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Petrizzelli F, Biagini T, Bianco SD, Liorni N, Napoli A, Castellana S, Mazza T. Connecting the dots: A practical evaluation of web-tools for describing protein dynamics as networks. FRONTIERS IN BIOINFORMATICS 2022; 2:1045368. [PMID: 36438625 PMCID: PMC9689706 DOI: 10.3389/fbinf.2022.1045368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 10/05/2022] [Indexed: 01/25/2023] Open
Abstract
Protein Structure Networks (PSNs) are a well-known mathematical model for estimation and analysis of the three-dimensional protein structure. Investigating the topological architecture of PSNs may help identify the crucial amino acid residues for protein stability and protein-protein interactions, as well as deduce any possible mutational effects. But because proteins go through conformational changes to give rise to essential biological functions, this has to be done dynamically over time. The most effective method to describe protein dynamics is molecular dynamics simulation, with the most popular software programs for manipulating simulations to infer interaction networks being RING, MD-TASK, and NAPS. Here, we compare the computational approaches used by these three tools-all of which are accessible as web servers-to understand the pathogenicity of missense mutations and talk about their potential applications as well as their advantages and disadvantages.
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Affiliation(s)
- Francesco Petrizzelli
- Bioinformatics Laboratory, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Tommaso Biagini
- Bioinformatics Laboratory, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Salvatore Daniele Bianco
- Bioinformatics Laboratory, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy,Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Niccolò Liorni
- Bioinformatics Laboratory, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy,Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Alessandro Napoli
- Bioinformatics Laboratory, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Stefano Castellana
- Bioinformatics Laboratory, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Tommaso Mazza
- Bioinformatics Laboratory, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy,*Correspondence: Tommaso Mazza,
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Olgun G, Gopalan V, Hannenhalli S. miRSCAPE - inferring miRNA expression from scRNA-seq data. iScience 2022; 25:104962. [PMID: 36060076 PMCID: PMC9437856 DOI: 10.1016/j.isci.2022.104962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 05/09/2022] [Accepted: 08/12/2022] [Indexed: 11/27/2022] Open
Abstract
Our understanding of miRNA activity at cellular resolution is thwarted by the inability of standard scRNA-seq protocols to capture miRNAs. We introduce a novel tool, miRSCAPE, to infer miRNA expression in a sample from its RNA-seq profile. We establish miRSCAPE's accuracy in 10 tumor and normal cohorts demonstrating its superiority over alternatives. miRSCAPE accurately infers cell type-specific miRNA activities (predicted versus observed fold-difference correlation ∼0.81) in two independent scRNA-seq datasets. We apply miRSCAPE to infer miRNA activities in scRNA clusters in pancreatic and lung adenocarcinomas, as well as in 56 cell types in the human cell landscape (HCL). In pancreatic and breast cancer scRNA-seq data, miRSCAPE recapitulates miRNAs associated with stemness and epithelial-mesenchymal transition (EMT) cell states, respectively. Overall, miRSCAPE recapitulates and refines miRNA biology at cellular resolution. miRSCAPE is freely available and is easily applicable to scRNA-seq data to infer miRNA activities at cellular resolution.
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Affiliation(s)
- Gulden Olgun
- Cancer Data Science Lab, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Vishaka Gopalan
- Cancer Data Science Lab, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sridhar Hannenhalli
- Cancer Data Science Lab, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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Song Z, Wang J. LncRNA ASMTL-AS1/microRNA-1270 differentiate prognostic groups in gastric cancer and influence cell proliferation, migration and invasion. Bioengineered 2022; 13:1507-1517. [PMID: 34986743 PMCID: PMC8805870 DOI: 10.1080/21655979.2021.2021063] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The objective of this study was to determine the expression levels of ASMTL-AS1 and miR-1270 in gastric cancer, and to explore whether ASMTL-AS1 and miR-1270 is associated with cancer prognosis and progression or not. ASMTL-AS1 and miR-1270 expression were quantified in gastric cancer tissues and adjacent normal tissues (n = 167) and cell lines. The potential of ASMTL-AS1 and miR-1270 as prognostic biomarkers was evaluated by the receiver operating characteristic (ROC) curve, Kaplan-Meier, and multivariate Cox regression analyses. The binding between ASMTL-AS1 and miR-1270 was verified by the Luciferase reporter assay and RNA pull-down assay. Functional roles of ASMTL-AS1/miR-1270 on cells were investigated in HGC-27 and NCI-N87 cells by MTS viability, Transwell migration, and Matrigel invasion assay. ASMTL-AS1 was significantly downregulated while miR-1270 was upregulated in gastric cancer tissues as compared with normal tissue and cell lines. According to the studies, ASMTL-AS1 and miR-1270 were related to unfavorable clinical parameters, such as the advanced TNM stage. Downregulated ASMTL-AS1 and upregulated miR-1270 were associated with reduced 5-year overall survival. Functional studies suggested that ASMTL-AS1 inhibits proliferation, migration, and invasion of HGC-27 and NCI-N87 cells by regulation of miR-1270. In summary, ASMTL-AS1 and miR-1270 are associated with poor prognosis of patients with gastric cancer. ASMTL-AS1 inhibited gastric cancer progression by regulating miR-1270. Therefore, ASMTL-AS1/miR-1270 may be a potential prognostic biomarker and novel strategy for gastric cancer targeted therapy.
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Affiliation(s)
- Zhenhe Song
- Department of Gastroenterology, Weihai Municipal Hospital, Cheeloo College of Medicine, Shandong University, Weihai, Shandong, China
| | - Jian Wang
- Department of Laboratory, Yidu Central Hospital of Weifang, Weifang, Shandong, China
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Nguyen L, Schilling D, Dobiasch S, Raulefs S, Santiago Franco M, Buschmann D, Pfaffl MW, Schmid TE, Combs SE. The Emerging Role of miRNAs for the Radiation Treatment of Pancreatic Cancer. Cancers (Basel) 2020; 12:cancers12123703. [PMID: 33317198 PMCID: PMC7763922 DOI: 10.3390/cancers12123703] [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: 10/21/2020] [Revised: 11/17/2020] [Accepted: 12/04/2020] [Indexed: 12/11/2022] Open
Abstract
Simple Summary Pancreatic cancer is an aggressive disease with a high mortality rate. Radiotherapy is one treatment option within a multimodal therapy approach for patients with locally advanced, non-resectable pancreatic tumors. However, radiotherapy is only effective in about one-third of the patients. Therefore, biomarkers that can predict the response to radiotherapy are of utmost importance. Recently, microRNAs, small non-coding RNAs regulating gene expression, have come into focus as there is growing evidence that microRNAs could serve as diagnostic, predictive and prognostic biomarkers in various cancer entities, including pancreatic cancer. Moreover, their high stability in body fluids such as serum and plasma render them attractive candidates for non-invasive biomarkers. This article describes the role of microRNAs as suitable blood biomarkers and outlines an overview of radiation-induced microRNAs changes and the association with radioresistance in pancreatic cancer. Abstract Today, pancreatic cancer is the seventh leading cause of cancer-related deaths worldwide with a five-year overall survival rate of less than 7%. Only 15–20% of patients are eligible for curative intent surgery at the time of diagnosis. Therefore, neoadjuvant treatment regimens have been introduced in order to downsize the tumor by chemotherapy and radiotherapy. To further increase the efficacy of radiotherapy, novel molecular biomarkers are urgently needed to define the subgroup of pancreatic cancer patients who would benefit most from radiotherapy. MicroRNAs (miRNAs) could have the potential to serve as novel predictive and prognostic biomarkers in patients with pancreatic cancer. In the present article, the role of miRNAs as blood biomarkers, which are associated with either radioresistance or radiation-induced changes of miRNAs in pancreatic cancer, is discussed. Furthermore, the manuscript provides own data of miRNAs identified in a pancreatic cancer mouse model as well as radiation-induced miRNA changes in the plasma of tumor-bearing mice.
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Affiliation(s)
- Lily Nguyen
- Institute of Radiation Medicine (IRM), Department of Radiation Sciences (DRS), Helmholtz Zentrum München, 85764 Neuherberg, Germany; (L.N.); (D.S.); (S.D.); (S.R.); (M.S.F.); (T.E.S.)
- Department of Radiation Oncology, School of Medicine, Technical University of Munich (TUM), Klinikum rechts der Isar, 81675 Munich, Germany
| | - Daniela Schilling
- Institute of Radiation Medicine (IRM), Department of Radiation Sciences (DRS), Helmholtz Zentrum München, 85764 Neuherberg, Germany; (L.N.); (D.S.); (S.D.); (S.R.); (M.S.F.); (T.E.S.)
- Department of Radiation Oncology, School of Medicine, Technical University of Munich (TUM), Klinikum rechts der Isar, 81675 Munich, Germany
| | - Sophie Dobiasch
- Institute of Radiation Medicine (IRM), Department of Radiation Sciences (DRS), Helmholtz Zentrum München, 85764 Neuherberg, Germany; (L.N.); (D.S.); (S.D.); (S.R.); (M.S.F.); (T.E.S.)
- Department of Radiation Oncology, School of Medicine, Technical University of Munich (TUM), Klinikum rechts der Isar, 81675 Munich, Germany
- Deutsches Konsortium für Translationale Krebsforschung (DKTK), Partner Site Munich, 81675 Munich, Germany
| | - Susanne Raulefs
- Institute of Radiation Medicine (IRM), Department of Radiation Sciences (DRS), Helmholtz Zentrum München, 85764 Neuherberg, Germany; (L.N.); (D.S.); (S.D.); (S.R.); (M.S.F.); (T.E.S.)
- Department of Radiation Oncology, School of Medicine, Technical University of Munich (TUM), Klinikum rechts der Isar, 81675 Munich, Germany
| | - Marina Santiago Franco
- Institute of Radiation Medicine (IRM), Department of Radiation Sciences (DRS), Helmholtz Zentrum München, 85764 Neuherberg, Germany; (L.N.); (D.S.); (S.D.); (S.R.); (M.S.F.); (T.E.S.)
| | - Dominik Buschmann
- Division of Animal Physiology and Immunology, TUM School of Life Sciences Weihenstephan, Technical University of Munich (TUM), 85354 Freising, Germany; (D.B.); (M.W.P.)
| | - Michael W. Pfaffl
- Division of Animal Physiology and Immunology, TUM School of Life Sciences Weihenstephan, Technical University of Munich (TUM), 85354 Freising, Germany; (D.B.); (M.W.P.)
| | - Thomas E. Schmid
- Institute of Radiation Medicine (IRM), Department of Radiation Sciences (DRS), Helmholtz Zentrum München, 85764 Neuherberg, Germany; (L.N.); (D.S.); (S.D.); (S.R.); (M.S.F.); (T.E.S.)
- Department of Radiation Oncology, School of Medicine, Technical University of Munich (TUM), Klinikum rechts der Isar, 81675 Munich, Germany
| | - Stephanie E. Combs
- Institute of Radiation Medicine (IRM), Department of Radiation Sciences (DRS), Helmholtz Zentrum München, 85764 Neuherberg, Germany; (L.N.); (D.S.); (S.D.); (S.R.); (M.S.F.); (T.E.S.)
- Department of Radiation Oncology, School of Medicine, Technical University of Munich (TUM), Klinikum rechts der Isar, 81675 Munich, Germany
- Deutsches Konsortium für Translationale Krebsforschung (DKTK), Partner Site Munich, 81675 Munich, Germany
- Correspondence: ; Tel.: +49-89-4140-4501
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Circular RNA hsa_circRNA_0007334 is Predicted to Promote MMP7 and COL1A1 Expression by Functioning as a miRNA Sponge in Pancreatic Ductal Adenocarcinoma. JOURNAL OF ONCOLOGY 2019; 2019:7630894. [PMID: 31428151 PMCID: PMC6681607 DOI: 10.1155/2019/7630894] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 06/11/2019] [Accepted: 06/17/2019] [Indexed: 01/03/2023]
Abstract
Pancreatic cancer remains one of the leading causes of cancer-related deaths worldwide. Pancreatic ductal adenocarcinoma (PDAC) is the most common type of pancreatic tumor. Many circular RNAs (circRNAs) have proven to play vital roles in the physiological and pathological processes of tumorigenesis; however, their biogenesis in PDAC remains unclear. In this study, the expression profiles of circRNAs from 10 PDAC tissues and their paired adjacent nontumor tissues were analyzed through RNA sequencing analysis. An enrichment analysis was employed to predict the functions of the differentially expressed circRNAs. Sequence alignment information and mRNA microarray projects were used to predict the RNA regulatory network. The knockdown of circRNAs by small interfering RNAs followed by wound healing and western blot assays was used to confirm their functions in a PDAC cell line. A total of 278 circRNAs were identified as differentially expressed in PDAC tissue. Of these, we found that hsa_circRNA_0007334 was significantly upregulated and may serve as a competing endogenous RNA to regulate matrix metallopeptidase 7 (MMP7) and collagen type I alpha 1 chain (COL1A1) by the competitive adsorption of hsa-miR-144-3p and hsa-miR-577 to enhance the expression and functions of MMP7 and COL1A1 in PDAC. In vitro experiments confirmed these results. The present study is the first to propose two regulatory pathways in PDAC: hsa_circRNA_0007334–hsa-miR-144-3p–MMP7 and hsa_circRNA_0007334–hsa-miR-577–COL1A1.
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Felix TF, Lopez Lapa RM, de Carvalho M, Bertoni N, Tokar T, Oliveira RA, M. Rodrigues MA, Hasimoto CN, Oliveira WK, Pelafsky L, Spadella CT, Llanos JC, F. Silva G, Lam WL, Rogatto SR, Amorim LS, Drigo SA, Carvalho RF, Reis PP. MicroRNA modulated networks of adaptive and innate immune response in pancreatic ductal adenocarcinoma. PLoS One 2019; 14:e0217421. [PMID: 31150430 PMCID: PMC6544344 DOI: 10.1371/journal.pone.0217421] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 05/10/2019] [Indexed: 12/14/2022] Open
Abstract
Despite progress in treatment strategies, only ~24% of pancreatic ductal adenocarcinoma (PDAC) patients survive >1 year. Our goal was to elucidate deregulated pathways modulated by microRNAs (miRNAs) in PDAC and Vater ampulla (AMP) cancers. Global miRNA expression was identified in 19 PDAC, 6 AMP and 25 paired, histologically normal pancreatic tissues using the GeneChip 4.0 miRNA arrays. Computational approaches were used for miRNA target prediction/identification of miRNA-regulated pathways. Target gene expression was validated in 178 pancreatic cancer and 4 pancreatic normal tissues from The Cancer Genome Atlas (TCGA). 20 miRNAs were significantly deregulated (FC≥2 and p<0.05) (15 down- and 5 up-regulated) in PDAC. miR-216 family (miR-216a-3p, miR-216a-5p, miR-216b-3p and miR-216b-5p) was consistently down-regulated in PDAC. miRNA-modulated pathways are associated with innate and adaptive immune system responses in PDAC. AMP cancers showed 8 down- and 1 up-regulated miRNAs (FDR p<0.05). Most enriched pathways (p<0.01) were RAS and Nerve Growth Factor signaling. PDAC and AMP display different global miRNA expression profiles and miRNA regulated networks/tumorigenesis pathways. The immune response was enriched in PDAC, suggesting the existence of immune checkpoint pathways more relevant to PDAC than AMP.
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Affiliation(s)
- Tainara F. Felix
- Department of Surgery and Orthopedics, Faculty of Medicine, São Paulo State University (UNESP), Botucatu, SP, Brazil
- Experimental Research Unity (UNIPEX), Faculty of Medicine, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Rainer M. Lopez Lapa
- Experimental Research Unity (UNIPEX), Faculty of Medicine, São Paulo State University (UNESP), Botucatu, SP, Brazil
- Department of Genetics, Institute of Biosciences, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Márcio de Carvalho
- Department of Veterinary Clinic, School of Veterinary Medicine and Animal Science, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Natália Bertoni
- Department of Surgery and Orthopedics, Faculty of Medicine, São Paulo State University (UNESP), Botucatu, SP, Brazil
- Experimental Research Unity (UNIPEX), Faculty of Medicine, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Tomas Tokar
- Krembil Research Institute, University Health Network, Toronto, ON, Canada
| | - Rogério A. Oliveira
- Department of Biostatistics, Institute of Biosciences, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Maria A. M. Rodrigues
- Department of Pathology, Faculty of Medicine, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Cláudia N. Hasimoto
- Department of Surgery and Orthopedics, Faculty of Medicine, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Walmar K. Oliveira
- Department of Surgery and Orthopedics, Faculty of Medicine, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Leonardo Pelafsky
- Department of Surgery and Orthopedics, Faculty of Medicine, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - César T. Spadella
- Department of Surgery and Orthopedics, Faculty of Medicine, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Juan C. Llanos
- Department of Surgery and Orthopedics, Faculty of Medicine, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Giovanni F. Silva
- Department of Clinics and Gastroenterology, Faculty of Medicine, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Wan L. Lam
- Genetics Unity, Integrative Oncology, British Columbia Cancer Center, Vancouver, BC, Canada
| | - Silvia Regina Rogatto
- Department of Clinical Genetics, Vejle Hospital, Institute of Regional Health Research, University of Southern Denmark, Denmark, DK
| | | | - Sandra A. Drigo
- Department of Surgery and Orthopedics, Faculty of Medicine, São Paulo State University (UNESP), Botucatu, SP, Brazil
- Experimental Research Unity (UNIPEX), Faculty of Medicine, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Robson F. Carvalho
- Department of Morphology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Patricia P. Reis
- Department of Surgery and Orthopedics, Faculty of Medicine, São Paulo State University (UNESP), Botucatu, SP, Brazil
- Experimental Research Unity (UNIPEX), Faculty of Medicine, São Paulo State University (UNESP), Botucatu, SP, Brazil
- * E-mail:
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