches the study population and identifies genetic/phenotypic commonalities that are important across diseases with pathological and molecular similarities. Our results show that ADIRF, SLC2A5, C3orf86, HSPA1B are among the most significant PCa biomarkers, while MTRNR2L1, EEPD1, TEPP and VN1R2 are jointly important biomarkers across prostate, breast and ovarian cancers. Our validation results have further shown that the discovered biomarkers can predict the disease state better than any randomly selected subset of differentially expressed prostate cancer genes.
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Affiliation(s)
- Kaiyue Zhou
- Department of Computer Science, Wayne State University, Detroit, 48201, USA
| | - Suzan Arslanturk
- Department of Computer Science, Wayne State University, Detroit, 48201, USA.
| | - Douglas B Craig
- Department of Oncology, Wayne State University, Detroit, 48201, USA
- Bioinformatics and Biostatistics Core, Barbara Ann Karmanos Cancer Institute, Detroit, 48201, USA
| | - Elisabeth Heath
- Department of Oncology, Wayne State University, Detroit, 48201, USA
- Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Detroit, 48201, USA
| | - Sorin Draghici
- Department of Computer Science, Wayne State University, Detroit, 48201, USA
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, 48201, USA
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31
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Choi YR, Shim J, Park JH, Kim YS, Kim MJ. Discovery of Orphan Olfactory Receptor 6M1 as a New Anticancer Target in MCF-7 Cells by a Combination of Surface Plasmon Resonance-Based and Cell-Based Systems. SENSORS 2021; 21:s21103468. [PMID: 34065710 PMCID: PMC8156394 DOI: 10.3390/s21103468] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 11/16/2022]
Abstract
Olfactory receptors (ORs) account for 49% of all G protein-coupled receptors (GPCRs), which are important targets for drug discovery, and hence ORs may also be potential drug targets. Various ORs are expressed in breast cancer cells; however, most of them are orphan receptors, and thus, their functions are unknown. Herein, we present an experimental strategy using a surface plasmon resonance (SPR) system and a cell-based assay that allowed the identification of orphan OR6M1 as a new anticancer target in the MCF-7 breast cancer cell line. After the construction of stable OR6M1-expressing cells, the SPR-based screening of 108 chemicals for ligand activity was performed against OR6M1-expressing whole cells (primary screening) or membrane fragments (secondary screening). As a result, anthraquinone (AQ) and rutin were discovered to be new OR6M1 ligands. Based on calcium imaging in OR6M1-expressing Hana3A cells, AQ and rutin were classified as an OR6M1 agonist and antagonist, respectively. Cell viability and live/dead assays showed that AQ induced the death of MCF-7 cells, which was inhibited by rutin. Therefore, OR6M1 may be considered an anticancer target, and AQ may be considered a chemotherapeutic agent. This combined method can be widely used to discover the ligands and functions of other orphan GPCRs.
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Affiliation(s)
- Yae Rim Choi
- Research Group of Natural Materials and Metabolism, Korea Food Research Institute, Wanju 55365, Korea; (Y.R.C.); (J.S.)
- Department of Food Science and Engineering, Ewha Womans University, Seoul 03760, Korea;
| | - Jaewon Shim
- Research Group of Natural Materials and Metabolism, Korea Food Research Institute, Wanju 55365, Korea; (Y.R.C.); (J.S.)
- Department of Biochemistry, Collage of Medicine, Kosin University, Busan 49267, Korea
| | - Jae-Ho Park
- Research Group of Healthcare, Korea Food Research Institute, Wanju 55365, Korea;
| | - Young-Suk Kim
- Department of Food Science and Engineering, Ewha Womans University, Seoul 03760, Korea;
| | - Min Jung Kim
- Research Group of Natural Materials and Metabolism, Korea Food Research Institute, Wanju 55365, Korea; (Y.R.C.); (J.S.)
- Correspondence: ; Tel.: +82-63-219-9380
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32
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Gao B, Baudis M. Signatures of Discriminative Copy Number Aberrations in 31 Cancer Subtypes. Front Genet 2021; 12:654887. [PMID: 34054918 PMCID: PMC8155688 DOI: 10.3389/fgene.2021.654887] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 04/15/2021] [Indexed: 12/13/2022] Open
Abstract
Copy number aberrations (CNA) are one of the most important classes of genomic mutations related to oncogenetic effects. In the past three decades, a vast amount of CNA data has been generated by molecular-cytogenetic and genome sequencing based methods. While this data has been instrumental in the identification of cancer-related genes and promoted research into the relation between CNA and histo-pathologically defined cancer types, the heterogeneity of source data and derived CNV profiles pose great challenges for data integration and comparative analysis. Furthermore, a majority of existing studies have been focused on the association of CNA to pre-selected "driver" genes with limited application to rare drivers and other genomic elements. In this study, we developed a bioinformatics pipeline to integrate a collection of 44,988 high-quality CNA profiles of high diversity. Using a hybrid model of neural networks and attention algorithm, we generated the CNA signatures of 31 cancer subtypes, depicting the uniqueness of their respective CNA landscapes. Finally, we constructed a multi-label classifier to identify the cancer type and the organ of origin from copy number profiling data. The investigation of the signatures suggested common patterns, not only of physiologically related cancer types but also of clinico-pathologically distant cancer types such as different cancers originating from the neural crest. Further experiments of classification models confirmed the effectiveness of the signatures in distinguishing different cancer types and demonstrated their potential in tumor classification.
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Affiliation(s)
- Bo Gao
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Michael Baudis
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Zurich, Switzerland
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van der Weyden L, Offord V, Turner G, Swiatkowska A, Speak AO, Adams DJ. Membrane protein regulators of melanoma pulmonary colonisation identified using a CRISPRa screen and spontaneous metastasis assay in mice. G3-GENES GENOMES GENETICS 2021; 11:6272227. [PMID: 33963380 PMCID: PMC8495943 DOI: 10.1093/g3journal/jkab157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 05/03/2021] [Indexed: 01/30/2023]
Abstract
Metastasis is the spread of cancer cells to a secondary site within the body, and is the leading cause of death for cancer patients. The lung is a common site of metastasis for many cancer types, including melanoma. Identifying the genes involved in aiding metastasis of melanoma cells to the lungs is critical for the development of better treatments. As the accessibility of cell surface proteins makes them attractive therapeutic targets, we performed a CRISPR activation screen using a library of guide RNAs (gRNAs) targeting the transcription start sites of 2195 membrane protein-encoding genes, to identify genes whose upregulated expression aided pulmonary metastasis. Immunodeficient mice were subcutaneously injected in the flank with murine B16-F0 melanoma cells expressing dCas9 and the membrane protein library gRNAs, and their lungs collected after 14–21 days. Analysis was performed to identify the gRNAs that were enriched in the lungs relative to those present in the cells at the time of administration (day 0). We identified six genes whose increased expression promotes lung metastasis. These genes included several with well-characterized pro-metastatic roles (Fut7, Mgat5, and Pcdh7) that have not previously been linked to melanoma progression, genes linked to tumor progression but that have not previously been described as involved in metastasis (Olfr322 and Olfr441), as well as novel genes (Tmem116). Thus, we have identified genes that, when upregulated in melanoma cells, can aid successful metastasis and colonization of the lung, and therefore may represent novel therapeutic targets to inhibit pulmonary metastasis.
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Affiliation(s)
- Louise van der Weyden
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Victoria Offord
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Gemma Turner
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Agnes Swiatkowska
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Anneliese O Speak
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - David J Adams
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
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Gilad Y, Eliaz Y, Yu Y, Dean AM, Han SJ, Qin L, O’Malley BW, Lonard DM. A genome-scale CRISPR Cas9 dropout screen identifies synthetically lethal targets in SRC-3 inhibited cancer cells. Commun Biol 2021; 4:399. [PMID: 33767353 PMCID: PMC7994904 DOI: 10.1038/s42003-021-01929-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 02/24/2021] [Indexed: 02/01/2023] Open
Abstract
Steroid receptor coactivator 3 (SRC-3/NCoA3/AIB1), is a key regulator of gene transcription and it plays a central role in breast cancer (BC) tumorigenesis, making it a potential therapeutic target. Beyond its function as an important regulator of estrogen receptor transcriptional activity, SRC-3 also functions as a coactivator for a wide range of other transcription factors, suggesting SRC-3 inhibition can be beneficial in hormone-independent cancers as well. The recent discovery of a potent SRC-3 small molecule inhibitor, SI-2, enabled the further development of additional related compounds. SI-12 is an improved version of SI-2 that like SI-2 has anti-proliferative activity in various cancer types, including BC. Here, we sought to identify gene targets, that when inhibited in the presence of SI-12, would lead to enhanced BC cell cytotoxicity. We performed a genome-scale CRISPR-Cas9 screen in MCF-7 BC cells under conditions of pharmacological pressure with SI-12. A parallel screen was performed with an ER inhibitor, fulvestrant, to shed light on both common and distinct activities between SRC-3 and ERα inhibition. Bearing in mind the key role of SRC-3 in tumorigenesis of other types of cancer, we extended our study by validating potential hits identified from the MCF-7 screen in other cancer cell lines.
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Affiliation(s)
- Yosi Gilad
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX USA
| | - Yossi Eliaz
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - Yang Yu
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX USA
| | - Adam M. Dean
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX USA
| | - San Jung Han
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX USA
| | - Li Qin
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX USA
| | - Bert W. O’Malley
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX USA
| | - David M. Lonard
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX USA
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35
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Wang Z, Yang X, Shen J, Xu J, Pan M, Liu J, Han S. Gene expression patterns associated with tumor-infiltrating CD4+ and CD8+ T cells in invasive breast carcinomas. Hum Immunol 2021; 82:279-287. [PMID: 33612391 DOI: 10.1016/j.humimm.2021.02.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/23/2021] [Accepted: 02/05/2021] [Indexed: 11/17/2022]
Abstract
BACKGROUND Breast carcinoma is one of the most common tumors in women. The immune microenvironment, especially T cell infiltration, is related to the occurrence and prognosis of breast carcinoma. OBJECTIVE This study investigated the gene expression patterns associated with tumor-infiltrating CD4+ and CD8+ T cells in invasive breast carcinomas. METHODS The gene expression data and corresponding clinical phenotype data from the Cancer Genome Atlas Breast Invasive Carcinoma (TCGA-BRCA) were downloaded. The stromal and immune score were calculated using ESTIMATE. The differentially expressed genes (DEGs) with a high vs. low stromal score and a high vs. low immune score were screened and then functionally enriched. The tumor-infiltrating immune cells were investigated using the Cibersort algorithm, and the CD4+ and CD8+ T cell-related genes were identified using a Spearman correlation test of infiltrating abundance with the DEGs. Moreover, the miRNA-mRNA pairs and lncRNA-miRNA pairs were predicted to construct the competing endogenous RNAs (ceRNA) network. Kaplan-Meier (K-M) survival curves were also plotted. RESULTS In total, 478 DEGs with a high vs. low stromal score and 796 DEGs with a high vs. low immune score were identified. In addition, 39 CD4+ T cell-related genes and 78 CD8+ T cell-related genes were identified; of these, 14 genes were significantly associated with the prognosis of BRCA patients. Moreover, for CD4+ T cell-related genes, the chr22-38_28785274-29006793.1-miR-34a/c-5p-CAPN6 axis was identified from the ceRNA network, whereas the chr22-38_28785274-29006793.1-miR-494-3p-SLC9A7 axis was identified for CD8+ T cell-related genes. CONCLUSIONS The chr22-38_28785274-29006793.1-miR-34a/c-5p-CAPN6 axis and the chr22-38_28785274-29006793.1-miR-494-3p-SLC9A7 axis might regulate cellular activities associated with CD4+ and CD8+ T cell infiltration, respectively, in BRCA.
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Affiliation(s)
- Zhanwei Wang
- Department of Breast Surgery, Huzhou Central Hospital, Affiliated Central Hospital HuZhou University, No. 1558, Sanhuan North Road, Wuxing District, Huzhou, Zhejiang Province 313000, China.
| | - Xi Yang
- Department of Medical Oncology, Huzhou Central Hospital, Affiliated Central Hospital HuZhou University, No. 1558, Sanhuan North Road, Wuxing District, Huzhou, Zhejiang Province 313000, China.
| | - Junjun Shen
- Department of Medical Oncology, Huzhou Central Hospital, Affiliated Central Hospital HuZhou University, No. 1558, Sanhuan North Road, Wuxing District, Huzhou, Zhejiang Province 313000, China.
| | - Jiamin Xu
- Graduate School of Nursing, Huzhou University, No. 1 Bachelor Road, Huzhou, Zhejiang Province 313000, China.
| | - Mingyue Pan
- Graduate School of Nursing, Huzhou University, NO.1 Bachelor Road, Huzhou, Zhejiang Province, 313000, China.
| | - Jin Liu
- Department of Pathology, Huzhou Central Hospital, Affiliated Central Hospital HuZhou University, No. 1558, Sanhuan North Road, Wuxing District, Huzhou, Zhejiang Province 313000, China.
| | - Shuwen Han
- Department of Medical Oncology, Huzhou Central Hospital, Affiliated Central Hospital HuZhou University, No. 1558, Sanhuan North Road, Wuxing District, Huzhou, Zhejiang Province 313000, China.
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Raka RN, Wu H, Xiao J, Hossen I, Cao Y, Huang M, Jin J. Human ectopic olfactory receptors and their food originated ligands: a review. Crit Rev Food Sci Nutr 2021; 62:5424-5443. [PMID: 33605814 DOI: 10.1080/10408398.2021.1885007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Ectopic olfactory receptors (EORs) are expressed in non-nasal tissues of human body. They belong to the G-protein coupled receptor (GPCR) superfamily. EORs may not be capable of differentiating odorants as nasal olfactory receptors (ORs), but still can be triggered by odorants and are involved in different biological processes such as anti-inflammation, energy metabolism, apoptosis etc. Consumption of strong flavored foods like celery, oranges, onions, and spices, is a good aid to attenuate inflammation and boost our immune system. During the digestion of these foods in human digestive system and the metabolization by gut microbiota, the odorants closely interacting with EORs, may play important roles in various bio-functions like serotonin release, appetite regulation etc., and ultimately impact health and diseases. Thus, EORs could be a potential target linking the ligands from food and their bioactivities. There have been related studies in different research fields of medicine and physiology, but still no systematic food oriented review. Our review portrays that EORs could be a potential target for functional food development. In this review, we summarized the EORs found in human tissues, their impacts on health and disease, ligands interacting with EORs exerting specific biological effects, and the mechanisms involved.
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Affiliation(s)
- Rifat Nowshin Raka
- Beijing Technology and Business University, Beijing, China.,Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing, China.,Beijing Engineering and Technology Research Center of Food Additives, Beijing, China.,Beijing Laboratory for Food Quality and Safety, Beijing, China.,Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing, China
| | - Hua Wu
- Beijing Technology and Business University, Beijing, China.,Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing, China.,Beijing Key Lab of Plant Resource Research and Development, Beijing, China
| | - Junsong Xiao
- Beijing Technology and Business University, Beijing, China.,Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing, China.,Beijing Engineering and Technology Research Center of Food Additives, Beijing, China.,Beijing Laboratory for Food Quality and Safety, Beijing, China.,Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing, China
| | - Imam Hossen
- Beijing Technology and Business University, Beijing, China.,Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing, China.,Beijing Engineering and Technology Research Center of Food Additives, Beijing, China.,Beijing Laboratory for Food Quality and Safety, Beijing, China.,Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing, China
| | - Yanping Cao
- Beijing Technology and Business University, Beijing, China.,Beijing Engineering and Technology Research Center of Food Additives, Beijing, China
| | - Mingquan Huang
- Beijing Technology and Business University, Beijing, China.,Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing, China
| | - Jianming Jin
- Beijing Technology and Business University, Beijing, China.,Beijing Key Lab of Plant Resource Research and Development, Beijing, China
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Kalra S, Mittal A, Bajoria M, Mishra T, Maryam S, Sengupta D, Ahuja G. Challenges and possible solutions for decoding extranasal olfactory receptors. FEBS J 2020; 288:4230-4241. [PMID: 33085840 DOI: 10.1111/febs.15606] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/29/2020] [Accepted: 10/13/2020] [Indexed: 12/15/2022]
Abstract
Olfactory receptors are primarily known to be expressed in the olfactory epithelium of the nasal cavity and therefore assist in odor perception. With the advent of high-throughput omics technologies such as tissue microarray or RNA sequencing, a large number of olfactory receptors have been reported to be expressed in the nonolfactory tissues. Although these technologies uncovered the expression of these olfactory receptors in the nonchemosensory tissues, unfortunately, they failed to reveal the information about their cell type of origin. Accurate characterization of the cell types should be the first step towards devising cell type-specific assays for their functional evaluation. Single-cell RNA-sequencing technology resolved some of these apparent limitations and opened new means to interrogate the expression of these extranasal olfactory receptors at the single-cell resolution. Moreover, the availability of large-scale, multi-organ/species single-cell expression atlases offer ample resources for the systematic reannotation of these receptors in a cell type-specific manner. In this Viewpoint article, we discuss some of the technical limitations that impede the in-depth understanding of these extranasal olfactory receptors, with a special focus on odorant receptors. Moreover, we also propose a list of single cell-based omics technologies that could further promulgate the opportunity to decipher the regulatory network that drives the odorant receptors expression at atypical locations.
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Affiliation(s)
- Siddhant Kalra
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India, India
| | - Aayushi Mittal
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India, India
| | - Manisha Bajoria
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India, India
| | - Tripti Mishra
- Pathfinder Research and Training Foundation, Greater Noida, India
| | - Sidrah Maryam
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India, India
| | - Debarka Sengupta
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India, India.,Department of Computer Science and Engineering, Indraprastha Institute of Information Technology, New Delhi, India, India.,Centre for Artificial Intelligence, Indraprastha Institute of Information Technology, New Delhi, India.,Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Gaurav Ahuja
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India, India
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Kalra S, Mittal A, Gupta K, Singhal V, Gupta A, Mishra T, Naidu S, Sengupta D, Ahuja G. Analysis of single-cell transcriptomes links enrichment of olfactory receptors with cancer cell differentiation status and prognosis. Commun Biol 2020; 3:506. [PMID: 32917933 PMCID: PMC7486295 DOI: 10.1038/s42003-020-01232-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 07/20/2020] [Indexed: 12/11/2022] Open
Abstract
Ectopically expressed olfactory receptors (ORs) have been linked with multiple clinically-relevant physiological processes. Previously used tissue-level expression estimation largely shadowed the potential role of ORs due to their overall low expression levels. Even after the introduction of the single-cell transcriptomics, a comprehensive delineation of expression dynamics of ORs in tumors remained unexplored. Our targeted investigation into single malignant cells revealed a complex landscape of combinatorial OR expression events. We observed differentiation-dependent decline in expressed OR counts per cell as well as their expression intensities in malignant cells. Further, we constructed expression signatures based on a large spectrum of ORs and tracked their enrichment in bulk expression profiles of tumor samples from The Cancer Genome Atlas (TCGA). TCGA tumor samples stratified based on OR-centric signatures exhibited divergent survival probabilities. In summary, our comprehensive analysis positions ORs at the cross-road of tumor cell differentiation status and cancer prognosis.
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Affiliation(s)
- Siddhant Kalra
- Department of Computational Biology, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), Okhla, Phase III, New Delhi, 110020, India
| | - Aayushi Mittal
- Department of Computational Biology, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), Okhla, Phase III, New Delhi, 110020, India
| | - Krishan Gupta
- Department of Computational Biology, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), Okhla, Phase III, New Delhi, 110020, India.,Department of Computer Science and Engineering, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), Okhla, Phase III, New Delhi, 110020, India
| | - Vrinda Singhal
- Department of Computational Biology, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), Okhla, Phase III, New Delhi, 110020, India
| | - Anku Gupta
- Department of Computer Science and Engineering, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), Okhla, Phase III, New Delhi, 110020, India
| | - Tripti Mishra
- Pathfinder Research and Training Foundation, 30/7 and 8, Knowledge Park III, Greater Noida, Uttar Pradesh, 201308, India
| | - Srivatsava Naidu
- Center for Biomedical Engineering, Indian Institute of Technology Ropar, Bara Phool, Birla Seed Farms, Rupnagar, Punjab, 140001, India
| | - Debarka Sengupta
- Department of Computational Biology, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), Okhla, Phase III, New Delhi, 110020, India. .,Department of Computer Science and Engineering, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), Okhla, Phase III, New Delhi, 110020, India. .,Centre for Artificial Intelligence, Indraprastha Institute of Information Technology, Okhla Phase III, New Delhi, 110020, India. .,Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia.
| | - Gaurav Ahuja
- Department of Computational Biology, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), Okhla, Phase III, New Delhi, 110020, India.
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Exploring Mechanism of Key Chinese Herbal Medicine on Breast Cancer by Data Mining and Network Pharmacology Methods. Chin J Integr Med 2020; 27:919-926. [PMID: 32572780 DOI: 10.1007/s11655-020-3422-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/22/2020] [Indexed: 12/26/2022]
Abstract
OBJECTIVE To screen the key Chinese Herbal Medicines (KCHMs) against breast cancer by data mining, and analyze the potential mechanism of KCHMs using network pharmacology method. METHODS Clinical prescriptions consisted of CHMs for treating breast cancer were screened, and then Traditional Chinese Medicine Inheritance Support System (TCMISS) was applied to obtain the KCHMs. Subsequently, active ingredients and corresponding target genes of KCHMs were searched by Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) database, and target genes of breast cancer were collected using OMIM and MalaCards. After that, the overlapping target genes of KCHMs and breast cancer were screened, and the protein-protein interaction (PPI) network was built. In addition, a network of "KCHMs-active ingredients-breast cancer-targets" was constructed by Cytoscape 3.7.1. Finally, Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analysis were performed with Database for Annotation, Visualization and Integrated Discovery (DAVID) database to reveal the action mechanism of KCHMs. RESULTS A total of 7 KCHMs were identified, whose active ingredients include quercetin, luteolin, nobiletin, kaempferol, isorhamnetin, naringenin, and be-ta-sitosterol, etc. Based on protein-protein interaction analysis, core targets were ESR1, MYC, CCND1, EGFR, CASP3, ERBB2, etc. Several KEGG pathways (e.g, PI3K-Akt, p53, ErbB, and HIF-1 signaling pathways) were found. CONCLUSION Based on the combination of the data mining method and network pharmacology approach, the therapeutic effect of KCHMs on breast cancer may be realized by acting on target genes and signaling pathways related to the formation and progression of breast cancer.
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