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Zertuche-Martínez C, Velázquez-Enríquez JM, González-García K, Santos-Álvarez JC, Romero-Tlalolini MDLÁ, Pina-Canseco S, Pérez-Campos Mayoral L, Muriel P, Villa-Treviño S, Baltiérrez-Hoyos R, Arellanes-Robledo J, Vásquez-Garzón VR. Discovery of candidate biomarkers from plasma-derived extracellular vesicles of patients with cirrhosis and hepatocellular carcinoma: an exploratory proteomic study. Mol Omics 2024; 20:483-495. [PMID: 39011654 DOI: 10.1039/d4mo00043a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
Extracellular vesicles (EVs) represent an attractive source of biomarkers due to their biomolecular cargo. The aim of this study was to identify candidate protein biomarkers from plasma-derived EVs of patients with liver cirrhosis (LC) and hepatocellular carcinoma (HCC). Plasma-derived EVs from healthy participants (HP), LC, and HCC patients (eight samples each) were subjected to label-free quantitative proteomic analysis using LC-MS/MS. A total of 248 proteins were identified, and differentially expressed proteins (DEPs) were obtained after pairwise comparison. We found that DEPs mainly involve complement cascade activation, coagulation pathways, cholesterol metabolism, and extracellular matrix components. By choosing a panel of up- and down-regulated proteins involved in cirrhotic and carcinogenesis processes, TGFBI, LGALS3BP, C7, SERPIND1, and APOC3 were found to be relevant for LC patients, while LRG1, TUBA1C, TUBB2B, ACTG1, C9, HP, FGA, FGG, FN1, PLG, APOB and ITIH2 were associated with HCC patients, which could discriminate both diseases. In addition, we identified the top shared proteins in both diseases, which included LCAT, SERPINF2, A2M, CRP, and VWF. Thus, our exploratory proteomic study revealed that these proteins might play an important role in the disease progression and represent a panel of candidate biomarkers for the prognosis and diagnosis of LC and HCC.
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Affiliation(s)
- Cecilia Zertuche-Martínez
- Laboratorio de Fibrosis y cáncer, Facultad de Medicina y Cirugía, Universidad Autónoma Benito Juárez de Oaxaca, Oaxaca de Juárez 68120, Oaxaca, Mexico
| | - Juan Manuel Velázquez-Enríquez
- Laboratorio de Fibrosis y cáncer, Facultad de Medicina y Cirugía, Universidad Autónoma Benito Juárez de Oaxaca, Oaxaca de Juárez 68120, Oaxaca, Mexico
| | - Karina González-García
- Laboratorio de Fibrosis y cáncer, Facultad de Medicina y Cirugía, Universidad Autónoma Benito Juárez de Oaxaca, Oaxaca de Juárez 68120, Oaxaca, Mexico
| | - Jovito Cesar Santos-Álvarez
- Laboratorio de Fibrosis y cáncer, Facultad de Medicina y Cirugía, Universidad Autónoma Benito Juárez de Oaxaca, Oaxaca de Juárez 68120, Oaxaca, Mexico
| | | | - Socorro Pina-Canseco
- Centro de Investigación Facultad de Medicina UNAM UABJO, Facultad de Medicina y Cirugía, Universidad Autónoma Benito Juárez de Oaxaca, Oaxaca de Juárez 68120, Oaxaca, Mexico
| | - Laura Pérez-Campos Mayoral
- Centro de Investigación Facultad de Medicina UNAM UABJO, Facultad de Medicina y Cirugía, Universidad Autónoma Benito Juárez de Oaxaca, Oaxaca de Juárez 68120, Oaxaca, Mexico
| | - Pablo Muriel
- Laboratorio de Hepatología Experimental, Departamento de Farmacología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Ciudad de México 07000, Mexico
| | - Saúl Villa-Treviño
- Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Ciudad de México 07360, Mexico
| | - Rafael Baltiérrez-Hoyos
- CONAHCYT-Facultad de Medicina y Cirugía, Universidad Autónoma Benito Juárez de Oaxaca, Oaxaca de Juárez 68120, Oaxaca, Mexico.
| | | | - Verónica Rocío Vásquez-Garzón
- CONAHCYT-Facultad de Medicina y Cirugía, Universidad Autónoma Benito Juárez de Oaxaca, Oaxaca de Juárez 68120, Oaxaca, Mexico.
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2
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Olbromski M, Mrozowska M, Piotrowska A, Kmiecik A, Smolarz B, Romanowicz H, Blasiak P, Maciejczyk A, Wojnar A, Dziegiel P. Prognostic significance of alpha-2-macrglobulin and low-density lipoprotein receptor-related protein-1 in various cancers. Am J Cancer Res 2024; 14:3036-3058. [PMID: 39005669 PMCID: PMC11236788 DOI: 10.62347/vujv9180] [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: 11/06/2023] [Accepted: 05/21/2024] [Indexed: 07/16/2024] Open
Abstract
Cancer is the leading cause of death worldwide. The World Health Organization (WHO) estimates that 10 million fatalities occurred in 2023. Breast cancer (BC) ranked first among malignancies with 2.26 million cases, lung cancer (LC) second with 2.21 million cases, and colon and rectum cancers (CC, CRC) third with 1.93 million cases. These results highlight the importance of investigating novel cancer prognoses and anti-cancer markers. In this study, we investigated the potential effects of alpha-2 macroglobulin and its receptor, LRP1, on the outcomes of breast, lung, and colorectal malignancies. Immunohistochemical staining was used to analyze the expression patterns of A2M and LRP1 in 545 cases of invasive ductal breast carcinoma (IDC) and 51 cases of mastopathies/fibrocystic breast disease (FBD); 256 cases of non-small cell lung carcinomas (NSCLCs) and 45 cases of non-malignant lung tissue (NMLT); and 108 cases of CRC and 25 cases of non-malignant colorectal tissue (NMCT). A2M and LRP1 expression levels were also investigated in breast (MCF-7, BT-474, SK-BR-3, T47D, MDA-MB-231, and MDA-MB-231/BO2), lung (NCI-H1703, NCI-H522, and A549), and colon (LS 180, Caco-2, HT-29, and LoVo) cancer cell lines. Based on our findings, A2M and LRP1 exhibited various expression patterns in the examined malignancies, which were related to one another. Additionally, the stroma of lung and colorectal cancer has increased levels of A2M/LRP1 areas, which explains the significance of the stroma in the development and maintenance of tumor homeostasis. A2M expression was shown to be downregulated in all types of malignancies under study and was positively linked with an increase in cell line aggressiveness. Although more invasive cells had higher levels of A2M expression, an IHC analysis showed the opposite results. This might be because exogenous alpha-2-macroglobulin is present, which has an inhibitory effect on several cancerous enzymes and receptor-dependent signaling pathways. Additionally, siRNA-induced suppression of the transcripts for A2M and LRPP1 revealed their connection, which provides fresh information on the function of the LRP1 receptor in A2M recurrence in cancer. Further studies on different forms of cancer may corroborate the fact that both A2M and LRP1 have high potential as innovative therapeutic agents.
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Affiliation(s)
- Mateusz Olbromski
- Department of Histology and Embryology, Department of Human Morphology and Embryology, Wroclaw Medical University Chalubinskiego 6A, 50-368 Wroclaw, Poland
| | - Monika Mrozowska
- Department of Histology and Embryology, Department of Human Morphology and Embryology, Wroclaw Medical University Chalubinskiego 6A, 50-368 Wroclaw, Poland
| | - Aleksandra Piotrowska
- Department of Histology and Embryology, Department of Human Morphology and Embryology, Wroclaw Medical University Chalubinskiego 6A, 50-368 Wroclaw, Poland
| | - Alicja Kmiecik
- Department of Histology and Embryology, Department of Human Morphology and Embryology, Wroclaw Medical University Chalubinskiego 6A, 50-368 Wroclaw, Poland
| | - Beata Smolarz
- Department of Pathology, Polish Mother's Memorial Hospital Research Institute Rzgowska 281/289, 93-338 Lodz, Poland
| | - Hanna Romanowicz
- Department of Pathology, Polish Mother's Memorial Hospital Research Institute Rzgowska 281/289, 93-338 Lodz, Poland
| | - Piotr Blasiak
- Department and Clinic of Thoracic Surgery, Wroclaw Medical University Grabiszynska 105, 53-439 Wroclaw, Poland
- Lower Silesian Center of Oncology, Pulmonology and Hematology Hirszfelda 12, 53-413 Wroclaw, Poland
| | - Adam Maciejczyk
- Lower Silesian Center of Oncology, Pulmonology and Hematology Hirszfelda 12, 53-413 Wroclaw, Poland
- Department of Oncology, Wroclaw Medical University Hirszfelda 12, 53-413 Wroclaw, Poland
| | - Andrzej Wojnar
- Department of Pathology, Lower Silesian Oncology Center Hirszfelda 12, 53-413 Wroclaw, Poland
| | - Piotr Dziegiel
- Department of Histology and Embryology, Department of Human Morphology and Embryology, Wroclaw Medical University Chalubinskiego 6A, 50-368 Wroclaw, Poland
- Department of Human Biology, Faculty of Physiotherapy, Wroclaw University of Health and Sport Sciences Paderewskiego 35, 51-612 Wroclaw, Poland
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3
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Wilk SS, Michalak K, Owczarek EP, Winiarczyk S, Zabielska-Koczywąs KA. Proteomic Analyses Reveal the Role of Alpha-2-Macroglobulin in Canine Osteosarcoma Cell Migration. Int J Mol Sci 2024; 25:3989. [PMID: 38612805 PMCID: PMC11011979 DOI: 10.3390/ijms25073989] [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: 02/13/2024] [Revised: 03/25/2024] [Accepted: 03/29/2024] [Indexed: 04/14/2024] Open
Abstract
Canine osteosarcoma (OSA) is an aggressive bone neoplasia with high metastatic potential. Metastasis is the main cause of death associated with OSA, and there is no current treatment available for metastatic disease. Proteomic analyses, including matrix-assisted laser desorption/ionisation-time of flight mass spectrometry (MALDI TOF/TOF MS), are widely used to select molecular targets and identify proteins that may play a key role in primary tumours and at various steps of the metastatic cascade. The main aim of this study was to identify proteins differently expressed in canine OSA cell lines with different malignancy phenotypes (OSCA-8 and OSCA-32) compared to canine osteoblasts (CnOb). The intermediate aim of the study was to compare canine OSA cell migration capacity and assess its correlation with the malignancy phenotypes of each cell line. Using MALDI-TOF/TOF MS analyses, we identified eight proteins that were significantly differentially expressed (p ≤ 0.05) in canine OSA cell lines compared to CnOb: cilia- and flagella-associated protein 298 (CFAP298), general transcription factor II-I (GTF2I), mirror-image polydactyly gene 1 protein (MIPOL1), alpha-2 macroglobulin (A2M), phosphoglycerate mutase 1 (PGAM1), ubiquitin (UB2L6), ectodysplasin-A receptor-associated adapter protein (EDARADD), and leucine-rich-repeat-containing protein 72 (LRRC72). Using the Simple Western technique, we confirmed high A2M expression in CnOb compared to OSCA-8 and OSCA-32 cell lines (with intermediate and low A2M expression, respectively). Then, we confirmed the role of A2M in cancer cell migration by demonstrating significantly inhibited OSA cell migration by treatment with A2M (both at 10 and 30 mM concentrations after 12 and 24 h) in a wound-healing assay. This study may be the first report indicating A2M's role in OSA cell metastasis; however, further in vitro and in vivo studies are needed to confirm its possible role as an anti-metastatic agent in this malignancy.
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Affiliation(s)
- Sylwia S. Wilk
- Department of Small Animal Diseases and Clinic, Institute of Veterinary Medicine, Warsaw University of Life Sciences, Nowoursynowska 159c, 02-787 Warsaw, Poland; (S.S.W.); (E.P.O.)
| | - Katarzyna Michalak
- Department of Epizootiology and Clinic of Infectious Diseases, University of Life Sciences, Głęboka 30, 20-612 Lublin, Poland; (K.M.); (S.W.)
| | - Ewelina P. Owczarek
- Department of Small Animal Diseases and Clinic, Institute of Veterinary Medicine, Warsaw University of Life Sciences, Nowoursynowska 159c, 02-787 Warsaw, Poland; (S.S.W.); (E.P.O.)
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology in Warsaw, 4 Ks. Trojdena, 02-109 Warsaw, Poland
| | - Stanisław Winiarczyk
- Department of Epizootiology and Clinic of Infectious Diseases, University of Life Sciences, Głęboka 30, 20-612 Lublin, Poland; (K.M.); (S.W.)
- National Veterinary Research Institute, Aleja Partyzantów 5, 24-100 Puławy, Poland
| | - Katarzyna A. Zabielska-Koczywąs
- Department of Small Animal Diseases and Clinic, Institute of Veterinary Medicine, Warsaw University of Life Sciences, Nowoursynowska 159c, 02-787 Warsaw, Poland; (S.S.W.); (E.P.O.)
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Mahmood N, Arakelian A, Szyf M, Rabbani SA. Methyl-CpG binding domain protein 2 (Mbd2) drives breast cancer progression through the modulation of epithelial-to-mesenchymal transition. Exp Mol Med 2024; 56:959-974. [PMID: 38556549 PMCID: PMC11058268 DOI: 10.1038/s12276-024-01205-2] [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: 12/04/2022] [Revised: 12/27/2023] [Accepted: 01/25/2024] [Indexed: 04/02/2024] Open
Abstract
Methyl-CpG-binding domain protein 2 (Mbd2), a reader of DNA methylation, has been implicated in different types of malignancies, including breast cancer. However, the exact role of Mbd2 in various stages of breast cancer growth and progression in vivo has not been determined. To test whether Mbd2 plays a causal role in mammary tumor growth and metastasis, we performed genetic knockout (KO) of Mbd2 in MMTV-PyMT transgenic mice and compared mammary tumor progression kinetics between the wild-type (PyMT-Mbd2+/+) and KO (PyMT-Mbd2-/-) groups. Our results demonstrated that deletion of Mbd2 in PyMT mice impedes primary tumor growth and lung metastasis at the experimental endpoint (postnatal week 20). Transcriptomic and proteomic analyses of primary tumors revealed that Mbd2 deletion abrogates the expression of several key determinants involved in epithelial-to-mesenchymal transition, such as neural cadherin (N-cadherin) and osteopontin. Importantly, loss of the Mbd2 gene impairs the activation of the PI3K/AKT pathway, which is required for PyMT-mediated oncogenic transformation, growth, and survival of breast tumor cells. Taken together, the results of this study provide a rationale for further development of epigenetic therapies targeting Mbd2 to inhibit the progression of breast cancer.
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Affiliation(s)
- Niaz Mahmood
- Department of Medicine, McGill University, Montréal, QC, H4A3J1, Canada
- Department of Biochemistry, McGill University, Montréal, QC, H3A1A3, Canada
| | - Ani Arakelian
- Department of Medicine, McGill University, Montréal, QC, H4A3J1, Canada
| | - Moshe Szyf
- Department of Pharmacology and Therapeutics, McGill University, Montréal, QC, H3G1Y6, Canada
| | - Shafaat A Rabbani
- Department of Medicine, McGill University, Montréal, QC, H4A3J1, Canada.
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5
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Di Cosimo S, Pizzamiglio S, Ciniselli CM, Duroni V, Cappelletti V, De Cecco L, De Marco C, Silvestri M, De Santis MC, Vingiani A, Paolini B, Orlandi R, Iorio MV, Pruneri G, Verderio P. A gene expression-based classifier for HER2-low breast cancer. Sci Rep 2024; 14:2628. [PMID: 38297001 PMCID: PMC10830477 DOI: 10.1038/s41598-024-52148-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 01/15/2024] [Indexed: 02/02/2024] Open
Abstract
In clinical trials evaluating antibody-conjugated drugs (ADCs), HER2-low breast cancer is defined through protein immunohistochemistry scoring (IHC) 1+ or 2+ without gene amplification. However, in daily practice, the accuracy of IHC is compromised by inter-observer variability. Herein, we aimed to identify HER2-low breast cancer primary tumors by leveraging gene expression profiling. A discovery approach was applied to gene expression profile of institutional INT1 (n = 125) and INT2 (n = 84) datasets. We identified differentially expressed genes (DEGs) in each specific HER2 IHC category 0, 1+, 2+ and 3+. Principal Component Analysis was used to generate a HER2-low signature whose performance was evaluated in the independent INT3 (n = 95), and in the publicly available TCGA and GSE81538 datasets. The association between the HER2-low signature and HER2 IHC categories was evaluated by Kruskal-Wallis test with post hoc pair-wise comparisons. The HER2-low signature discriminatory capability was assessed by estimating the area under the receiver operating characteristic curve (AUC). Gene Ontology and KEGG analyses were performed to evaluate the HER2-low signature genes functional enrichment. A HER2-low signature was computed based on HER2 IHC category-specific DEGs. The twenty genes included in the signature were significantly enriched with lipid and steroid metabolism pathways, peptidase regulation, and humoral immune response. The HER2-low signature values showed a bell-shaped distribution across IHC categories (low values in 0 and 3+; high values in 1+ and 2+), effectively distinguishing HER2-low from 0 (p < 0.001) to 3+ (p < 0.001). Notably, the signature values were higher in tumors scored with 1+ as compared to 0. The HER2-low signature association with IHC categories and its bell-shaped distribution was confirmed in the independent INT3, TCGA and GSE81538 datasets. In the combined INT1 and INT3 datasets, the HER2-low signature achieved an AUC value of 0.74 (95% confidence interval, CI 0.67-0.81) in distinguishing HER2-low vs. the other categories, outperforming the individual ERBB2 mRNA AUC value of 0.52 (95% CI 0.43-0.60). These results represent a proof-of-concept for an observer-independent gene-expression-based classifier of HER2-low status. The herein identified 20-gene signature shows promise in distinguishing between HER2 0 and HER2-low expressing tumors, including those scored as 1+ at IHC, and in developing a selection approach for ADCs candidates.
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Affiliation(s)
- Serena Di Cosimo
- Department of Advanced Diagnostics, Fondazione IRCCS Istituto Nazionale Dei Tumori, Milan, Italy
| | - Sara Pizzamiglio
- Bioinformatics and Biostatistics Unit, Department of Epidemiology and Data Science, Fondazione IRCCS Istituto Nazionale Dei Tumori, Milan, Italy.
| | - Chiara Maura Ciniselli
- Bioinformatics and Biostatistics Unit, Department of Epidemiology and Data Science, Fondazione IRCCS Istituto Nazionale Dei Tumori, Milan, Italy
| | - Valeria Duroni
- Bioinformatics and Biostatistics Unit, Department of Epidemiology and Data Science, Fondazione IRCCS Istituto Nazionale Dei Tumori, Milan, Italy
| | - Vera Cappelletti
- Department of Advanced Diagnostics, Fondazione IRCCS Istituto Nazionale Dei Tumori, Milan, Italy
| | - Loris De Cecco
- Molecular Mechanisms Unit, Department of Research, Fondazione IRCCS Istituto Nazionale Dei Tumori, Milan, Italy
| | - Cinzia De Marco
- Department of Advanced Diagnostics, Fondazione IRCCS Istituto Nazionale Dei Tumori, Milan, Italy
| | - Marco Silvestri
- Department of Advanced Diagnostics, Fondazione IRCCS Istituto Nazionale Dei Tumori, Milan, Italy
| | - Maria Carmen De Santis
- Radiation Oncology 1, Fondazione IRCCS Istituto Nazionale Dei Tumori, Milan, Italy
- Breast Unit, Fondazione IRCCS Istituto Nazionale Dei Tumori, Milan, Italy
| | - Andrea Vingiani
- Department of Advanced Diagnostics, Fondazione IRCCS Istituto Nazionale Dei Tumori, Milan, Italy
- Breast Unit, Fondazione IRCCS Istituto Nazionale Dei Tumori, Milan, Italy
| | - Biagio Paolini
- Department of Pathology, Fondazione IRCCS Istituto Nazionale Dei Tumori, Milan, Italy
| | - Rosaria Orlandi
- Molecular Targeting Unit, Department of Research, Fondazione IRCCS Istituto Nazionale Dei Tumori, Milan, Italy
| | - Marilena Valeria Iorio
- Molecular Targeting Unit, Department of Research, Fondazione IRCCS Istituto Nazionale Dei Tumori, Milan, Italy
| | - Giancarlo Pruneri
- Department of Advanced Diagnostics, Fondazione IRCCS Istituto Nazionale Dei Tumori, Milan, Italy
- Breast Unit, Fondazione IRCCS Istituto Nazionale Dei Tumori, Milan, Italy
| | - Paolo Verderio
- Bioinformatics and Biostatistics Unit, Department of Epidemiology and Data Science, Fondazione IRCCS Istituto Nazionale Dei Tumori, Milan, Italy
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Skvortsova L, Abdikerim S, Yergali K, Mit N, Perfilyeva A, Omarbayeva N, Zhunussova A, Kachiyeva Z, Sadykova T, Bekmanov B, Kaidarova D, Djansugurova L, Zhunussova G. Association of Genetic Markers with the Risk of Early-Onset Breast Cancer in Kazakh Women. Genes (Basel) 2024; 15:108. [PMID: 38254997 PMCID: PMC10815330 DOI: 10.3390/genes15010108] [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: 12/11/2023] [Revised: 01/10/2024] [Accepted: 01/15/2024] [Indexed: 01/24/2024] Open
Abstract
Breast cancer is a global health problem. It is an age-dependent disease, but cases of early-onset breast cancer (eBC) are gradually increasing. There are many unresolved questions regarding eBC risk factors, mechanisms of development and screening. Only 10% of eBC cases are due to mutations in the BRCA1/BRCA2 genes, and 90% have a more complex genetic background. This poses a significant challenge to timely cancer detection in young women and highlights the need for research and awareness. Therefore, identifying genetic risk factors for eBC is essential to solving these problems. This study represents an association analysis of 144 eBC cases and 163 control participants to identify genetic markers associated with eBC risks in Kazakh women. We performed a two-stage approach in association analysis to assess genetic predisposition to eBC. First-stage genome-wide association analysis revealed two risk intronic loci in the CHI3L2 gene (p = 5.2 × 10-6) and MGAT5 gene (p = 8.4 × 10-6). Second-stage exonic polymorphisms haplotype analysis showed significant risks for seven haplotypes (p < 9.4 × 10-4). These results point to the importance of studying medium- and low-penetrant genetic markers in their haplotype combinations for a detailed understanding of the role of detected genetic markers in eBC development and prediction.
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Affiliation(s)
- Liliya Skvortsova
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty 050060, Kazakhstan; (L.S.); (S.A.); (K.Y.); (N.M.); (A.P.); (A.Z.); (B.B.); (L.D.)
| | - Saltanat Abdikerim
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty 050060, Kazakhstan; (L.S.); (S.A.); (K.Y.); (N.M.); (A.P.); (A.Z.); (B.B.); (L.D.)
- Department of Molecular Biology and Genetics, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Kanagat Yergali
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty 050060, Kazakhstan; (L.S.); (S.A.); (K.Y.); (N.M.); (A.P.); (A.Z.); (B.B.); (L.D.)
| | - Natalya Mit
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty 050060, Kazakhstan; (L.S.); (S.A.); (K.Y.); (N.M.); (A.P.); (A.Z.); (B.B.); (L.D.)
| | - Anastassiya Perfilyeva
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty 050060, Kazakhstan; (L.S.); (S.A.); (K.Y.); (N.M.); (A.P.); (A.Z.); (B.B.); (L.D.)
| | - Nazgul Omarbayeva
- Breast Cancer Department, Kazakh Institute of Oncology and Radiology, Almaty 050060, Kazakhstan; (N.O.); (T.S.); (D.K.)
- Oncology Department, Asfendiyarov Kazakh National Medical University, Almaty 050012, Kazakhstan
| | - Aigul Zhunussova
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty 050060, Kazakhstan; (L.S.); (S.A.); (K.Y.); (N.M.); (A.P.); (A.Z.); (B.B.); (L.D.)
| | - Zulfiya Kachiyeva
- Research Institute of Applied and Fundamental Medicine, Asfendiyarov Kazakh National Medical University, Almaty 050012, Kazakhstan;
| | - Tolkyn Sadykova
- Breast Cancer Department, Kazakh Institute of Oncology and Radiology, Almaty 050060, Kazakhstan; (N.O.); (T.S.); (D.K.)
- Oncology Department, Asfendiyarov Kazakh National Medical University, Almaty 050012, Kazakhstan
| | - Bakhytzhan Bekmanov
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty 050060, Kazakhstan; (L.S.); (S.A.); (K.Y.); (N.M.); (A.P.); (A.Z.); (B.B.); (L.D.)
- Department of Molecular Biology and Genetics, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Dilyara Kaidarova
- Breast Cancer Department, Kazakh Institute of Oncology and Radiology, Almaty 050060, Kazakhstan; (N.O.); (T.S.); (D.K.)
- Oncology Department, Asfendiyarov Kazakh National Medical University, Almaty 050012, Kazakhstan
| | - Leyla Djansugurova
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty 050060, Kazakhstan; (L.S.); (S.A.); (K.Y.); (N.M.); (A.P.); (A.Z.); (B.B.); (L.D.)
- Department of Molecular Biology and Genetics, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Gulnur Zhunussova
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty 050060, Kazakhstan; (L.S.); (S.A.); (K.Y.); (N.M.); (A.P.); (A.Z.); (B.B.); (L.D.)
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7
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Biţă A, Scorei IR, Bălşeanu TA, Rău G, Ciocîlteu MV, Mogoşanu GD. Zinc-Boron Complex-Based Dietary Supplements for Longevity and Healthy Life. CURRENT HEALTH SCIENCES JOURNAL 2023; 49:381-387. [PMID: 38314211 PMCID: PMC10832868 DOI: 10.12865/chsj.49.03.10] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 08/18/2023] [Indexed: 02/06/2024]
Abstract
The nutritional role of zinc (Zn) and boron (B) in the plant-animal-human food chain is highly topical worldwide research. Our data indicated that Zn-B complex (ZBC)-based dietary supplements can be used as stable non-toxic formulations, with high intestinal absorption rate, inducing alpha2-macroglobulin (A2M) expression for longevity and healthy life. ZBC is metabolized by hydrolysis, mainly at the absorption site (intestinal level), and most of it is excreted in the urine. Within seven hours from the administration in mice, almost the entire amount of orally absorbed ZBC is eliminated in a metabolized form. The highest amount of A2M protein in mouse liver was determined by immunoabsorbance assay in the chronic experiment (1000mg/kg of ZBC), followed by the subchronic experiment (at the same dose of ZBC), and by the acute experiment (5000mg/kg of ZBC).
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Affiliation(s)
- Andrei Biţă
- Department of Biochemistry, BioBoron Research Institute, S.C. Natural Research S.R.L., Podari, Dolj County, Romania
- Department of Pharmacognosy & Phytotherapy, Faculty of Pharmacy, University of Medicine and Pharmacy of Craiova, Romania
| | - Ion Romulus Scorei
- Department of Biochemistry, BioBoron Research Institute, S.C. Natural Research S.R.L., Podari, Dolj County, Romania
| | - Tudor Adrian Bălşeanu
- Department of Biochemistry, BioBoron Research Institute, S.C. Natural Research S.R.L., Podari, Dolj County, Romania
- Department of Physiology, Faculty of Medicine, University of Medicine and Pharmacy of Craiova, Romania
| | - Gabriela Rău
- Department of Biochemistry, BioBoron Research Institute, S.C. Natural Research S.R.L., Podari, Dolj County, Romania
- Department of Organic Chemistry, Faculty of Pharmacy, University of Medicine and Pharmacy of Craiova, Romania
| | - Maria Viorica Ciocîlteu
- Department of Biochemistry, BioBoron Research Institute, S.C. Natural Research S.R.L., Podari, Dolj County, Romania
- Department of Analytical Chemistry, Faculty of Pharmacy, University of Medicine and Pharmacy of Craiova, Romania
| | - George Dan Mogoşanu
- Department of Biochemistry, BioBoron Research Institute, S.C. Natural Research S.R.L., Podari, Dolj County, Romania
- Department of Pharmacognosy & Phytotherapy, Faculty of Pharmacy, University of Medicine and Pharmacy of Craiova, Romania
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8
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Liu X, Liu H, Wang Y, Li M, Ji L, Wang K, Wei C, Li W, Chen C, Yu L, Zhu X, Hong X. Chromosome-Level Analysis of the Pelochelys cantorii Genome Provides Insights to Its Immunity, Growth and Longevity. BIOLOGY 2023; 12:939. [PMID: 37508370 PMCID: PMC10376104 DOI: 10.3390/biology12070939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 06/19/2023] [Accepted: 06/29/2023] [Indexed: 07/30/2023]
Abstract
The Asian giant soft-shelled turtle, Pelochelys cantorii (Trionychidae), is one of the largest aquatic turtles in China and was designated as a First-Grade Protected Animal in China in 1989. Previous investigation based on a combination of Illumina short-read, PacBio long-read and Hi-C scaffolding technologies acquired a high-quality chromosome-level genome of Pc. cantorii. In this study, comparative genomic analysis between Pc. cantorii and 16 other vertebrate genomes indicated that turtles separated from the ancestor of archosaurians approximately 256.6 (95% highest posterior density interval, 263.6-251.9) million years ago (Mya) (Upper Permian to Triassic) and that Pc. cantorii separated from the ancestor of Pd. sinensis and R. swinhoei approximately 59.3 (95% highest posterior density interval, 64.3-54.3) Mya. Moreover, several candidate genes, such as VWA5A, ABCG2, A2M and IGSF1, associated with tumor suppression, growth and age were expanded, implicating their potential roles in the exceptional longevity of turtles. This new chromosome-level assembly has important scientific value in the study of conservation of Pc. cantorii and also enriches the evolutionary investigation of turtle species.
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Affiliation(s)
- Xiaoli Liu
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Haiyang Liu
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Yakun Wang
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Mingzhi Li
- Guangzhou Bio & Data Technology Co., Ltd., Guangzhou 510555, China
| | - Liqin Ji
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Kaikuo Wang
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
- College of Life Science and Fisheries, Shanghai Ocean University, Shanghai 201306, China
| | - Chengqing Wei
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Wei Li
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Chen Chen
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Lingyun Yu
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Xinping Zhu
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
- College of Life Science and Fisheries, Shanghai Ocean University, Shanghai 201306, China
| | - Xiaoyou Hong
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
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9
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Miranda-Galvis M, Carneiro Soares C, Moretto Carnielli C, Ramalho Buttura J, Sales de Sá R, Kaminagakura E, Marchi FA, Paes Leme AF, Lópes Pinto CA, Santos-Silva AR, Moraes Castilho R, Kowalski LP, Squarize CH. New Insights into the Impact of Human Papillomavirus on Oral Cancer in Young Patients: Proteomic Approach Reveals a Novel Role for S100A8. Cells 2023; 12:cells12091323. [PMID: 37174723 PMCID: PMC10177374 DOI: 10.3390/cells12091323] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/29/2023] [Accepted: 05/02/2023] [Indexed: 05/15/2023] Open
Abstract
Human papillomavirus (HPV) infection has recently been linked to a subset of cancers affecting the oral cavity. However, the molecular mechanisms underlying HPV-driven oral squamous cell carcinoma (OSCC) onset and progression are poorly understood. METHODS We performed MS-based proteomics profiling based on HPV status in OSCC in young patients, following biological characterization and cell assays to explore the proteome functional landscape. RESULTS Thirty-nine proteins are differentially abundant between HPV (+) and HPV (-) OSCC. Among them, COPS3, DYHC1, and S100A8 are unfavorable for tumor recurrence and survival, in contrast to A2M and Serpine1, low levels of which show an association with better DFS. Remarkably, S100A8 is considered an independent prognostic factor for lower survival rates, and at high levels, it alters tumor-associated immune profiling, showing a lower proportion of M1 macrophages and dendritic cells. HPV (+) OSCC also displayed the pathogen-associated patterns receptor that, when activated, triggered the S100A8 and NFκB inflammatory responses. CONCLUSION HPV (+) OSCC has a peculiar microenvironment pattern distinctive from HPV (-), involving the expression of pathogen-associated pattern receptors, S100A8 overexpression, and NFκB activation and responses, which has important consequences in prognosis and may guide therapeutic decisions.
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Affiliation(s)
- Marisol Miranda-Galvis
- Laboratory of Epithelial Biology, Department of Periodontics and Oral Medicine, University of Michigan School of Dentistry, Ann Arbor, MI 48109, USA
- Oral Diagnosis Department, Piracicaba Dental School, University of Campinas (UNICAMP), Piracicaba 13414-903, SP, Brazil
| | - Carolina Carneiro Soares
- Oral Diagnosis Department, Piracicaba Dental School, University of Campinas (UNICAMP), Piracicaba 13414-903, SP, Brazil
- Department of Microbiology, Immune Biology, and Genetics, Center for Molecular Biology, University of Vienna, 1030 Vienna, Austria
| | - Carolina Moretto Carnielli
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas 13083-970, SP, Brazil
| | - Jaqueline Ramalho Buttura
- Laboratory of Bioinformatics and Computational Biology, A.C.Camargo Cancer Center (CIPE), São Paulo 01508-010, SP, Brazil
| | - Raisa Sales de Sá
- Oral Diagnosis Department, Piracicaba Dental School, University of Campinas (UNICAMP), Piracicaba 13414-903, SP, Brazil
| | - Estela Kaminagakura
- Department of Bioscience and Oral Diagnosis, Science and Technology Institute, University of São Paulo State (UNESP), São José dos Campos 01049-010, SP, Brazil
| | - Fabio Albuquerque Marchi
- Center for Translational Research in Oncology, Cancer Institute of the State of São Paulo (ICESP), São Paulo 01246-000, SP, Brazil
- Comprehensive Center for Precision Oncology, University of São Paulo, São Paulo 05508-900, SP, Brazil
| | - Adriana Franco Paes Leme
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas 13083-970, SP, Brazil
| | - Clóvis A Lópes Pinto
- Department of Anatomic Pathology, A.C.Camargo Cancer Center, São Paulo 01509-001, SP, Brazil
| | - Alan Roger Santos-Silva
- Oral Diagnosis Department, Piracicaba Dental School, University of Campinas (UNICAMP), Piracicaba 13414-903, SP, Brazil
| | - Rogerio Moraes Castilho
- Laboratory of Epithelial Biology, Department of Periodontics and Oral Medicine, University of Michigan School of Dentistry, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Luiz Paulo Kowalski
- Head and Neck Surgery Department, Medical School, University of São Paulo, São Paulo 05508-900, SP, Brazil
- Department of Head and Neck Surgery and Otorhinolaryngology, A.C.Camargo Cancer Center, São Paulo 01509-001, SP, Brazil
| | - Cristiane Helena Squarize
- Laboratory of Epithelial Biology, Department of Periodontics and Oral Medicine, University of Michigan School of Dentistry, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
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10
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Kennedy BM, Harris RE. Cyclooxygenase and Lipoxygenase Gene Expression in the Inflammogenesis of Colorectal Cancer: Correlated Expression of EGFR, JAK STAT and Src Genes, and a Natural Antisense Transcript, RP11-C67.2.2. Cancers (Basel) 2023; 15:cancers15082380. [PMID: 37190308 DOI: 10.3390/cancers15082380] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/13/2023] [Accepted: 04/18/2023] [Indexed: 05/17/2023] Open
Abstract
We examined the expression of major inflammatory genes, cyclooxygenase-1, 2 (COX1, COX2), arachidonate-5-lipoxygenase (ALOX5), and arachidonate-5-lipoxygenase activating protein (ALOX5AP) among 469 tumor specimens of colorectal cancer in The Cancer Genome Atlas (TCGA). Among 411 specimens without mutations in mismatch repair (MMR) genes, the mean expression of each of the inflammatory genes ranked above the 80th percentile, and the overall mean cyclooxygenase expression (COX1+COX2) ranked in the upper 99th percentile of all genes. Similar levels were observed for 58 cases with MMR mutations. Pearson correlation coefficients exceeding r = 0.70 were observed between COX and LOX mRNA levels with genes of major cell-signaling pathways involved in tumorigenesis (Src, JAK STAT, MAPK, PI3K). We observed a novel association (r = 0.78) between ALOX5 expression and a natural antisense transcript (NAT), RP11-67C2.2, a long non-coding mRNA gene, 462 base pairs in length that is located within the terminal intron of the ALOX5 gene on chromosome 10q11.21. Tumor-promoting genes highly correlated with the expression of COX1, COX2, ALOX5 and ALOX5AP are known to increase mitogenesis, mutagenesis, angiogenesis, cell survival, immunosuppression and metastasis in the inflammogenesis of colorectal cancer. These genes and the novel NAT, RP1167C2.2 are potential molecular targets for chemoprevention and therapy of colorectal cancer.
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Affiliation(s)
- Brian M Kennedy
- Colleges of Public Health and Medicine, The Ohio State University Comprehensive Cancer Center, The Ohio State University, 1841 Neil Avenue, Columbus, OH 43210-1351, USA
| | - Randall E Harris
- Colleges of Public Health and Medicine, The Ohio State University Comprehensive Cancer Center, The Ohio State University, 1841 Neil Avenue, Columbus, OH 43210-1351, USA
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11
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Potential anti-cancer effects of hibernating common carp (Cyprinus carpio) plasma on B16-F10 murine melanoma: In vitro and in vivo studies. Int J Biol Macromol 2023; 238:124058. [PMID: 36931484 DOI: 10.1016/j.ijbiomac.2023.124058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 03/12/2023] [Accepted: 03/13/2023] [Indexed: 03/17/2023]
Abstract
Melanoma is the major type of skin cancer, which its treatment is still a challenge in the world. In recent years, interest in hibernation-based therapeutic approaches for various biomedical applications has been increased. Many studies indicated that some factors in the blood plasma of hibernating animals such as alpha-2-macroglobulin (A2M) cause anti-proliferative effects. Considering that, the present study was conducted to investigate the anti-cancer effects of hibernating common carp plasma (HCCP) on murine melanoma (B16-F10) in vitro and in vivo. The effect of HCCP on cell viability, migration, apoptosis rate, and cell cycle distribution of B16-F10 cells, tumor growth, and rate of survival were evaluated. To investigate the role of A2M in the anti-cancer effects of HCCP, the gene of interest and proteins in HCCP and non-hibernating common carp plasma (NHCCP) were evaluated by quantitative reverse transcription-polymerase chain reaction (qRT-PCR) assay as well as sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and mass spectrometry analysis. Based on our findings, HCCP significantly decreased B16-F10 cell viability. Moreover, HCCP caused morphological alternations, inhibition of migration, induction of apoptosis, and significantly induced the cell cycle arrest at the G2/M phase. In addition, A2M level was significantly increased in HCCP compared with NHCCP. Taken together, our findings suggested that HCCP had the potential to be a promising novel therapeutic target for cancer treatment because of its anti-cancer properties.
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12
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Ye F, Zhang G, E. W, Chen H, Yu C, Yang L, Fu Y, Li J, Fu S, Sun Z, Fei L, Guo Q, Wang J, Xiao Y, Wang X, Zhang P, Ma L, Ge D, Xu S, Caballero-Pérez J, Cruz-Ramírez A, Zhou Y, Chen M, Fei JF, Han X, Guo G. Construction of the axolotl cell landscape using combinatorial hybridization sequencing at single-cell resolution. Nat Commun 2022; 13:4228. [PMID: 35869072 PMCID: PMC9307617 DOI: 10.1038/s41467-022-31879-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 07/08/2022] [Indexed: 01/01/2023] Open
Abstract
The Mexican axolotl (Ambystoma mexicanum) is a well-established tetrapod model for regeneration and developmental studies. Remarkably, neotenic axolotls may undergo metamorphosis, a process that triggers many dramatic changes in diverse organs, accompanied by gradually decline of their regeneration capacity and lifespan. However, the molecular regulation and cellular changes in neotenic and metamorphosed axolotls are still poorly investigated. Here, we develop a single-cell sequencing method based on combinatorial hybridization to generate a tissue-based transcriptomic landscape of the neotenic and metamorphosed axolotls. We perform gene expression profiling of over 1 million single cells across 19 tissues to construct the first adult axolotl cell landscape. Comparison of single-cell transcriptomes between the tissues of neotenic and metamorphosed axolotls reveal the heterogeneity of non-immune parenchymal cells in different tissues and established their regulatory network. Furthermore, we describe dynamic gene expression patterns during limb development in neotenic axolotls. This system-level single-cell analysis of molecular characteristics in neotenic and metamorphosed axolotls, serves as a resource to explore the molecular identity of the axolotl and facilitates better understanding of metamorphosis. The Mexican axolotl is a well-established tetrapod model for regeneration and development. Here the authors report a scRNA-seq method to profile neotenic, metamorphic and limb development stages, highlighting unique perturbation patterns of cell type-related gene expression throughout metamorphosis.
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13
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Lee J, Park HS, Han SR, Kang YH, Mun JY, Shin DW, Oh HW, Cho YK, Lee MS, Park J. Alpha-2-macroglobulin as a novel diagnostic biomarker for human bladder cancer in urinary extracellular vesicles. Front Oncol 2022; 12:976407. [PMID: 36176383 PMCID: PMC9513419 DOI: 10.3389/fonc.2022.976407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 08/17/2022] [Indexed: 11/13/2022] Open
Abstract
Extracellular vesicles (EVs) derived from urine are promising tools for the diagnosis of urogenital cancers. Urinary EVs (uEVs) are considered potential biomarkers for bladder cancer (BC) because urine is in direct contact with the BC tumor microenvironment and thus reflects the current state of the disease. However, challenges associated with the effective isolation and analysis of uEVs complicate the clinical detection of uEV-associated protein biomarkers. Herein, we identified uEV-derived alpha-2-macroglobulin (a2M) as a novel diagnostic biomarker for BC through comparative analysis of uEVs obtained from patients with BC pre- and post-operation using an antibody array. Furthermore, enzyme-linked immunosorbent assay of uEVs isolated from patients with BC (n=60) and non-cancer control subjects (n=23) validated the significant upregulation of a2M expression in patient uEVs (p<0.0001). There was no significant difference in whole urine a2M levels between patients with BC and controls (p=0.317). We observed that compared to classical differential centrifugation, ExoDisc, a centrifugal microfluidic tangential flow filtration device, was a significantly more effective separation method for uEV protein analysis. We expect that our approach for EV analysis will provide an efficient route for the identification of clinically meaningful uEV-based biomarkers for cancer diagnosis.
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Affiliation(s)
- Jisu Lee
- Department of Microbiology and Immunology, Eulji University School of Medicine, Daejeon, South Korea
| | - Hyun Sik Park
- Department of Urology, Eulji University Hospital, Eulji University School of Medicine, Daejeon, South Korea
| | - Seung Ro Han
- Department of Microbiology and Immunology, Eulji University School of Medicine, Daejeon, South Korea
- Eulji Biomedical Science Research Institute, Eulji University School of Medicine, Daejeon, South Korea
| | - Yun Hee Kang
- Department of Microbiology and Immunology, Eulji University School of Medicine, Daejeon, South Korea
- Eulji Biomedical Science Research Institute, Eulji University School of Medicine, Daejeon, South Korea
| | - Ji Young Mun
- Neural Circuit Research Group, Korea Brain Research Institute, Daegu, South Korea
| | - Dong Wook Shin
- Department of Family Medicine/Supportive Care Center, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Hyun-Woo Oh
- Core Facility Management Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Yoon-Kyoung Cho
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
- Center for Soft and Living Matter, Institute for Basic Science (IBS), Ulsan, South Korea
| | - Myung-Shin Lee
- Department of Microbiology and Immunology, Eulji University School of Medicine, Daejeon, South Korea
- Eulji Biomedical Science Research Institute, Eulji University School of Medicine, Daejeon, South Korea
- *Correspondence: Myung-Shin Lee, ; Jinsung Park,
| | - Jinsung Park
- Department of Urology, Eulji University Hospital, Eulji University School of Medicine, Daejeon, South Korea
- Department of Urology, Uijeongbu Eulji Medical Center, Eulji University, Uijeongbu-si, South Korea
- *Correspondence: Myung-Shin Lee, ; Jinsung Park,
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14
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Bianchi L, Altera A, Barone V, Bonente D, Bacci T, De Benedetto E, Bini L, Tosi GM, Galvagni F, Bertelli E. Untangling the Extracellular Matrix of Idiopathic Epiretinal Membrane: A Path Winding among Structure, Interactomics and Translational Medicine. Cells 2022; 11:cells11162531. [PMID: 36010606 PMCID: PMC9406781 DOI: 10.3390/cells11162531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/10/2022] [Accepted: 08/12/2022] [Indexed: 12/16/2022] Open
Abstract
Idiopathic epiretinal membranes (iERMs) are fibrocellular sheets of tissue that develop at the vitreoretinal interface. The iERMs consist of cells and an extracellular matrix (ECM) formed by a complex array of structural proteins and a large number of proteins that regulate cell–matrix interaction, matrix deposition and remodelling. Many components of the ECM tend to produce a layered pattern that can influence the tractional properties of the membranes. We applied a bioinformatics approach on a list of proteins previously identified with an MS-based proteomic analysis on samples of iERM to report the interactome of some key proteins. The performed pathway analysis highlights interactions occurring among ECM molecules, their cell receptors and intra- or extracellular proteins that may play a role in matrix biology in this special context. In particular, integrin β1, cathepsin B, epidermal growth factor receptor, protein-glutamine gamma-glutamyltransferase 2 and prolow-density lipoprotein receptor-related protein 1 are key hubs in the outlined protein–protein cross-talks. A section on the biomarkers that can be found in the vitreous humor of patients affected by iERM and that can modulate matrix deposition is also presented. Finally, translational medicine in iERM treatment has been summed up taking stock of the techniques that have been proposed for pharmacologic vitreolysis.
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Affiliation(s)
- Laura Bianchi
- Department of Life Sciences, University of Siena, 53100 Siena, Italy
| | - Annalisa Altera
- Department of Life Sciences, University of Siena, 53100 Siena, Italy
- Department of Molecular and Developmental Medicine, University of Siena, 53100 Siena, Italy
| | - Virginia Barone
- Department of Molecular and Developmental Medicine, University of Siena, 53100 Siena, Italy
| | - Denise Bonente
- Department of Life Sciences, University of Siena, 53100 Siena, Italy
- Department of Molecular and Developmental Medicine, University of Siena, 53100 Siena, Italy
| | - Tommaso Bacci
- Department of Medicine, Surgery and Neuroscience, University of Siena, 53100 Siena, Italy
| | - Elena De Benedetto
- Department of Medicine, Surgery and Neuroscience, University of Siena, 53100 Siena, Italy
| | - Luca Bini
- Department of Life Sciences, University of Siena, 53100 Siena, Italy
| | - Gian Marco Tosi
- Department of Medicine, Surgery and Neuroscience, University of Siena, 53100 Siena, Italy
| | - Federico Galvagni
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
| | - Eugenio Bertelli
- Department of Molecular and Developmental Medicine, University of Siena, 53100 Siena, Italy
- Correspondence:
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15
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Kisipan ML, Ojoo RO, Kanui TI, Abelson KSP. Bodyweight, locomotion, and behavioral responses of the naked mole rat (Heterocephalus glaber) to lipopolysaccharide administration. J Comp Physiol A Neuroethol Sens Neural Behav Physiol 2022; 208:493-504. [PMID: 35731263 PMCID: PMC9250917 DOI: 10.1007/s00359-022-01557-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 06/10/2022] [Indexed: 11/26/2022]
Abstract
The naked mole rat has unique biologic characteristics that include atypical inflammatory responses. Lipopolysaccharide induces inflammation which triggers brain centers controlling feeding, and behavior to result in “sick animal behavior”. We characterized the bodyweight, locomotor, and other behavioral responses of this rodent to lipopolysaccharide administration. Lipopolysaccharide caused weight losses, which were not prevented by TAK 242. In the open field test, lipopolysaccharide did not depress locomotion, while urination, defecation, and activity freezing were rare. The animals exhibited walling but not rearing and fast backward movements that were unaffected by lipopolysaccharide. Failure to depress locomotion suggests either a unique immunity-brain crosstalk or motor responses/centers that tolerate depressive effects of inflammation. The absence of activity freezing and rarity of urination and defecation suggests that novel environments or lipopolysaccharide do not induce anxiety, or that anxiety is expressed differently in the animal. The absence of rearing could be due to the design of the animal’s locomotor apparatus while fast backward movement could be a mechanism for quick escape from threats in the tunnels of their habitat. Our results elucidate the unique biology of this rodent, which elicits interest in the animal as a model for inflammatory research, although the findings require mechanistic corroborations.
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Affiliation(s)
- Mosiany Letura Kisipan
- Department of Experimental Medicine, University of Copenhagen, Copenhagen, Denmark.
- Department of Veterinary Anatomy and Physiology, Egerton University, Njoro, Kenya.
| | - Rodi Omondi Ojoo
- Department of Veterinary Anatomy and Physiology, University of Nairobi, Nairobi, Kenya
| | - Titus Ikusya Kanui
- Department of Agricultural Sciences, South Eastern Kenya University, Kitui, Kenya
| | - Klas S P Abelson
- Department of Experimental Medicine, University of Copenhagen, Copenhagen, Denmark
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16
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Lee HC, Chang CY, Huang YC, Wu KL, Chiang HH, Chang YY, Liu LX, Hung JY, Hsu YL, Wu YY, Tsai YM. Downregulated ADAMTS1 Incorporating A2M Contributes to Tumorigenesis and Alters Tumor Immune Microenvironment in Lung Adenocarcinoma. BIOLOGY 2022; 11:biology11050760. [PMID: 35625488 PMCID: PMC9139094 DOI: 10.3390/biology11050760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/03/2022] [Accepted: 05/11/2022] [Indexed: 11/23/2022]
Abstract
Simple Summary Lung cancer is the most dreadful cancer type and has the worst cancer-related clinical outcomes. This study used specimens from the in-house lung cancer cohort and public cohort to verify the roles of downregulated ADAMTS1, a protease remodeling extracellular matrix, to facilitate cancer promotion and progress. Based on the clinical specimens, cell and animal study with the aid of the public databases, we concluded that downregulated expression of ADAMTS1 might promote tumor progression and metastasis and modify the tumor microenvironment in lung cancer. Further investigation would be required for its application in treating lung cancer. Abstract Lung adenocarcinoma (LUAD) still holds the most dreadful clinical outcomes worldwide. Despite advanced treatment strategies, there are still some unmet needs. Next-generation sequencing of large-scale cancer genomics discovery projects combined with bioinformatics provides the opportunity to take a step forward in meeting clinical conditions. Based on in-house and The Cancer Genome Atlas (TCGA) cohorts, the results showed decreased levels of ADAMTS1 conferred poor survival compared with normal parts. Gene set enrichment analyses (GSEA) indicated the negative correlation between ADAMTS1 and the potential roles of epithelial–mesenchymal transition (EMT), metastasis, and poor prognosis in LUAD patients. With the knockdown of ADAMTS1, A549 lung cancer cells exhibited more aggressive behaviors such as EMT and increased migration, resulting in cancer metastasis in a mouse model. The pathway interaction network disclosed the linkage of downregulated α2-macroglobulin (A2M), which regulates EMT and metastasis. Furthermore, immune components analysis indicated a positive relationship between ADAMTS1 and the infiltrating levels of multiple immune cells, especially anticancer CD4+ T cells in LUAD. Notably, ADAMTS1 expression was also inversely correlated with the accumulation of immunosuppressive myeloid-derived suppressor cells and regulatory T cells, implying the downregulated ADAMTS1 mediated immune adjustment to fit the tumor survival disadvantages in LUAD patients. In conclusion, our study indicates that ADAMTS1 interacts with A2M in regulating EMT and metastasis in LUAD. Additionally, ADAMTS1 contributes to poor prognosis and immune infiltration in LUAD patients
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Affiliation(s)
- Hsiao-Chen Lee
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (H.-C.L.); (C.-Y.C.); (Y.-C.H.); (K.-L.W.); (L.-X.L.); (J.-Y.H.); (Y.-L.H.)
- Division of Plastic Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Chao-Yuan Chang
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (H.-C.L.); (C.-Y.C.); (Y.-C.H.); (K.-L.W.); (L.-X.L.); (J.-Y.H.); (Y.-L.H.)
- Department of Anatomy, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Yung-Chi Huang
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (H.-C.L.); (C.-Y.C.); (Y.-C.H.); (K.-L.W.); (L.-X.L.); (J.-Y.H.); (Y.-L.H.)
| | - Kuan-Li Wu
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (H.-C.L.); (C.-Y.C.); (Y.-C.H.); (K.-L.W.); (L.-X.L.); (J.-Y.H.); (Y.-L.H.)
- Division of Pulmonary and Critical Care Medicine, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan;
| | - Hung-Hsing Chiang
- Division of Thoracic Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
| | - Yung-Yun Chang
- Division of Pulmonary and Critical Care Medicine, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan;
- Division of General Medicine, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
| | - Lian-Xiu Liu
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (H.-C.L.); (C.-Y.C.); (Y.-C.H.); (K.-L.W.); (L.-X.L.); (J.-Y.H.); (Y.-L.H.)
| | - Jen-Yu Hung
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (H.-C.L.); (C.-Y.C.); (Y.-C.H.); (K.-L.W.); (L.-X.L.); (J.-Y.H.); (Y.-L.H.)
- Division of Pulmonary and Critical Care Medicine, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan;
- Department of Internal Medicine, Kaohsiung Municipal Ta-Tung Hospital, Kaohsiung 807, Taiwan
| | - Ya-Ling Hsu
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (H.-C.L.); (C.-Y.C.); (Y.-C.H.); (K.-L.W.); (L.-X.L.); (J.-Y.H.); (Y.-L.H.)
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
- Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Yu-Yuan Wu
- School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
| | - Ying-Ming Tsai
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (H.-C.L.); (C.-Y.C.); (Y.-C.H.); (K.-L.W.); (L.-X.L.); (J.-Y.H.); (Y.-L.H.)
- Division of Pulmonary and Critical Care Medicine, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan;
- Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
- Correspondence:
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17
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Golpich M, Amini E, Kefayat A, Fesharaki M, Moshtaghian J. In vitro and in vivo anti-cancer effects of hibernating common carp (Cyprinus carpio) plasma on metastatic triple-negative breast cancer. Sci Rep 2022; 12:2855. [PMID: 35190572 PMCID: PMC8861139 DOI: 10.1038/s41598-022-06368-4] [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: 10/07/2021] [Accepted: 01/28/2022] [Indexed: 11/28/2022] Open
Abstract
Uncontrollable proliferation is a hallmark of cancer cells. Cell proliferation and migration are significantly depressed during hibernation state. Many studies believe some factors in the plasma of hibernating animals cause these effects. This study aimed to assess the anti-cancer effects of hibernating common carp (Cyprinus carpio) plasma on 4T1 cancer cells in vitro and in vivo. The effect of hibernating plasma on cell viability, morphology, migration, apoptosis rate, and cell cycle distribution of 4T1 cells was investigated in vitro and in vivo. Hibernating plasma at a concentration of 16 mg/ml significantly reduced the viability of 4T1 cancer cells, without any toxicity on L929 normal fibroblast cells. It could change the morphology of cancer cells, induced apoptosis and cell cycle arrest at the G2/M phase, and inhibited migration. Furthermore, intratumoral injection of hibernating plasma (200 µl, 16 mg/ml) in the tumor-bearing mice caused a significant inhibition of 4T1 breast tumors volume (46.9%) and weight (58.8%) compared with controls. A significant decrease in the number of metastatic colonies at the lungs (80%) and liver (52.8%) of hibernating plasma-treated animals was detected which increased the survival time (21.9%) compared to the control groups. Immunohistochemical analysis revealed a considerable reduction in the Ki-67-positive cells in the tumor section of the hibernating plasma-treated animals compared with controls. Taken together, the SDS-PAGE and mass spectrometry analysis indicated the alpha-2-macroglobulin level in the hibernating fish plasma was significantly increased. It could exert an anti-cancer effect on breast cancer cells and suggested as a novel cancer treatment strategy.
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18
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Celsi F, Monasta L, Arrigoni G, Battisti I, Licastro D, Aloisio M, Di Lorenzo G, Romano F, Ricci G, Ura B. Gel-Based Proteomic Identification of Suprabasin as a Potential New Candidate Biomarker in Endometrial Cancer. Int J Mol Sci 2022; 23:ijms23042076. [PMID: 35216190 PMCID: PMC8880426 DOI: 10.3390/ijms23042076] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 02/04/2022] [Accepted: 02/07/2022] [Indexed: 02/01/2023] Open
Abstract
Endometrial cancer (EC) is the most frequent gynaecologic cancer in postmenopausal women. We used 2D-DIGE and mass spectrometry to identify candidate biomarkers in endometrial cancer, analysing the serum protein contents of 10 patients versus 10 control subjects. Using gel-based proteomics, we identified 24 candidate biomarkers, considering only spots with a fold change in volume percentage ≥ 1.5 or intensity change ≤ 0.6, which were significantly different between cases and controls (p < 0.05). We used Western blotting analysis both in the serum and tissue of 43 patients for data validation. Among the identified proteins, we selected Suprabasin (SBSN), an oncogene previously associated with poor prognosis in different cancers. SBSN principal isoforms were subjected to Western blotting analysis in serum and surgery-excised tissue: both isoforms were downregulated in the tissue. However, in serum, isoform 1 was upregulated, while isoform 2 was downregulated. Data-mining on the TCGA and GTEx projects, using the GEPIA2.0 interface, indicated a diminished SBSN expression in the Uterine Corpus Endometrial Cancer (UCEC) database compared to normal tissue, confirming proteomic results. These results suggest that SBSN, specifically isoform 2, in tissue or serum, could be a potential novel biomarker in endometrial cancer.
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Affiliation(s)
- Fulvio Celsi
- Institute for Maternal and Child Health—IRCCS Burlo Garofolo, 65/1 Via dell’Istria, 34137 Trieste, Italy; (F.C.); (L.M.); (M.A.); (G.D.L.); (F.R.); (G.R.)
| | - Lorenzo Monasta
- Institute for Maternal and Child Health—IRCCS Burlo Garofolo, 65/1 Via dell’Istria, 34137 Trieste, Italy; (F.C.); (L.M.); (M.A.); (G.D.L.); (F.R.); (G.R.)
| | - Giorgio Arrigoni
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy;
- Proteomics Centre, University of Padova and Azienda Ospedaliera di Padova, 35131 Padova, Italy
- CRIBI Biotechnology Center, University of Padova, 35131 Padova, Italy
- Correspondence: (G.A.); (B.U.)
| | - Ilaria Battisti
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy;
- Proteomics Centre, University of Padova and Azienda Ospedaliera di Padova, 35131 Padova, Italy
| | - Danilo Licastro
- ARGO Laboratorio Genomica ed Epigenomica, AREA Science Park, Basovizza, 34149 Trieste, Italy;
| | - Michelangelo Aloisio
- Institute for Maternal and Child Health—IRCCS Burlo Garofolo, 65/1 Via dell’Istria, 34137 Trieste, Italy; (F.C.); (L.M.); (M.A.); (G.D.L.); (F.R.); (G.R.)
| | - Giovanni Di Lorenzo
- Institute for Maternal and Child Health—IRCCS Burlo Garofolo, 65/1 Via dell’Istria, 34137 Trieste, Italy; (F.C.); (L.M.); (M.A.); (G.D.L.); (F.R.); (G.R.)
| | - Federico Romano
- Institute for Maternal and Child Health—IRCCS Burlo Garofolo, 65/1 Via dell’Istria, 34137 Trieste, Italy; (F.C.); (L.M.); (M.A.); (G.D.L.); (F.R.); (G.R.)
| | - Giuseppe Ricci
- Institute for Maternal and Child Health—IRCCS Burlo Garofolo, 65/1 Via dell’Istria, 34137 Trieste, Italy; (F.C.); (L.M.); (M.A.); (G.D.L.); (F.R.); (G.R.)
- Department of Medicine, Surgery and Health Sciences, University of Trieste, 34129 Trieste, Italy
| | - Blendi Ura
- Institute for Maternal and Child Health—IRCCS Burlo Garofolo, 65/1 Via dell’Istria, 34137 Trieste, Italy; (F.C.); (L.M.); (M.A.); (G.D.L.); (F.R.); (G.R.)
- Correspondence: (G.A.); (B.U.)
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19
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Li F, Chen Q, Yang Y, Li M, Zhang L, Yan Z, Zhang J, Wang K. ESR1 as a recurrence-related gene in intrahepatic cholangiocarcinoma: a weighted gene coexpression network analysis. Cancer Cell Int 2021; 21:225. [PMID: 33865377 PMCID: PMC8052670 DOI: 10.1186/s12935-021-01929-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 04/07/2021] [Indexed: 02/06/2023] Open
Abstract
Background Intrahepatic cholangiocarcinoma (iCCA) is the second most common malignant hepatic tumor and has a high postoperative recurrence rate and a poor prognosis. The key roles of most tumor recurrence-associated molecules in iCCA remain unclear. This study aimed to explore hub genes related to the postsurgical recurrence of iCCA. Method Differentially expressed genes (DEGs) between iCCA samples and normal liver samples were screened from The Cancer Genome Atlas (TCGA) database and used to construct a weighted gene coexpression network. Module-trait correlations were calculated to identify the key module related to recurrence in iCCA patients. Genes in the key module were subjected to functional enrichment analysis, and candidate hub genes were filtered through coexpression and protein–protein interaction (PPI) network analysis. Validation studies were conducted to detect the “real” hub gene. Furthermore, the biological functions and the underlying mechanism of the real hub gene in iCCA tumorigenesis and progression were determined via in vitro experiments. Results A total of 1019 DEGs were filtered and used to construct four coexpression modules. The red module, which showed the highest correlations with the recurrence status, family history, and day to death of patients, was identified as the key module. Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses demonstrated that genes in the red module were enriched in genes and pathways related to tumorigenesis and tumor progression. We performed validation studies and identified estrogen receptor 1 (ESR1), which significantly impacted the prognosis of iCCA patients, as the real hub gene related to the recurrence of iCCA. The in vitro experiments demonstrated that ESR1 overexpression significantly suppressed cell proliferation, migration, and invasion, whereas ESR1 knockdown elicited opposite effects. Further investigation into the mechanism demonstrated that ESR1 acts as a tumor suppressor by inhibiting the JAK/STAT3 signaling pathway. Conclusions ESR1 was identified as the real hub gene related to the recurrence of iCCA that plays a critical tumor suppressor role in iCCA progression. ESR1 significantly impacts the prognosis of iCCA patients and markedly suppresses cholangiocarcinoma cell proliferation, migration and invasion by inhibiting JAK/STAT3 signaling pathway. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-021-01929-5.
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Affiliation(s)
- Fengwei Li
- Department of Hepatic Surgery (II) of the Eastern Hepatobiliary Surgery Hospital, Navy Medical University, (Second Military Medical University), #225 Changhai Road, Shanghai, 200438, China
| | - Qinjunjie Chen
- Department of Hepatic Surgery (IV) of the Eastern Hepatobiliary Surgery Hospital, Navy Medical University, Shanghai, China
| | - Yang Yang
- Department of Hepatic Surgery (VI) of the Eastern Hepatobiliary Surgery Hospital, Navy Medical University, Shanghai, China
| | - Meihui Li
- Department of Obstetrics and Gynecology, Changhai Hospital, Naval Military Medical University, #168, Changhai Road, Yangpu District, Shanghai, 200433, China
| | - Lei Zhang
- Department of Hepatic Surgery (II) of the Eastern Hepatobiliary Surgery Hospital, Navy Medical University, (Second Military Medical University), #225 Changhai Road, Shanghai, 200438, China
| | - Zhenlin Yan
- Department of Hepatic Surgery (IV) of the Eastern Hepatobiliary Surgery Hospital, Navy Medical University, Shanghai, China
| | - Junjie Zhang
- Department of Obstetrics and Gynecology, Changhai Hospital, Naval Military Medical University, #168, Changhai Road, Yangpu District, Shanghai, 200433, China.
| | - Kui Wang
- Department of Hepatic Surgery (II) of the Eastern Hepatobiliary Surgery Hospital, Navy Medical University, (Second Military Medical University), #225 Changhai Road, Shanghai, 200438, China.
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20
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Using proteomic and transcriptomic data to assess activation of intracellular molecular pathways. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2021; 127:1-53. [PMID: 34340765 DOI: 10.1016/bs.apcsb.2021.02.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Analysis of molecular pathway activation is the recent instrument that helps to quantize activities of various intracellular signaling, structural, DNA synthesis and repair, and biochemical processes. This may have a deep impact in fundamental research, bioindustry, and medicine. Unlike gene ontology analyses and numerous qualitative methods that can establish whether a pathway is affected in principle, the quantitative approach has the advantage of exactly measuring the extent of a pathway up/downregulation. This results in emergence of a new generation of molecular biomarkers-pathway activation levels, which reflect concentration changes of all measurable pathway components. The input data can be the high-throughput proteomic or transcriptomic profiles, and the output numbers take both positive and negative values and positively reflect overall pathway activation. Due to their nature, the pathway activation levels are more robust biomarkers compared to the individual gene products/protein levels. Here, we review the current knowledge of the quantitative gene expression interrogation methods and their applications for the molecular pathway quantization. We consider enclosed bioinformatic algorithms and their applications for solving real-world problems. Besides a plethora of applications in basic life sciences, the quantitative pathway analysis can improve molecular design and clinical investigations in pharmaceutical industry, can help finding new active biotechnological components and can significantly contribute to the progressive evolution of personalized medicine. In addition to the theoretical principles and concepts, we also propose publicly available software for the use of large-scale protein/RNA expression data to assess the human pathway activation levels.
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21
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Wu Z, Tao H, Zhang S, Wang X, Ma J, Li R, Liu Z, Wang J, Cui P, Chen S, Di H, Huang Z, Zheng X, Hu Y. Efficacy and safety of anti-PD-1-based therapy in combination with PARP inhibitors for patients with advanced solid tumors in a real-world setting. Cancer Immunol Immunother 2021; 70:2971-2980. [PMID: 33740125 PMCID: PMC8423634 DOI: 10.1007/s00262-021-02852-4] [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: 03/30/2020] [Accepted: 01/05/2021] [Indexed: 01/05/2023]
Abstract
Background Rationale exists for combining immune checkpoint inhibitors and PARP inhibitors (PARPi), and results of clinical trials in ovarian cancer are promising, but data in other cancers are limited. Method Efficacy and safety of PARPi/anti-PD-1 in advanced solid tumors were retrospectively analyzed. The efficacy measures included objective response rate (ORR), disease control rate (DCR), progression-free survival (PFS) and overall survival (OS). Results This retrospective study included data from 40 patients. The ORR was 27.5% (95% CI, 13.0–42.0%), with a DCR of 85.0% (95% CI, 73.4–96.6%). Except four patients in first-line treatment (three with PR and one with SD), the ORR of ≥second-line treatment, non-small cell lung cancer (NSCLC) and small cell lung cancer (SCLC) was 22.2%, 23.1% and 28.6%, and the DCR was 83.3%, 84.6% and 71.4%, separately. The median PFS of all patients, ≥second-line treatment, NSCLC and SCLC was 4.6 m, 4.2 m, 4.5 m and 3.7 m. The median OS was 9.4 m, 11.4 m, 12.7 m and 5.4 m, respectively. Multivariable analysis revealed that BRCA1/2 mutation was positively correlated with ORR (P = 0.008), and LDH≥250U/L was negatively correlated with lowered DCR (P = 0.018), while lymphocyte number, ECOG and LDH significantly influenced both PFS and OS. We found that the possible resistant mechanisms were sarcomatous degeneration and secondary mutation, including BRCA2 truncation mutation, A2M, JAK1,T790M, KEAP1 and mTOR mutation. 37.5% patients had ≥grade 3 adverse events. Conclusion PARPi/anti-PD-1 is an effective and tolerable method for patients with advanced solid tumors, and BRCA1/2 is a potential biomarker. Supplementary Information The online version of this article (10.1007/s00262-021-02852-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhaozhen Wu
- Department of Medical Oncology, Chinese PLA General Hospital, Beijing, 100853, China.,Beijing Chest Hospital, Beijing, 101149, China.,School of Medicine, Nankai Universitiy, Tianjin, 300071, China
| | - Haitao Tao
- Department of Medical Oncology, Chinese PLA General Hospital, Beijing, 100853, China
| | - Sujie Zhang
- Department of Medical Oncology, Chinese PLA General Hospital, Beijing, 100853, China
| | - Xiao Wang
- School of Medicine, Oregon Health & Science University, Oregon, 97239-3098, USA
| | - Junxun Ma
- Department of Medical Oncology, Chinese PLA General Hospital, Beijing, 100853, China
| | - Ruixin Li
- Department of Medical Oncology, Chinese PLA General Hospital, Beijing, 100853, China
| | - Zhefeng Liu
- Department of Medical Oncology, Chinese PLA General Hospital, Beijing, 100853, China
| | - Jinliang Wang
- Department of Medical Oncology, Chinese PLA General Hospital, Beijing, 100853, China
| | - Pengfei Cui
- Department of Medical Oncology, Chinese PLA General Hospital, Beijing, 100853, China
| | - Shixue Chen
- Department of Medical Oncology, Chinese PLA General Hospital, Beijing, 100853, China
| | - Huang Di
- Department of Medical Oncology, Chinese PLA General Hospital, Beijing, 100853, China.,School of Medicine, Nankai Universitiy, Tianjin, 300071, China
| | - Ziwei Huang
- Department of Medical Oncology, Chinese PLA General Hospital, Beijing, 100853, China.,School of Medicine, Nankai Universitiy, Tianjin, 300071, China
| | - Xuan Zheng
- Department of Medical Oncology, Chinese PLA General Hospital, Beijing, 100853, China
| | - Yi Hu
- Department of Medical Oncology, Chinese PLA General Hospital, Beijing, 100853, China. .,School of Medicine, Nankai Universitiy, Tianjin, 300071, China.
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22
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Harman RM, Das SP, Bartlett AP, Rauner G, Donahue LR, Van de Walle GR. Beyond tradition and convention: benefits of non-traditional model organisms in cancer research. Cancer Metastasis Rev 2020; 40:47-69. [PMID: 33111160 DOI: 10.1007/s10555-020-09930-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 09/01/2020] [Indexed: 02/07/2023]
Abstract
Traditional laboratory model organisms are indispensable for cancer research and have provided insight into numerous mechanisms that contribute to cancer development and progression in humans. However, these models do have some limitations, most notably related to successful drug translation, because traditional model organisms are often short-lived, small-bodied, genetically homogeneous, often immunocompromised, are not exposed to natural environments shared with humans, and usually do not develop cancer spontaneously. We propose that assimilating information from a variety of long-lived, large, genetically diverse, and immunocompetent species that live in natural environments and do develop cancer spontaneously (or do not develop cancer at all) will lead to a more comprehensive understanding of human cancers. These non-traditional model organisms can also serve as sentinels for environmental risk factors that contribute to human cancers. Ultimately, expanding the range of animal models that can be used to study cancer will lead to improved insights into cancer development, progression and metastasis, tumor microenvironment, as well as improved therapies and diagnostics, and will consequently reduce the negative impacts of the wide variety of cancers afflicting humans overall.
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Affiliation(s)
- Rebecca M Harman
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Sanjna P Das
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Arianna P Bartlett
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Gat Rauner
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Leanne R Donahue
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Gerlinde R Van de Walle
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA.
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23
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Rchiad Z, Haidar M, Ansari HR, Tajeri S, Mfarrej S, Ben Rached F, Kaushik A, Langsley G, Pain A. Novel tumour suppressor roles for GZMA and RASGRP1 in Theileria annulata-transformed macrophages and human B lymphoma cells. Cell Microbiol 2020; 22:e13255. [PMID: 32830401 PMCID: PMC7685166 DOI: 10.1111/cmi.13255] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 08/03/2020] [Accepted: 08/07/2020] [Indexed: 12/22/2022]
Abstract
Theileria annulata is a tick-transmitted apicomplexan parasite that infects and transforms bovine leukocytes into disseminating tumours that cause a disease called tropical theileriosis. Using comparative transcriptomics we identified genes transcriptionally perturbed during Theileria-induced leukocyte transformation. Dataset comparisons highlighted a small set of genes associated with Theileria-transformed leukocyte dissemination. The roles of Granzyme A (GZMA) and RAS guanyl-releasing protein 1 (RASGRP1) were verified by CRISPR/Cas9-mediated knockdown. Knocking down expression of GZMA and RASGRP1 in attenuated macrophages led to a regain in their dissemination in Rag2/γC mice confirming their role as dissemination suppressors in vivo. We further evaluated the roles of GZMA and RASGRP1 in human B lymphomas by comparing the transcriptome of 934 human cancer cell lines to that of Theileria-transformed bovine host cells. We confirmed dampened dissemination potential of human B lymphomas that overexpress GZMA and RASGRP1. Our results provide evidence that GZMA and RASGRP1 have a novel tumour suppressor function in both T. annulata-infected bovine host leukocytes and in human B lymphomas.
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Affiliation(s)
- Zineb Rchiad
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,Laboratoire de Biologie Comparative des Apicomplexes, Faculté de Médecine, Université Paris Descartes - Sorbonne Paris Cité, Paris, France.,INSERM U1016, CNRS UMR8104, Cochin Institute, Paris, France.,Centre de Coalition, Innovation, et de prévention des Epidémies au Maroc (CIPEM), Mohammed VI Polytechnic University (UM6P), Ben Guerir, Morocco
| | - Malak Haidar
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,Laboratoire de Biologie Comparative des Apicomplexes, Faculté de Médecine, Université Paris Descartes - Sorbonne Paris Cité, Paris, France.,INSERM U1016, CNRS UMR8104, Cochin Institute, Paris, France
| | - Hifzur Rahman Ansari
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,King Abdullah International Medical Research Center (KAIMRC), King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Jeddah, Saudi Arabia
| | - Shahin Tajeri
- Laboratoire de Biologie Comparative des Apicomplexes, Faculté de Médecine, Université Paris Descartes - Sorbonne Paris Cité, Paris, France.,INSERM U1016, CNRS UMR8104, Cochin Institute, Paris, France
| | - Sara Mfarrej
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Fathia Ben Rached
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Abhinav Kaushik
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Gordon Langsley
- Laboratoire de Biologie Comparative des Apicomplexes, Faculté de Médecine, Université Paris Descartes - Sorbonne Paris Cité, Paris, France.,INSERM U1016, CNRS UMR8104, Cochin Institute, Paris, France
| | - Arnab Pain
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo, Japan
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24
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Wilkinson M, Sinclair P, Dellatorre-Teixeira L, Swan P, Brennan E, Moran B, Wedekind D, Downey P, Sheahan K, Conroy E, Gallagher WM, Docherty N, le Roux C, Brennan DJ. The Molecular Effects of a High Fat Diet on Endometrial Tumour Biology. Life (Basel) 2020; 10:life10090188. [PMID: 32927694 PMCID: PMC7554710 DOI: 10.3390/life10090188] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 08/30/2020] [Accepted: 09/02/2020] [Indexed: 01/03/2023] Open
Abstract
We sought to validate the BDII/Han rat model as a model for diet-induced obesity in endometrial cancer (EC) and determine if transcriptomic changes induced by a high fat diet (HFD) in an EC rat model can be used to identify novel biomarkers in human EC. Nineteen BDII/Han rats were included. Group A (n = 7) were given ad lib access to a normal calorie, normal chow diet (NCD) while Group B (n = 12) were given ad lib access to a calorie rich HFD for 15 months. RNAseq was performed on endometrial tumours from both groups. The top-ranking differentially expressed genes (DEGs) were examined in the human EC using The Cancer Genome Atlas (TCGA) to assess if the BDII/Han rat model is an appropriate model for human obesity-induced carcinogenesis. Weight gain in HFD rats was double the weight gain of NCD rats (50 g vs. 25 g). The incidence of cancer was similar in both groups (4/7-57% vs. 4/12-33%; p = 0.37). All tumours were equivalent to a Stage 1A, Grade 2 human endometrioid carcinoma. A total of 368 DEGs were identified between the tumours in the HFD group compared to the NCD group. We identified two upstream regulators of the DEGs, mir-33 and Brd4, and a pathway analysis identified downstream enrichment of the colorectal cancer metastasis and ovarian cancer metastasis pathways. Top-ranking DEGs included Tex14, A2M, Hmgcs2, Adamts5, Pdk4, Crabp2, Capn12, Npw, Idi1 and Gpt. A2M expression was decreased in HFD tumours. Consistent with these findings, we found a significant negative correlation between A2M mRNA expression levels and BMI in the TCGA cohort (Spearman's Rho = -0.263, p < 0.001). A2M expression was associated with improved overall survival (HR = 0.45, 95% CI 0.23-0.9, p = 0.024). Crabp2 expression was increased in HFD tumours. In human EC, CRABP2 expression was associated with reduced overall survival (HR = 3.554, 95% CI 1.875-6.753, p < 0.001). Diet-induced obesity can alter EC transcriptomic profiles. The BDII/Han rat model is a suitable model of diet-induced obesity in endometrial cancer and can be used to identify clinically relevant biomarkers in human EC.
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Affiliation(s)
- Michael Wilkinson
- Department of Gynaecological Oncology, UCD School of Medicine, Mater Misericordiae Universtity Hospital, Eccles Street, Dublin 7, D07 AX57 Dublin, Ireland;
- UCD Diabetes Complications Research Centre, UCD Conway Institute, University College Dublin, D14 NN96 Dublin, Ireland; (P.S.); (L.D.-T.); (P.S.); (E.B.); (N.D.)
| | - Piriyah Sinclair
- UCD Diabetes Complications Research Centre, UCD Conway Institute, University College Dublin, D14 NN96 Dublin, Ireland; (P.S.); (L.D.-T.); (P.S.); (E.B.); (N.D.)
| | - Ludmilla Dellatorre-Teixeira
- UCD Diabetes Complications Research Centre, UCD Conway Institute, University College Dublin, D14 NN96 Dublin, Ireland; (P.S.); (L.D.-T.); (P.S.); (E.B.); (N.D.)
| | - Patrick Swan
- UCD Diabetes Complications Research Centre, UCD Conway Institute, University College Dublin, D14 NN96 Dublin, Ireland; (P.S.); (L.D.-T.); (P.S.); (E.B.); (N.D.)
| | - Eoin Brennan
- UCD Diabetes Complications Research Centre, UCD Conway Institute, University College Dublin, D14 NN96 Dublin, Ireland; (P.S.); (L.D.-T.); (P.S.); (E.B.); (N.D.)
| | - Bruce Moran
- Department of Pathology, St Vincent’s University Hospital, Elm Park, Dublin 4, D04 YN63 Dublin, Ireland; (B.M.); (K.S.)
| | - Dirk Wedekind
- Biomedical Facility, Hanover Medical School, 30625 Hanover, Germany;
| | - Paul Downey
- Department of Pathology, National Maternity Hospital, Holles Street, Dublin 2, D02 YH21 Dublin, Ireland;
| | - Kieran Sheahan
- Department of Pathology, St Vincent’s University Hospital, Elm Park, Dublin 4, D04 YN63 Dublin, Ireland; (B.M.); (K.S.)
| | - Emer Conroy
- Cancer Biology and Therapeutic Laboratory, UCD School of Biomolecular and Biomedical Science Ireland, UCD Conway Institute, University College Dublin, D14 NN96 Dublin, Ireland; (E.C.); (W.M.G.)
| | - William M. Gallagher
- Cancer Biology and Therapeutic Laboratory, UCD School of Biomolecular and Biomedical Science Ireland, UCD Conway Institute, University College Dublin, D14 NN96 Dublin, Ireland; (E.C.); (W.M.G.)
| | - Neil Docherty
- UCD Diabetes Complications Research Centre, UCD Conway Institute, University College Dublin, D14 NN96 Dublin, Ireland; (P.S.); (L.D.-T.); (P.S.); (E.B.); (N.D.)
| | - Carel le Roux
- UCD Diabetes Complications Research Centre, UCD Conway Institute, University College Dublin, D14 NN96 Dublin, Ireland; (P.S.); (L.D.-T.); (P.S.); (E.B.); (N.D.)
- Department of Pathology, St Vincent’s University Hospital, Elm Park, Dublin 4, D04 YN63 Dublin, Ireland; (B.M.); (K.S.)
- Correspondence: (C.l.R.); (D.J.B.)
| | - Donal J. Brennan
- Department of Gynaecological Oncology, UCD School of Medicine, Mater Misericordiae Universtity Hospital, Eccles Street, Dublin 7, D07 AX57 Dublin, Ireland;
- UCD Diabetes Complications Research Centre, UCD Conway Institute, University College Dublin, D14 NN96 Dublin, Ireland; (P.S.); (L.D.-T.); (P.S.); (E.B.); (N.D.)
- Cancer Biology and Therapeutic Laboratory, UCD School of Biomolecular and Biomedical Science Ireland, UCD Conway Institute, University College Dublin, D14 NN96 Dublin, Ireland; (E.C.); (W.M.G.)
- Systems Biology Ireland, UCD School of Medicine, Belfield, Dublin 4, D14 NN96 Dublin, Ireland
- Correspondence: (C.l.R.); (D.J.B.)
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25
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Shepard A, Kissil JL. The use of non-traditional models in the study of cancer resistance-the case of the naked mole rat. Oncogene 2020; 39:5083-5097. [PMID: 32535616 DOI: 10.1038/s41388-020-1355-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 05/15/2020] [Accepted: 06/03/2020] [Indexed: 12/16/2022]
Abstract
Non-traditional model organisms are typically defined as any model the deviates from the typical laboratory animals, such as mouse, rat, and worm. These models are becoming increasingly important in human disease research, such as cancer, as they often display unusual biological features. Naked mole rats (NMRs) are currently one of the most popular non-traditional model, particularly in the longevity and cancer research fields. NMRs display an exceptionally long lifespan (~30 years), yet have been observed to display a low incidence of cancer, making them excellent candidates for understanding endogenous cancer resistance mechanisms. Over the past decade, many potential resistance mechanisms have been characterized. These include unique biological mechanisms involved in genome stability, protein stability, oxidative metabolism, and other cellular mechanisms such as cell cycle regulation and senescence. This review aims to summarize the many identified cancer resistance mechanisms to understand some of the main hypotheses that have thus far been generated. Many of these proposed mechanisms remain to be fully characterized or confirmed in vivo, giving the field a direction to grow and further understand the complex biology displayed by the NMR.
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Affiliation(s)
- Alyssa Shepard
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Joseph L Kissil
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, 33458, USA.
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26
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Agioutantis PC, Loutrari H, Kolisis FN. Computational Analysis of Transcriptomic and Proteomic Data for Deciphering Molecular Heterogeneity and Drug Responsiveness in Model Human Hepatocellular Carcinoma Cell Lines. Genes (Basel) 2020; 11:E623. [PMID: 32517019 PMCID: PMC7349788 DOI: 10.3390/genes11060623] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 05/21/2020] [Accepted: 06/02/2020] [Indexed: 12/11/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is associated with high mortality due to its inherent heterogeneity, aggressiveness, and limited therapeutic regimes. Herein, we analyzed 21 human HCC cell lines (HCC lines) to explore intertumor molecular diversity and pertinent drug sensitivity. We used an integrative computational approach based on exploratory and single-sample gene-set enrichment analysis of transcriptome and proteome data from the Cancer Cell Line Encyclopedia, followed by correlation analysis of drug-screening data from the Cancer Therapeutics Response Portal with curated gene-set enrichment scores. Acquired results classified HCC lines into two groups, a poorly and a well-differentiated group, displaying lower/higher enrichment scores in a "Specifically Upregulated in Liver" gene-set, respectively. Hierarchical clustering based on a published epithelial-mesenchymal transition gene expression signature further supported this stratification. Between-group comparisons of gene and protein expression unveiled distinctive patterns, whereas downstream functional analysis significantly associated differentially expressed genes with crucial cancer-related biological processes/pathways and revealed concrete driver-gene signatures. Finally, correlation analysis highlighted a diverse effectiveness of specific drugs against poorly compared to well-differentiated HCC lines, possibly applicable in clinical research with patients with analogous characteristics. Overall, this study expanded the knowledge on the molecular profiles, differentiation status, and drug responsiveness of HCC lines, and proposes a cost-effective computational approach to precision anti-HCC therapies.
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Affiliation(s)
- Panagiotis C. Agioutantis
- Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, 5 Iroon Polytechniou Str., Zografou Campus, 15780 Athens, Greece;
- G.P. Livanos and M. Simou Laboratories, 1st Department of Critical Care Medicine & Pulmonary Services, Evangelismos Hospital, Medical School, National Kapodistrian University of Athens, 3 Ploutarchou Str., 10675 Athens, Greece
| | - Heleni Loutrari
- G.P. Livanos and M. Simou Laboratories, 1st Department of Critical Care Medicine & Pulmonary Services, Evangelismos Hospital, Medical School, National Kapodistrian University of Athens, 3 Ploutarchou Str., 10675 Athens, Greece
| | - Fragiskos N. Kolisis
- Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, 5 Iroon Polytechniou Str., Zografou Campus, 15780 Athens, Greece;
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27
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Gemoll T, Rozanova S, Röder C, Hartwig S, Kalthoff H, Lehr S, ElSharawy A, Habermann J. Protein Profiling of Serum Extracellular Vesicles Reveals Qualitative and Quantitative Differences After Differential Ultracentrifugation and ExoQuick TM Isolation. J Clin Med 2020; 9:jcm9051429. [PMID: 32408476 PMCID: PMC7290673 DOI: 10.3390/jcm9051429] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 05/04/2020] [Accepted: 05/07/2020] [Indexed: 12/11/2022] Open
Abstract
Solid tumor biopsies are the current standard for precision medicine. However, the procedure is invasive and not always feasible. In contrast, liquid biopsies, such as serum enriched for extracellular vesicles (EVs) represent a non-invasive source of cancer biomarkers. In this study, we compared two EV isolation methods in the context of the protein biomarker detection in inflammatory bowel disease (IBD) and colorectal cancer (CRC). Using serum samples of a healthy cohort as well as CRC and IBD patients, EVs were isolated by ultracentrifugation and ExoQuick™ in parallel. EV associated protein profiles were compared by multiplex-fluorescence two-dimensional difference gel electrophoresis (2D-DIGE) and subsequent identification by mass spectrometry. Validation of gelsolin (GSN) was performed using fluorescence-quantitative western blot. 2D-DIGE resolved 936 protein spots in all serum-enriched EVs isolated by ultracentrifugation or ExoQuick™. Hereof, 93 spots were differently expressed between isolation approaches. Higher levels of GSN in EVs obtained with ExoQuick™ compared to ultracentrifugation were confirmed by western blot (p = 0.0006). Although patient groups were distinguishable after both EV isolation approaches, sample preparation strongly influences EVs’ protein profile and thus impacts on inter-study reproducibility, biomarker identification and validation. The results stress the need for strict SOPs in EV research before clinical implementation can be reached.
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Affiliation(s)
- Timo Gemoll
- Section for Translational Surgical Oncology & Biobanking, Department of Surgery, University of Lübeck and University Hospital Schleswig-Holstein, 23562 Lübeck, Germany; (S.R.); (J.H.)
- Correspondence: ; Tel.: +49-0451-500-40431
| | - Svitlana Rozanova
- Section for Translational Surgical Oncology & Biobanking, Department of Surgery, University of Lübeck and University Hospital Schleswig-Holstein, 23562 Lübeck, Germany; (S.R.); (J.H.)
| | - Christian Röder
- Institute for Experimental Cancer Research, University of Kiel, 24105 Kiel, Germany; (C.R.); (H.K.)
| | - Sonja Hartwig
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center at the Heinrich-Heine-University Düsseldorf, Leibniz Center for Diabetes Research, 40225 Düsseldorf, Germany; (S.H.); (S.L.)
- German Center for Diabetes Research (DZD), 85764 München-Neuherberg, Germany
| | - Holger Kalthoff
- Institute for Experimental Cancer Research, University of Kiel, 24105 Kiel, Germany; (C.R.); (H.K.)
| | - Stefan Lehr
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center at the Heinrich-Heine-University Düsseldorf, Leibniz Center for Diabetes Research, 40225 Düsseldorf, Germany; (S.H.); (S.L.)
- German Center for Diabetes Research (DZD), 85764 München-Neuherberg, Germany
| | - Abdou ElSharawy
- Institute of Clinical Molecular Biology, Center of Molecular Sciences, University of Kiel, 24118 Kiel, Germany;
- Division of Biochemistry, Chemistry Department, Faculty of Sciences, Damietta University, New Damietta City 34511, Egypt
| | - Jens Habermann
- Section for Translational Surgical Oncology & Biobanking, Department of Surgery, University of Lübeck and University Hospital Schleswig-Holstein, 23562 Lübeck, Germany; (S.R.); (J.H.)
- Interdisciplinary Center for Biobanking-Lübeck (ICB-L), University of Lübeck, 23562 Lübeck, Germany
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28
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Mutation Enrichment and Transcriptomic Activation Signatures of 419 Molecular Pathways in Cancer. Cancers (Basel) 2020; 12:cancers12020271. [PMID: 31979117 PMCID: PMC7073226 DOI: 10.3390/cancers12020271] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 01/16/2020] [Accepted: 01/20/2020] [Indexed: 12/13/2022] Open
Abstract
Carcinogenesis is linked with massive changes in regulation of gene networks. We used high throughput mutation and gene expression data to interrogate involvement of 278 signaling, 72 metabolic, 48 DNA repair and 47 cytoskeleton molecular pathways in cancer. Totally, we analyzed 4910 primary tumor samples with individual cancer RNA sequencing and whole exome sequencing profiles including ~1.3 million DNA mutations and representing thirteen cancer types. Gene expression in cancers was compared with the corresponding 655 normal tissue profiles. For the first time, we calculated mutation enrichment values and activation levels for these pathways. We found that pathway activation profiles were largely congruent among the different cancer types. However, we observed no correlation between mutation enrichment and expression changes both at the gene and at the pathway levels. Overall, positive median cancer-specific activation levels were seen in the DNA repair, versus similar slightly negative values in the other types of pathways. The DNA repair pathways also demonstrated the highest values of mutation enrichment. However, the signaling and cytoskeleton pathways had the biggest proportions of representatives among the outstandingly frequently mutated genes thus suggesting their initiator roles in carcinogenesis and the auxiliary/supporting roles for the other groups of molecular pathways.
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29
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Zolotovskaia M, Sorokin M, Garazha A, Borisov N, Buzdin A. Molecular Pathway Analysis of Mutation Data for Biomarkers Discovery and Scoring of Target Cancer Drugs. Methods Mol Biol 2020; 2063:207-234. [PMID: 31667773 DOI: 10.1007/978-1-0716-0138-9_16] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
DNA mutations govern cancer development. Cancer mutation profiles vary dramatically among the individuals. In some cases, they may serve as the predictors of disease progression and response to therapies. However, the biomarker potential of cancer mutations can be dramatically (several orders of magnitude) enhanced by applying molecular pathway-based approach. We developed Oncobox system for calculation of pathway instability (PI) values for the molecular pathways that are aggregated mutation frequencies of the pathway members normalized on gene lengths and on number of genes in the pathway. PI scores can be effective biomarkers in different types of comparisons, for example, as the cancer type biomarkers and as the predictors of tumor response to target therapies. The latter option is implemented using mutation drug score (MDS) values, which algorithmically rank the drugs capacity of interfering with the mutated molecular pathways. Here, describe the mathematical basis and algorithms for PI and MDS values calculation, validation and implementation. The example analysis is provided encompassing 5956 human tumor mutation profiles of 15 cancer types from The Cancer Genome Atlas (TCGA) project, that totally make 2,316,670 mutations in 19,872 genes and 1748 molecular pathways, thus enabling ranking of 128 clinically approved target drugs. Our results evidence that the Oncobox PI and MDS approaches are highly useful for basic and applied aspects of molecular oncology and pharmacology research.
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Affiliation(s)
- Marianna Zolotovskaia
- Omicsway Corp., Walnut, CA, USA
- Department of Oncology, Hematology and Radiotherapy of Pediatric Faculty, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Maxim Sorokin
- Omicsway Corp., Walnut, CA, USA
- Laboratory of Clinical Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | | | - Nikolay Borisov
- Omicsway Corp., Walnut, CA, USA
- Laboratory of Clinical Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Anton Buzdin
- Omicsway Corp., Walnut, CA, USA.
- Laboratory of Clinical Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow, Russia.
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.
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30
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Cole JE, Steeil JC, Sarro SJ, Kerns KL, Cartoceti A. Chordoma of the sacrum of an adult naked mole-rat. J Vet Diagn Invest 2019; 32:132-135. [PMID: 31838959 DOI: 10.1177/1040638719894985] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The naked mole-rat (NMR; Heterocephalus glaber)-a small, eusocial, subterranean rodent native to East Africa-is distinguished by its capability to live long and resist changes associated with the aging process. Notably, a growing amount of research has been dedicated to NMRs' multifactorial capacity to resist cancer. Since 2016, however, zoos have begun to document various neoplasms in a handful of individuals. We present herein radiographic, gross anatomic, and histopathologic features of a case of a sacral chordoma in a geriatric female. Chordomas originate in notochordal remnants. These spinal tumors are most commonly seen in ferrets; chordomas are rare in humans, can be difficult to treat, and need wide surgical margins.
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Affiliation(s)
- Jordan E Cole
- Wildlife Health Sciences (Cole, Steeil, Cartoceti), Smithsonian Conservation and Biology Institute, National Zoological Park, Washington, DC, USA.,Animal Care Sciences (Kerns, Sarro), Smithsonian Conservation and Biology Institute, National Zoological Park, Washington, DC
| | - James C Steeil
- Wildlife Health Sciences (Cole, Steeil, Cartoceti), Smithsonian Conservation and Biology Institute, National Zoological Park, Washington, DC, USA.,Animal Care Sciences (Kerns, Sarro), Smithsonian Conservation and Biology Institute, National Zoological Park, Washington, DC
| | - Steven J Sarro
- Wildlife Health Sciences (Cole, Steeil, Cartoceti), Smithsonian Conservation and Biology Institute, National Zoological Park, Washington, DC, USA.,Animal Care Sciences (Kerns, Sarro), Smithsonian Conservation and Biology Institute, National Zoological Park, Washington, DC
| | - Kenton L Kerns
- Wildlife Health Sciences (Cole, Steeil, Cartoceti), Smithsonian Conservation and Biology Institute, National Zoological Park, Washington, DC, USA.,Animal Care Sciences (Kerns, Sarro), Smithsonian Conservation and Biology Institute, National Zoological Park, Washington, DC
| | - Andrew Cartoceti
- Wildlife Health Sciences (Cole, Steeil, Cartoceti), Smithsonian Conservation and Biology Institute, National Zoological Park, Washington, DC, USA.,Animal Care Sciences (Kerns, Sarro), Smithsonian Conservation and Biology Institute, National Zoological Park, Washington, DC
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31
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Ma Q, Xu Y, Liao H, Cai Y, Xu L, Xiao D, Liu C, Pu W, Zhong X, Guo X. Identification and validation of key genes associated with non-small-cell lung cancer. J Cell Physiol 2019; 234:22742-22752. [PMID: 31127628 DOI: 10.1002/jcp.28839] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 04/30/2019] [Accepted: 05/01/2019] [Indexed: 12/24/2022]
Abstract
Non-small-cell lung cancer (NSCLC) is one of the main causes of death induced by cancer globally. However, the molecular aberrations in NSCLC patients remain unclearly. In the present study, four messenger RNA microarray datasets (GSE18842, GSE40275, GSE43458, and GSE102287) were downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) between NSCLC tissues and adjacent lung tissues were obtained from GEO2R and the overlapping DEGs were identified. Moreover, functional and pathway enrichment were performed by Funrich, while the protein-protein interaction (PPI) network construction were obtained from STRING and hub genes were visualized and identified by Cytoscape software. Furthermore, validation, overall survival (OS) and tumor staging analysis of selected hub genes were performed by GEPIA. A total of 367 DEGs (95 upregulated and 272 downregulated) were obtained through gene integration analysis. The PPI network consisted of 94 nodes and 1036 edges in the upregulated DEGs and 272 nodes and 464 edges in the downregulated DEGs, respectively. The PPI network identified 46 upregulated and 27 downregulated hub genes among the DEGs, and six (such as CENPE, NCAPH, MYH11, LRRK2, HSD17B6, and A2M) of that have not been identified to be associated with NSCLC so far. Moreover, the expression differences of the mentioned hub genes were consistent with that in lung adenocarcinoma and lung squamous cell carcinoma in the TCGA database. Further analysis showed that all the six hub genes were associated with tumor staging except MYH11, while only the upregulated DEG CENPE was associated with the worse OS of patients with NSCLC. In conclusion, the current study showed that CENPE, NCAPH, MYH11, LRRK2, HSD17B6, and A2M might be the key genes contributed to tumorigenesis or tumor progression in NSCLC, further functional study is needed to explore the involved mechanisms.
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Affiliation(s)
- Qiang Ma
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Nanchong, China.,Translational Medicine Research Center, North Sichuan Medical College, Nanchong, China.,Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, Sichuan, China
| | - Yuan Xu
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Nanchong, China.,Translational Medicine Research Center, North Sichuan Medical College, Nanchong, China.,Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, Sichuan, China
| | - Hebin Liao
- Translational Medicine Research Center, North Sichuan Medical College, Nanchong, China
| | - Yan Cai
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Nanchong, China.,Translational Medicine Research Center, North Sichuan Medical College, Nanchong, China.,Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, Sichuan, China
| | - Lei Xu
- Translational Medicine Research Center, North Sichuan Medical College, Nanchong, China
| | - Dan Xiao
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Nanchong, China.,Translational Medicine Research Center, North Sichuan Medical College, Nanchong, China.,Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, Sichuan, China
| | - Chang Liu
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Nanchong, China.,Translational Medicine Research Center, North Sichuan Medical College, Nanchong, China.,Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, Sichuan, China
| | - Wenjie Pu
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Nanchong, China.,Translational Medicine Research Center, North Sichuan Medical College, Nanchong, China.,Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, Sichuan, China
| | - Xiaowu Zhong
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Nanchong, China.,Translational Medicine Research Center, North Sichuan Medical College, Nanchong, China.,Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, Sichuan, China
| | - Xiaolan Guo
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Nanchong, China.,Translational Medicine Research Center, North Sichuan Medical College, Nanchong, China.,Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, Sichuan, China
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32
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Zhang N, Wang H, Xie Q, Cao H, Wu F, Di Wu DB, Wan Y. Identification of potential diagnostic and therapeutic target genes for lung squamous cell carcinoma. Oncol Lett 2019; 18:169-180. [PMID: 31289486 PMCID: PMC6539486 DOI: 10.3892/ol.2019.10300] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 03/19/2019] [Indexed: 12/19/2022] Open
Abstract
The purpose of this study was to identify potential molecular markers of lung squamous cell carcinoma (LUSC). Three datasets containing LUSC mRNA sequencing data were downloaded from the Gene Expression Omnibus, The Cancer Genome Atlas and the Gene Expression Profiling Interactive Analysis databases. These datasets were used to identify significantly differentially expressed genes (DEGs) in LUSC. A protein-protein interaction network of the DEGs was constructed followed by Gene Ontology, Kyoto Encyclopedia of Genes and Genomes and overall survival analyses of the DEGs. A total of 37 DEGs between LUSC and normal tissues were identified, including 26 downregulated genes and 11 upregulated genes. Biological Process enrichment analysis revealed that the DEGs were mainly enriched in ‘cell adhesion’, ‘cell-matrix adhesion’, ‘anatomical structure morphogenesis’, ‘ECM-receptor interaction’ and ‘focal adhesion’. Overall survival analysis demonstrated that transcription factor 21, α-2-macroglobulin, acyl-CoA synthetase long chain family member 5, integrin subunit β8, meiotic nuclear divisions 1 and secretoglobin family 1A member 1 were significantly associated with the occurrence and development of lung cancer, and these genes were selected as hub genes. The results obtained in the present study may aid the elucidation of the molecular mechanisms involved in the development of LUSC and may provide potential targets for LUSC treatment.
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Affiliation(s)
- Nana Zhang
- Department of Respiration, Second Hospital of Lanzhou University, Lanzhou, Gansu 730000, P.R. China
| | - Hong Wang
- Department of Respiration, Second Hospital of Lanzhou University, Lanzhou, Gansu 730000, P.R. China
| | - Qiqi Xie
- Department of Orthopaedics, Second Hospital of Lanzhou University, Lanzhou, Gansu 730000, P.R. China
| | - Hua Cao
- Department of Respiration, Second Hospital of Lanzhou University, Lanzhou, Gansu 730000, P.R. China
| | - Fanqi Wu
- Department of Respiration, Second Hospital of Lanzhou University, Lanzhou, Gansu 730000, P.R. China
| | - Dan Bei Di Wu
- Department of Respiration, Second Hospital of Lanzhou University, Lanzhou, Gansu 730000, P.R. China
| | - Yixin Wan
- Department of Respiration, Second Hospital of Lanzhou University, Lanzhou, Gansu 730000, P.R. China
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33
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Zolotovskaia MA, Sorokin MI, Emelianova AA, Borisov NM, Kuzmin DV, Borger P, Garazha AV, Buzdin AA. Pathway Based Analysis of Mutation Data Is Efficient for Scoring Target Cancer Drugs. Front Pharmacol 2019; 10:1. [PMID: 30728774 PMCID: PMC6351482 DOI: 10.3389/fphar.2019.00001] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 01/03/2019] [Indexed: 12/20/2022] Open
Abstract
Despite the significant achievements in chemotherapy, cancer remains one of the leading causes of death. Target therapy revolutionized this field, but efficiencies of target drugs show dramatic variation among individual patients. Personalization of target therapies remains, therefore, a challenge in oncology. Here, we proposed molecular pathway-based algorithm for scoring of target drugs using high throughput mutation data to personalize their clinical efficacies. This algorithm was validated on 3,800 exome mutation profiles from The Cancer Genome Atlas (TCGA) project for 128 target drugs. The output values termed Mutational Drug Scores (MDS) showed positive correlation with the published drug efficiencies in clinical trials. We also used MDS approach to simulate all known protein coding genes as the putative drug targets. The model used was built on the basis of 18,273 mutation profiles from COSMIC database for eight cancer types. We found that the MDS algorithm-predicted hits frequently coincide with those already used as targets of the existing cancer drugs, but several novel candidates can be considered promising for further developments. Our results evidence that the MDS is applicable to ranking of anticancer drugs and can be applied for the identification of novel molecular targets.
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Affiliation(s)
- Marianna A Zolotovskaia
- Oncobox Ltd., Moscow, Russia.,Department of Oncology, Hematology and Radiotherapy of Pediatric Faculty, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Maxim I Sorokin
- The Laboratory of Clinical Bioinformatics, IM Sechenov First Moscow State Medical University, Moscow, Russia.,Omicsway Corp., Walnut, CA, United States.,Science-Educational Center Department, M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Anna A Emelianova
- Science-Educational Center Department, M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Nikolay M Borisov
- The Laboratory of Clinical Bioinformatics, IM Sechenov First Moscow State Medical University, Moscow, Russia.,Omicsway Corp., Walnut, CA, United States
| | - Denis V Kuzmin
- Science-Educational Center Department, M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Pieter Borger
- Laboratory of the Swiss Hepato-Pancreato-Biliary, Department of Surgery, Transplantation Center, University Hospital Zurich, Zurich, Switzerland
| | | | - Anton A Buzdin
- Oncobox Ltd., Moscow, Russia.,The Laboratory of Clinical Bioinformatics, IM Sechenov First Moscow State Medical University, Moscow, Russia.,Science-Educational Center Department, M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
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34
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Molecular pathway activation – New type of biomarkers for tumor morphology and personalized selection of target drugs. Semin Cancer Biol 2018; 53:110-124. [DOI: 10.1016/j.semcancer.2018.06.003] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 06/19/2018] [Accepted: 06/19/2018] [Indexed: 02/06/2023]
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35
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|