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Lambroia L, Conca Dioguardi CM, Puccio S, Pansa A, Alvisi G, Basso G, Cibella J, Colombo FS, Marano S, Basato S, Alfieri R, Giudici S, Castoro C, Peano C. Definition of a Multi-Omics Signature for Esophageal Adenocarcinoma Prognosis Prediction. Cancers (Basel) 2024; 16:2748. [PMID: 39123475 PMCID: PMC11311406 DOI: 10.3390/cancers16152748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2024] [Revised: 07/29/2024] [Accepted: 07/31/2024] [Indexed: 08/12/2024] Open
Abstract
Esophageal cancer is a highly lethal malignancy, representing 5% of all cancer-related deaths. The two main subtypes are esophageal squamous cell carcinoma (ESCC) and esophageal adenocarcinoma (EAC). While most research has focused on ESCC, few studies have analyzed EAC for transcriptional signatures linked to diagnosis or prognosis. In this study, we utilized single-cell RNA sequencing and bulk RNA sequencing to identify specific immune cell types that contribute to anti-tumor responses, as well as differentially expressed genes (DEGs). We have characterized transcriptional signatures, validated against a wide cohort of TCGA patients, that are capable of predicting clinical outcomes and the prognosis of EAC post-surgery with efficacy comparable to the currently accepted prognostic factors. In conclusion, our findings provide insights into the immune landscape and therapeutic targets of EAC, proposing novel immunological biomarkers for predicting prognosis, aiding in patient stratification for post-surgical outcomes, follow-up, and personalized adjuvant therapy decisions.
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Affiliation(s)
- Luca Lambroia
- Humanitas Research Hospital-IRCCS, 20072 Rozzano, Italy;
| | | | - Simone Puccio
- Institute of Genetic and Biomedical Research, National Research Council, UoS of Milan, 20072 Milan, Italy;
- Laboratory of Translational Immunology and Humanitas Flow Cytometry Core, Humanitas Research Hospital, 20072 Milan, Italy (F.S.C.)
| | - Andrea Pansa
- Upper Gastrointestinal Surgery Unit, IRCCS Humanitas Research Hospital, 20089 Milan, Italy; (A.P.)
| | - Giorgia Alvisi
- Laboratory of Translational Immunology and Humanitas Flow Cytometry Core, Humanitas Research Hospital, 20072 Milan, Italy (F.S.C.)
| | - Gianluca Basso
- Genomic Unit, Humanitas Research Hospital, 20072 Milan, Italy
| | - Javier Cibella
- Human Technopole, 20157 Milan, Italy; (C.M.C.D.); (J.C.)
| | - Federico Simone Colombo
- Laboratory of Translational Immunology and Humanitas Flow Cytometry Core, Humanitas Research Hospital, 20072 Milan, Italy (F.S.C.)
| | - Salvatore Marano
- Upper Gastrointestinal Surgery Unit, IRCCS Humanitas Research Hospital, 20089 Milan, Italy; (A.P.)
| | - Silvia Basato
- Upper Gastrointestinal Surgery Unit, IRCCS Humanitas Research Hospital, 20089 Milan, Italy; (A.P.)
| | - Rita Alfieri
- Upper Gastrointestinal Surgery Unit, IRCCS Humanitas Research Hospital, 20089 Milan, Italy; (A.P.)
| | - Simone Giudici
- Upper Gastrointestinal Surgery Unit, IRCCS Humanitas Research Hospital, 20089 Milan, Italy; (A.P.)
| | - Carlo Castoro
- Upper Gastrointestinal Surgery Unit, IRCCS Humanitas Research Hospital, 20089 Milan, Italy; (A.P.)
- Department of Biomedical Sciences, Humanitas University, 20072 Milan, Italy
| | - Clelia Peano
- Human Technopole, 20157 Milan, Italy; (C.M.C.D.); (J.C.)
- Institute of Genetic and Biomedical Research, National Research Council, UoS of Milan, 20072 Milan, Italy;
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Brejová B, Gagie T, Herencsárová E, Vinař T. Maximum-scoring path sets on pangenome graphs of constant treewidth. FRONTIERS IN BIOINFORMATICS 2024; 4:1391086. [PMID: 39011297 PMCID: PMC11246863 DOI: 10.3389/fbinf.2024.1391086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Accepted: 06/03/2024] [Indexed: 07/17/2024] Open
Abstract
We generalize a problem of finding maximum-scoring segment sets, previously studied by Csűrös (IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2004, 1, 139-150), from sequences to graphs. Namely, given a vertex-weighted graph G and a non-negative startup penalty c, we can find a set of vertex-disjoint paths in G with maximum total score when each path's score is its vertices' total weight minus c. We call this new problem maximum-scoring path sets (MSPS). We present an algorithm that has a linear-time complexity for graphs with a constant treewidth. Generalization from sequences to graphs allows the algorithm to be used on pangenome graphs representing several related genomes and can be seen as a common abstraction for several biological problems on pangenomes, including searching for CpG islands, ChIP-seq data analysis, analysis of region enrichment for functional elements, or simple chaining problems.
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Affiliation(s)
- Broňa Brejová
- Department of Computer Science, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Bratislava, Slovakia
| | - Travis Gagie
- Faculty of Computer Science, Dalhousie University, Halifax, NS, Canada
| | - Eva Herencsárová
- Department of Computer Science, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Bratislava, Slovakia
| | - Tomáš Vinař
- Department of Applied Informatics, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Bratislava, Slovakia
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Kurmyshkina OV, Dobrynin PV, Kovchur PI, Volkova TO. Sequencing-based transcriptome analysis reveals diversification of immune response- and angiogenesis-related expression patterns of early-stage cervical carcinoma as compared with high-grade CIN. Front Immunol 2023; 14:1215607. [PMID: 37731500 PMCID: PMC10507244 DOI: 10.3389/fimmu.2023.1215607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 07/31/2023] [Indexed: 09/22/2023] Open
Abstract
Background Molecular diversity of virus-associated cervical cancer remains a relatively underexplored issue, and interrelations of immunologic and angiogenic features during the establishment of a particular landscape of the cervical cancer microenvironment are not well-characterized, especially for its earliest clinical stages, although this may provide insight into the mechanisms behind the differences in tumor aggressiveness, treatment responsiveness and prognosis. In this research, we were aimed at identifying transcriptomic landscapes of early-stage cervical carcinoma that differ substantially in their immune-related characteristics, patterns of signaling pathways and composition of the microenvironment in comparison with immediate precursor (intraepithelial) lesions. Methods We performed the Illumina platform-based RNA sequencing using a panel of fresh tissue samples that included human papillomavirus-positive cervical intraepithelial neoplastic lesions (CIN), invasive squamous carcinoma of the cervix of FIGO IA1-IIB stages, and morphologically normal epithelium. The derived transcriptomic profiles were bioinformatically analyzed and compared by patterns of signaling pathway activation, distribution of tumor-infiltrating cell populations, and genomic regions involved. Result According to hierarchical cluster analysis of the whole-transcriptome profiles, tissue samples were distributed between three groups, or gene expression patterns (the one comprising most pre-cancer cases and the other two encompassing mostly early-stage invasive cancer cases). Differentially expressed genes were retrieved in each intergroup pairwise comparison followed by Gene Ontology analysis. Gene set enrichment analysis of the two groups of tumor samples in comparison with the CIN group identified substantial differences in immunological and angiogenic properties between tumorous groups suggesting the development of different molecular phenotypes. Cell composition analysis confirmed the diverse changes in the abundancies of immune and non-immune populations and, accordingly, different impacts of the immune and stromal compartments on the tumor microenvironment in these two groups of tumors compared to CIN. Positional gene expression analysis demonstrated that the identified transcriptomic differences were linked to different chromosomal regions and co-localized with particular gene families implicated in immune regulation, inflammation, cell differentiation, and tumor invasion. Conclusions Overall, detection of different transcriptomic patterns of invasive cervical carcinoma at its earliest stages supports the diverse impacts of immune response- and angiogenesis-related mechanisms on the onset of tumor invasion and progression. This may provide new options for broadening the applicability and increasing the efficiency of target anti-angiogenic and immune-based therapy of virus-associated cervical carcinoma.
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Affiliation(s)
- Olga V. Kurmyshkina
- Laboratory of Molecular Genetics of Innate Immunity, Institute of Medicine, Petrozavodsk State University, Petrozavodsk, Russia
| | - Pavel V. Dobrynin
- Human Genetics Laboratory, Vavilov Institute of General Genetics of Russian Academy of Sciences, Moscow, Russia
| | - Pavel I. Kovchur
- Department of Hospital Surgery, Oncology, Urology, Institute of Medicine, Petrozavodsk State University, Petrozavodsk, Russia
- Hospital Admitting Department, The Republican Oncological Dispensary, Petrozavodsk, Russia
| | - Tatyana O. Volkova
- Department of Biomedical Chemistry, Immunology and Laboratory Diagnostics, Institute of Medicine, Petrozavodsk State University, Petrozavodsk, Russia
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4
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3D microenvironment attenuates simulated microgravity-mediated changes in T cell transcriptome. Cell Mol Life Sci 2022; 79:508. [PMID: 36063234 DOI: 10.1007/s00018-022-04531-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 08/05/2022] [Accepted: 08/17/2022] [Indexed: 11/03/2022]
Abstract
Human space travel and exploration are of interest to both the industrial and scientific community. However, there are many adverse effects of spaceflight on human physiology. In particular, there is a lack of understanding of the extent to which microgravity affects the immune system. T cells, key players of the adaptive immune system and long-term immunity, are present not only in blood circulation but also reside within the tissue. As of yet, studies investigating the effects of microgravity on T cells are limited to peripheral blood or traditional 2D cell culture that recapitulates circulating blood. To better mimic interstitial tissue, 3D cell culture has been well established for physiologically and pathologically relevant models. In this work, we utilize 2D cell culture and 3D collagen matrices to gain an understanding of how simulated microgravity, using a random positioning machine, affects both circulating and tissue-resident T cells. T cells were studied in both resting and activated stages. We found that 3D cell culture attenuates the effects of simulated microgravity on the T cells transcriptome and nuclear irregularities compared to 2D cell culture. Interestingly, simulated microgravity appears to have less effect on activated T cells compared to those in the resting stage. Overall, our work provides novel insights into the effects of simulated microgravity on circulating and tissue-resident T cells which could provide benefits for the health of space travellers.
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Naidoo M, Jones L, Conboy B, Hamarneh W, D’Souza D, Anthony K, Machado LR. Duchenne muscular dystrophy gene expression is an independent prognostic marker for IDH mutant low-grade glioma. Sci Rep 2022; 12:3200. [PMID: 35217778 PMCID: PMC8881458 DOI: 10.1038/s41598-022-07223-2] [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: 07/20/2021] [Accepted: 02/04/2022] [Indexed: 11/18/2022] Open
Abstract
Alterations in the expression of the Duchenne muscular dystrophy (DMD) gene have been associated with the development, progression and survival outcomes of numerous cancers including tumours of the central nervous system. We undertook a detailed bioinformatic analysis of low-grade glioma (LGG) bulk RNAseq data to characterise the association between DMD expression and LGG survival outcomes. High DMD expression was significantly associated with poor survival in LGG with a difference in median overall survival between high and low DMD groups of over 7 years (P = < 0.0001). In a multivariate model, DMD expression remained significant (P = 0.02) and was an independent prognostic marker for LGG. The effect of DMD expression on overall survival was only apparent in isocitrate dehydrogenase (IDH) mutant cases where non-1p/19q co-deleted LGG patients could be further stratified into high/low DMD groups. Patients in the high DMD group had a median overall survival time almost halve that of the low DMD group. The expression of the individual DMD gene products Dp71, Dp71ab and Dp427m were also significantly associated with overall survival in LGG which have differential biological effects relevant to the pathogenesis of LGG. Differential gene expression and pathway analysis identifies dysregulated biological processes relating to ribosome biogenesis, synaptic signalling, neurodevelopment, morphogenesis and immune pathways. Genes spanning almost the entirety of chromosome 1p are upregulated in patients with high overall DMD, Dp71 and Dp427m expression which worsens survival outcomes for these patients. We confirmed dystrophin protein is variably expressed in LGG tumour tissue by immunohistochemistry and, overall, demonstrate that DMD expression has potential utility as an independent prognostic marker which can further stratify IDH mutant LGG to identify those at risk of poor survival. This knowledge may improve risk stratification and management of LGG.
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Affiliation(s)
- Michael Naidoo
- grid.44870.3fCentre for Physical Activity and Life Sciences, University of Northampton, University Drive, Northampton, NN1 5PH UK
| | - Leanne Jones
- grid.44870.3fCentre for Physical Activity and Life Sciences, University of Northampton, University Drive, Northampton, NN1 5PH UK
| | - Benjamin Conboy
- grid.44870.3fCentre for Physical Activity and Life Sciences, University of Northampton, University Drive, Northampton, NN1 5PH UK
| | - Wael Hamarneh
- grid.500651.7Northampton General Hospital NHS Trust, Northampton, NN1 5BD UK
| | - Darwin D’Souza
- grid.59734.3c0000 0001 0670 2351Icahn School of Medicine at Mount Sinai, New York City, USA
| | - Karen Anthony
- grid.44870.3fCentre for Physical Activity and Life Sciences, University of Northampton, University Drive, Northampton, NN1 5PH UK
| | - Lee R. Machado
- grid.44870.3fCentre for Physical Activity and Life Sciences, University of Northampton, University Drive, Northampton, NN1 5PH UK ,grid.9918.90000 0004 1936 8411Department of Genetics and Genome Science, University of Leicester, Leicester, LE1 7RH UK
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O’Reilly J, Ono‐Moore KD, Chintapalli SV, Rutkowsky JM, Tolentino T, Lloyd KCK, Olfert IM, Adams SH. Sex differences in skeletal muscle revealed through fiber type, capillarity, and transcriptomics profiling in mice. Physiol Rep 2021; 9:e15031. [PMID: 34545692 PMCID: PMC8453262 DOI: 10.14814/phy2.15031] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 08/19/2021] [Indexed: 12/03/2022] Open
Abstract
Skeletal muscle anatomy and physiology are sexually dimorphic but molecular underpinnings and muscle-specificity are not well-established. Variances in metabolic health, fitness level, sedentary behavior, genetics, and age make it difficult to discern inherent sex effects in humans. Therefore, mice under well-controlled conditions were used to determine female and male (n = 19/sex) skeletal muscle fiber type/size and capillarity in superficial and deep gastrocnemius (GA-s, GA-d), soleus (SOL), extensor digitorum longus (EDL), and plantaris (PLT), and transcriptome patterns were also determined (GA, SOL). Summed muscle weight strongly correlated with lean body mass (r2 = 0.67, p < 0.0001, both sexes). Other phenotypes were muscle-specific: e.g., capillarity (higher density, male GA-s), myofiber size (higher, male EDL), and fiber type (higher, lower type I and type II prevalences, respectively, in female SOL). There were broad differences in transcriptomics, with >6000 (GA) and >4000 (SOL) mRNAs differentially-expressed by sex; only a minority of these were shared across GA and SOL. Pathway analyses revealed differences in ribosome biology, transcription, and RNA processing. Curation of sexually dimorphic muscle transcripts shared in GA and SOL, and literature datasets from mice and humans, identified 11 genes that we propose are canonical to innate sex differences in muscle: Xist, Kdm6a, Grb10, Oas2, Rps4x (higher, females) and Ddx3y, Kdm5d, Irx3, Wwp1, Aldh1a1, Cd24a (higher, males). These genes and those with the highest "sex-biased" expression in our study do not contain estrogen-response elements (exception, Greb1), but a subset are proposed to be regulated through androgen response elements. We hypothesize that innate muscle sexual dimorphism in mice and humans is triggered and then maintained by classic X inactivation (Xist, females) and Y activation (Ddx3y, males), with coincident engagement of X encoded (Kdm6a) and Y encoded (Kdm5d) demethylase epigenetic regulators that are complemented by modulation at some regions of the genome that respond to androgen.
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Affiliation(s)
- Juliana O’Reilly
- Division of Exercise PhysiologyWest Virginia University School of MedicineMorgantownWest VirginiaUSA
| | | | - Sree V. Chintapalli
- Arkansas Children’s Nutrition CenterLittle RockArkansasUSA
- Department of PediatricsUniversity of Arkansas for Medical SciencesLittle RockArkansasUSA
| | - Jennifer M. Rutkowsky
- Department of Molecular Biosciences, University of California Davis School of Veterinary MedicineDavisCaliforniaUSA
- Mouse Metabolic Phenotyping CenterUniversity of CaliforniaDavisCaliforniaUSA
| | - Todd Tolentino
- Mouse Metabolic Phenotyping CenterUniversity of CaliforniaDavisCaliforniaUSA
- Mouse Biology ProgramUniversity of CaliforniaDavisCaliforniaUSA
| | - K. C. Kent Lloyd
- Mouse Metabolic Phenotyping CenterUniversity of CaliforniaDavisCaliforniaUSA
- Mouse Biology ProgramUniversity of CaliforniaDavisCaliforniaUSA
- Department of SurgeryUniversity of California Davis School of MedicineSacramentoCaliforniaUSA
| | - I. Mark Olfert
- Division of Exercise PhysiologyWest Virginia University School of MedicineMorgantownWest VirginiaUSA
| | - Sean H. Adams
- Department of SurgeryUniversity of California Davis School of MedicineSacramentoCaliforniaUSA
- Center for Alimentary and Metabolic ScienceUniversity of California Davis School of MedicineSacramentoCaliforniaUSA
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Li M, Wu W, Deng S, Shao Z, Jin X. TRAIP modulates the IGFBP3/AKT pathway to enhance the invasion and proliferation of osteosarcoma by promoting KANK1 degradation. Cell Death Dis 2021; 12:767. [PMID: 34349117 PMCID: PMC8339131 DOI: 10.1038/s41419-021-04057-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/21/2021] [Accepted: 07/21/2021] [Indexed: 01/03/2023]
Abstract
Osteosarcoma is one of the most common primary malignancies in bones and is characterized by high metastatic rates. Circulating tumor cells (CTCs) derived from solid tumors can give rise to metastatic lesions, increasing the risk of death in patients with cancer. Here, we used bioinformatics tools to compare the gene expression between CTCs and metastatic lesions in osteosarcoma to identify novel molecular mechanisms underlying osteosarcoma metastasis. We identified TRAIP as a key differentially expressed gene with prognostic significance in osteosarcoma. We demonstrated that TRAIP regulated the proliferation and invasion of osteosarcoma cells. In addition, we found that TRAIP promoted KANK1 polyubiquitination and subsequent degradation, downregulating IGFBP3 and activating the AKT pathway in osteosarcoma cells. These results support the critical role of the TRAIP/KANK1/IGFBP3/AKT signaling axis in osteosarcoma progression and suggest that TRAIP may represent a promising therapeutic target for osteosarcoma.
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Affiliation(s)
- Mi Li
- Department of Orthopedics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wei Wu
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Sisi Deng
- Cancer center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zengwu Shao
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Xin Jin
- Department of Urology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.
- Uro-Oncology Institute of Central South University, Changsha, Hunan, China.
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8
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Liang Z, Zhang Y, Chen Q, Hao J, Wang H, Li Y, Yan Y. Analysis of MCM Proteins' Role as a Potential Target of Statins in Patients with Acute Type A Aortic Dissection through Bioinformatics. Genes (Basel) 2021; 12:387. [PMID: 33803192 PMCID: PMC7998850 DOI: 10.3390/genes12030387] [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: 02/01/2021] [Revised: 02/27/2021] [Accepted: 03/02/2021] [Indexed: 11/18/2022] Open
Abstract
Acute aortic dissection is one of the most severe vascular diseases. The molecular mechanisms of aortic expansion and dissection are unclear. Clinical studies have found that statins play a protective role in aortic dissection development and therapy; however, the mechanism of statins' effects on the aorta is unknown. The Gene Expression Omnibus (GEO) dataset GSE52093, GSE2450and GSE8686 were analyzed, and genes expressed differentially between aortic dissection samples and normal samples were determined using the Networkanalyst and iDEP tools. Weight gene correlation network analysis (WGCNA), functional annotation, pathway enrichment analysis, and the analysis of the regional variations of genomic features were then performed. We found that the minichromosome maintenance proteins (MCMs), a family of proteins targeted by statins, were upregulated in dissected aortic wall tissues and play a central role in cell-cycle and mitosis regulation in aortic dissection patients. Our results indicate a potential molecular target and mechanism for statins' effects in patients with acute type A aortic dissection.
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Affiliation(s)
- Zheyong Liang
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, China; (Y.Z.); (Q.C.); (J.H.); (H.W.); (Y.L.); (Y.Y.)
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9
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Takeda H, Takai A, Iguchi E, Mishima M, Arasawa S, Kumagai K, Eso Y, Shimizu T, Takahashi K, Ueda Y, Taura K, Hatano E, Iijima H, Aoyagi H, Aizaki H, Marusawa H, Wakita T, Seno H. Oncogenic transcriptomic profile is sustained in the liver after the eradication of the hepatitis C virus. Carcinogenesis 2021; 42:672-684. [PMID: 33617626 DOI: 10.1093/carcin/bgab014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 01/12/2021] [Accepted: 02/16/2021] [Indexed: 02/07/2023] Open
Abstract
Hepatocellular carcinoma (HCC) developing after hepatitis C virus (HCV) eradication is a serious clinical concern. However, molecular basis for the hepatocarcinogenesis after sustained virologic response (SVR) remains unclear. In this study, we aimed to unveil the transcriptomic profile of post-SVR liver tissues and explore the molecules associated with post-SVR carcinogenesis. We analysed 90 RNA sequencing datasets, consisting of non-cancerous liver tissues including 20 post-SVR, 40 HCV-positive and 7 normal livers, along with Huh7 cell line specimens before and after HCV infection and eradication. Comparative analysis demonstrated that cell cycle- and mitochondrial function-associated pathways were altered only in HCV-positive non-cancerous liver tissues, whereas some cancer-related pathways were up-regulated in the non-cancerous liver tissues of both post-SVR and HCV-positive cases. The persistent up-regulation of carcinogenesis-associated gene clusters after viral clearance was reconfirmed through in vitro experiments, of which, CYR61, associated with liver fibrosis and carcinogenesis in several cancer types, was the top enriched gene and co-expressed with cell proliferation-associated gene modules. To evaluate whether this molecule could be a predictor of hepatocarcinogenesis after cure of HCV infection, we also examined 127 sera from independent HCV-positive cohorts treated with direct-acting antivirals (DAAs), including 60 post-SVR-HCC patients, and found that the elevated serum Cyr61 was significantly associated with early carcinogenesis after receiving DAA therapy. In conclusion, some oncogenic transcriptomic profiles are sustained in liver tissues after HCV eradication, which might be a molecular basis for the liver cancer development even after viral clearance. Among them, up-regulated CYR61 could be a possible biomarker for post-SVR-HCC.
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Affiliation(s)
- Haruhiko Takeda
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Atsushi Takai
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Eriko Iguchi
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masako Mishima
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Soichi Arasawa
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Ken Kumagai
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yuji Eso
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takahiro Shimizu
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Ken Takahashi
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yoshihide Ueda
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kobe University, Kobe, Japan
| | - Kojiro Taura
- Division of Hepato-Biliary-Pancreatic and Transplant Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Etsuro Hatano
- Division of Hepato-Biliary-Pancreatic and Transplant Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Department of Gastroenterological Surgery, Hyogo College of Medicine, Nishinomiya, Japan
| | - Hiroko Iijima
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Hyogo College of Medicine, Nishinomiya, Japan
| | - Haruyo Aoyagi
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hideki Aizaki
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hiroyuki Marusawa
- Department of Gastroenterology and Hepatology, Osaka Red Cross Hospital, Osaka, Japan
| | - Takaji Wakita
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hiroshi Seno
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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10
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Puccio S, Grillo G, Licciulli F, Severgnini M, Liuni S, Bicciato S, De Bellis G, Ferrari F, Peano C. WoPPER: Web server for Position Related data analysis of gene Expression in Prokaryotes. Nucleic Acids Res 2019; 45:W109-W115. [PMID: 28460063 PMCID: PMC5570229 DOI: 10.1093/nar/gkx329] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 04/14/2017] [Indexed: 12/26/2022] Open
Abstract
The structural and conformational organization of chromosomes is crucial for gene expression regulation in eukaryotes and prokaryotes as well. Up to date, gene expression data generated using either microarray or RNA-sequencing are available for many bacterial genomes. However, differential gene expression is usually investigated with methods considering each gene independently, thus not taking into account the physical localization of genes along a bacterial chromosome. Here, we present WoPPER, a web tool integrating gene expression and genomic annotations to identify differentially expressed chromosomal regions in bacteria. RNA-sequencing or microarray-based gene expression data are provided as input, along with gene annotations. The user can select genomic annotations from an internal database including 2780 bacterial strains, or provide custom genomic annotations. The analysis produces as output the lists of positionally related genes showing a coordinated trend of differential expression. Graphical representations, including a circular plot of the analyzed chromosome, allow intuitive browsing of the results. The analysis procedure is based on our previously published R-package PREDA. The release of this tool is timely and relevant for the scientific community, as WoPPER will fill an existing gap in prokaryotic gene expression data analysis and visualization tools. WoPPER is open to all users and can be reached at the following URL: https://WoPPER.ba.itb.cnr.it
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Affiliation(s)
- Simone Puccio
- Institute of Biomedical Technologies, National Research Council, Segrate, 20090, Milan, Italy
| | - Giorgio Grillo
- Institute of Biomedical Technologies, National Research Council, 70126, Bari, Italy
| | - Flavio Licciulli
- Institute of Biomedical Technologies, National Research Council, 70126, Bari, Italy
| | - Marco Severgnini
- Institute of Biomedical Technologies, National Research Council, Segrate, 20090, Milan, Italy
| | - Sabino Liuni
- Institute of Biomedical Technologies, National Research Council, 70126, Bari, Italy
| | - Silvio Bicciato
- Department of Life Sciences, Center for Genome Research, University of Modena and Reggio Emilia, 41125, Modena, Italy
| | - Gianluca De Bellis
- Institute of Biomedical Technologies, National Research Council, Segrate, 20090, Milan, Italy
| | - Francesco Ferrari
- IFOM, the FIRC Institute of Molecular Oncology, 20139, Milan, Italy.,Institute of Molecular Genetics, National Research Council, 27100, Pavia, Italy
| | - Clelia Peano
- Institute of Biomedical Technologies, National Research Council, Segrate, 20090, Milan, Italy
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Ge SX, Son EW, Yao R. iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data. BMC Bioinformatics 2018; 19:534. [PMID: 30567491 PMCID: PMC6299935 DOI: 10.1186/s12859-018-2486-6] [Citation(s) in RCA: 740] [Impact Index Per Article: 123.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 11/12/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND RNA-seq is widely used for transcriptomic profiling, but the bioinformatics analysis of resultant data can be time-consuming and challenging, especially for biologists. We aim to streamline the bioinformatic analyses of gene-level data by developing a user-friendly, interactive web application for exploratory data analysis, differential expression, and pathway analysis. RESULTS iDEP (integrated Differential Expression and Pathway analysis) seamlessly connects 63 R/Bioconductor packages, 2 web services, and comprehensive annotation and pathway databases for 220 plant and animal species. The workflow can be reproduced by downloading customized R code and related pathway files. As an example, we analyzed an RNA-Seq dataset of lung fibroblasts with Hoxa1 knockdown and revealed the possible roles of SP1 and E2F1 and their target genes, including microRNAs, in blocking G1/S transition. In another example, our analysis shows that in mouse B cells without functional p53, ionizing radiation activates the MYC pathway and its downstream genes involved in cell proliferation, ribosome biogenesis, and non-coding RNA metabolism. In wildtype B cells, radiation induces p53-mediated apoptosis and DNA repair while suppressing the target genes of MYC and E2F1, and leads to growth and cell cycle arrest. iDEP helps unveil the multifaceted functions of p53 and the possible involvement of several microRNAs such as miR-92a, miR-504, and miR-30a. In both examples, we validated known molecular pathways and generated novel, testable hypotheses. CONCLUSIONS Combining comprehensive analytic functionalities with massive annotation databases, iDEP ( http://ge-lab.org/idep/ ) enables biologists to easily translate transcriptomic and proteomic data into actionable insights.
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Affiliation(s)
- Steven Xijin Ge
- Department of Mathematics and Statistics, South Dakota State University, Box 2225, Brookings, SD 57007 USA
| | - Eun Wo Son
- Department of Mathematics and Statistics, South Dakota State University, Box 2225, Brookings, SD 57007 USA
| | - Runan Yao
- Department of Mathematics and Statistics, South Dakota State University, Box 2225, Brookings, SD 57007 USA
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Lomiento M, Mammoli F, Mazza EMC, Bicciato S, Ferrari S. Chromosome positioning in interphase nuclei of hematopoietic stem cell and myeloid precursor. Hematol Rep 2018; 10:7515. [PMID: 29721254 PMCID: PMC5907646 DOI: 10.4081/hr.2018.7515] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 01/18/2018] [Indexed: 12/16/2022] Open
Abstract
Human myelopoiesis is an intriguing biological process during which multipotent stem cells limit their differentiation potential generating precursors that evolve into terminally differentiated cells. The differentiation process is correlated with differential gene expression and changes in nuclear architecture. In interphase, chromosomes are distinct entities known as chromosome territories and they show a radial localization that could result in a constrain of inter-homologous distance. This element plays a role in genome stability and gene expression. Here, we provide the first experimental evidence of 3D chromosomal arrangement considering two steps of human normal myelopoiesis. Specifically, multicolor 3D-FISH and 3D image analysis revealed that, in both normal human hematopoietic stem cells and myelod precursors CD14-, chromosomal position is correlated with gene density. However, we observed that inter-homologue distances are totally different during differentiation. This could be associated with differential gene expression that we found comparing the two cell types. Our results disclose an unprecedented framework relevant for deciphering the genomic mechanisms at the base of normal human myelopoiesis.
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Affiliation(s)
- Mariana Lomiento
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Fabiana Mammoli
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | | | - Silvio Bicciato
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Sergio Ferrari
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
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Salati S, Zini R, Nuzzo S, Guglielmelli P, Pennucci V, Prudente Z, Ruberti S, Rontauroli S, Norfo R, Bianchi E, Bogani C, Rotunno G, Fanelli T, Mannarelli C, Rosti V, Salmoiraghi S, Pietra D, Ferrari S, Barosi G, Rambaldi A, Cazzola M, Bicciato S, Tagliafico E, Vannucchi AM, Manfredini R. Integrative analysis of copy number and gene expression data suggests novel pathogenetic mechanisms in primary myelofibrosis. Int J Cancer 2016; 138:1657-69. [PMID: 26547506 DOI: 10.1002/ijc.29920] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Revised: 10/15/2015] [Accepted: 10/23/2015] [Indexed: 12/27/2022]
Abstract
Primary myelofibrosis (PMF) is a Myeloproliferative Neoplasm (MPN) characterized by megakaryocyte hyperplasia, progressive bone marrow fibrosis, extramedullary hematopoiesis and transformation to Acute Myeloid Leukemia (AML). A number of phenotypic driver (JAK2, CALR, MPL) and additional subclonal mutations have been described in PMF, pointing to a complex genomic landscape. To discover novel genomic lesions that can contribute to disease phenotype and/or development, gene expression and copy number signals were integrated and several genomic abnormalities leading to a concordant alteration in gene expression levels were identified. In particular, copy number gain in the polyamine oxidase (PAOX) gene locus was accompanied by a coordinated transcriptional up-regulation in PMF patients. PAOX inhibition resulted in rapid cell death of PMF progenitor cells, while sparing normal cells, suggesting that PAOX inhibition could represent a therapeutic strategy to selectively target PMF cells without affecting normal hematopoietic cells' survival. Moreover, copy number loss in the chromatin modifier HMGXB4 gene correlates with a concomitant transcriptional down-regulation in PMF patients. Interestingly, silencing of HMGXB4 induces megakaryocyte differentiation, while inhibiting erythroid development, in human hematopoietic stem/progenitor cells. These results highlight a previously un-reported, yet potentially interesting role of HMGXB4 in the hematopoietic system and suggest that genomic and transcriptional imbalances of HMGXB4 could contribute to the aberrant expansion of the megakaryocytic lineage that characterizes PMF patients.
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Affiliation(s)
- Simona Salati
- Life Sciences Department University of Modena and Reggio Emilia, Centre for Regenerative Medicine, via Gottardi N.100, Modena, 41125, Italy
| | - Roberta Zini
- Life Sciences Department University of Modena and Reggio Emilia, Centre for Regenerative Medicine, via Gottardi N.100, Modena, 41125, Italy
| | - Simona Nuzzo
- Center for Genome Research, University of Modena and Reggio Emilia, via Campi N.287, Modena, 41125, Italy
| | - Paola Guglielmelli
- Department of Experimental and Clinical Medicine, Laboratorio Congiunto MMPC, University of Florence, Azienda Ospedaliera Universitaria Careggi, Florence, Italy
| | - Valentina Pennucci
- Life Sciences Department University of Modena and Reggio Emilia, Centre for Regenerative Medicine, via Gottardi N.100, Modena, 41125, Italy
| | - Zelia Prudente
- Life Sciences Department University of Modena and Reggio Emilia, Centre for Regenerative Medicine, via Gottardi N.100, Modena, 41125, Italy
| | - Samantha Ruberti
- Life Sciences Department University of Modena and Reggio Emilia, Centre for Regenerative Medicine, via Gottardi N.100, Modena, 41125, Italy
| | - Sebastiano Rontauroli
- Life Sciences Department University of Modena and Reggio Emilia, Centre for Regenerative Medicine, via Gottardi N.100, Modena, 41125, Italy
| | - Ruggiero Norfo
- Life Sciences Department University of Modena and Reggio Emilia, Centre for Regenerative Medicine, via Gottardi N.100, Modena, 41125, Italy
| | - Elisa Bianchi
- Life Sciences Department University of Modena and Reggio Emilia, Centre for Regenerative Medicine, via Gottardi N.100, Modena, 41125, Italy
| | - Costanza Bogani
- Department of Experimental and Clinical Medicine, Laboratorio Congiunto MMPC, University of Florence, Azienda Ospedaliera Universitaria Careggi, Florence, Italy
| | - Giada Rotunno
- Department of Experimental and Clinical Medicine, Laboratorio Congiunto MMPC, University of Florence, Azienda Ospedaliera Universitaria Careggi, Florence, Italy
| | - Tiziana Fanelli
- Department of Experimental and Clinical Medicine, Laboratorio Congiunto MMPC, University of Florence, Azienda Ospedaliera Universitaria Careggi, Florence, Italy
| | - Carmela Mannarelli
- Department of Experimental and Clinical Medicine, Laboratorio Congiunto MMPC, University of Florence, Azienda Ospedaliera Universitaria Careggi, Florence, Italy
| | - Vittorio Rosti
- IRCCS Policlinico S.Matteo Foundation, Center for the Study of Myelofibrosis, Pavia, Italy
| | | | - Daniela Pietra
- Department of Hematology Oncology, IRCCS Policlinico San Matteo Foundation & University of Pavia, Pavia, Italy
| | - Sergio Ferrari
- Center for Genome Research, University of Modena and Reggio Emilia, via Campi N.287, Modena, 41125, Italy
| | - Giovanni Barosi
- IRCCS Policlinico S.Matteo Foundation, Center for the Study of Myelofibrosis, Pavia, Italy
| | | | - Mario Cazzola
- Department of Hematology Oncology, IRCCS Policlinico San Matteo Foundation & University of Pavia, Pavia, Italy
| | - Silvio Bicciato
- Center for Genome Research, University of Modena and Reggio Emilia, via Campi N.287, Modena, 41125, Italy
| | - Enrico Tagliafico
- Center for Genome Research, University of Modena and Reggio Emilia, via Campi N.287, Modena, 41125, Italy
| | - Alessandro M Vannucchi
- Department of Experimental and Clinical Medicine, Laboratorio Congiunto MMPC, University of Florence, Azienda Ospedaliera Universitaria Careggi, Florence, Italy
| | - Rossella Manfredini
- Life Sciences Department University of Modena and Reggio Emilia, Centre for Regenerative Medicine, via Gottardi N.100, Modena, 41125, Italy
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Guarneri V, Dieci MV, Frassoldati A, Maiorana A, Ficarra G, Bettelli S, Tagliafico E, Bicciato S, Generali DG, Cagossi K, Bisagni G, Sarti S, Musolino A, Ellis C, Crescenzo R, Conte P. Prospective Biomarker Analysis of the Randomized CHER-LOB Study Evaluating the Dual Anti-HER2 Treatment With Trastuzumab and Lapatinib Plus Chemotherapy as Neoadjuvant Therapy for HER2-Positive Breast Cancer. Oncologist 2015; 20:1001-10. [PMID: 26245675 DOI: 10.1634/theoncologist.2015-0138] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 06/26/2015] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND The CHER-LOB randomized phase II study showed that the combination of lapatinib and trastuzumab plus chemotherapy increases the pathologic complete remission (pCR) rate compared with chemotherapy plus either trastuzumab or lapatinib. A biomarker program was prospectively planned to identify potential predictors of sensitivity to different treatments and to evaluate treatment effect on tumor biomarkers. MATERIALS AND METHODS Overall, 121 breast cancer patients positive for human epidermal growth factor 2 (HER2) were randomly assigned to neoadjuvant chemotherapy plus trastuzumab, lapatinib, or both trastuzumab and lapatinib. Pre- and post-treatment samples were centrally evaluated for HER2, p95-HER2, phosphorylated AKT (pAKT), phosphatase and tensin homolog, Ki67, apoptosis, and PIK3CA mutations. Fresh-frozen tissue samples were collected for genomic analyses. RESULTS A mutation in PIK3CA exon 20 or 9 was documented in 20% of cases. Overall, the pCR rates were similar in PIK3CA wild-type and PIK3CA-mutated patients (33.3% vs. 22.7%; p = .323). For patients receiving trastuzumab plus lapatinib, the probability of pCR was higher in PIK3CA wild-type tumors (48.4% vs. 12.5%; p = .06). Ki67, pAKT, and apoptosis measured on the residual disease were significantly reduced from baseline. The degree of Ki67 inhibition was significantly higher in patients receiving the dual anti-HER2 blockade. The integrated analysis of gene expression and copy number data demonstrated that a 50-gene signature specifically predicted the lapatinib-induced pCR. CONCLUSION PIK3CA mutations seem to identify patients who are less likely to benefit from dual anti-HER2 inhibition. p95-HER2 and markers of phosphoinositide 3-kinase pathway deregulation are not confirmed as markers of different sensitivity to trastuzumab or lapatinib. IMPLICATIONS FOR PRACTICE HER2 is currently the only validated marker to select breast cancer patients for anti-HER2 treatment; however, it is becoming evident that HER2-positive breast cancer is a heterogeneous disease. In addition, more and more new anti-HER2 treatments are becoming available. There is a need to identify markers of sensitivity to different treatments to move in the direction of treatment personalization. This study identified PIK3CA mutations as a potential predictive marker of resistance to dual anti-HER2 treatment that should be further studied in breast cancer.
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Affiliation(s)
- Valentina Guarneri
- Department of Surgery, Oncology and Gastroenterology, University of Padua, Padua, Italy; Division of Medical Oncology 2, Istituto Oncologico Veneto Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Padua, Italy; Division of Oncology, University Hospital, Ferrara, Italy; Division of Pathology, Modena University Hospital, Modena, Italy; Center for Genome Research, University of Modena and Reggio Emilia, Modena, Italy; Unità Operativa Multidisciplinare di Patologia Mammaria, Azienda Ospedaliera Istituti Ospitalieri di Cremona, Cremona, Italy; Division of Medical Oncology, Ramazzini Hospital, Carpi, Italy; Department of Medical Oncology, Azienda Ospedaliera ASMN, IRCCS, Reggio Emilia, Italy; Division of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori IRCCS, Meldola, Italy; Division of Medical Oncology, University Hospital, Parma, Italy; GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | - Maria Vittoria Dieci
- Department of Surgery, Oncology and Gastroenterology, University of Padua, Padua, Italy; Division of Medical Oncology 2, Istituto Oncologico Veneto Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Padua, Italy; Division of Oncology, University Hospital, Ferrara, Italy; Division of Pathology, Modena University Hospital, Modena, Italy; Center for Genome Research, University of Modena and Reggio Emilia, Modena, Italy; Unità Operativa Multidisciplinare di Patologia Mammaria, Azienda Ospedaliera Istituti Ospitalieri di Cremona, Cremona, Italy; Division of Medical Oncology, Ramazzini Hospital, Carpi, Italy; Department of Medical Oncology, Azienda Ospedaliera ASMN, IRCCS, Reggio Emilia, Italy; Division of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori IRCCS, Meldola, Italy; Division of Medical Oncology, University Hospital, Parma, Italy; GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | - Antonio Frassoldati
- Department of Surgery, Oncology and Gastroenterology, University of Padua, Padua, Italy; Division of Medical Oncology 2, Istituto Oncologico Veneto Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Padua, Italy; Division of Oncology, University Hospital, Ferrara, Italy; Division of Pathology, Modena University Hospital, Modena, Italy; Center for Genome Research, University of Modena and Reggio Emilia, Modena, Italy; Unità Operativa Multidisciplinare di Patologia Mammaria, Azienda Ospedaliera Istituti Ospitalieri di Cremona, Cremona, Italy; Division of Medical Oncology, Ramazzini Hospital, Carpi, Italy; Department of Medical Oncology, Azienda Ospedaliera ASMN, IRCCS, Reggio Emilia, Italy; Division of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori IRCCS, Meldola, Italy; Division of Medical Oncology, University Hospital, Parma, Italy; GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | - Antonino Maiorana
- Department of Surgery, Oncology and Gastroenterology, University of Padua, Padua, Italy; Division of Medical Oncology 2, Istituto Oncologico Veneto Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Padua, Italy; Division of Oncology, University Hospital, Ferrara, Italy; Division of Pathology, Modena University Hospital, Modena, Italy; Center for Genome Research, University of Modena and Reggio Emilia, Modena, Italy; Unità Operativa Multidisciplinare di Patologia Mammaria, Azienda Ospedaliera Istituti Ospitalieri di Cremona, Cremona, Italy; Division of Medical Oncology, Ramazzini Hospital, Carpi, Italy; Department of Medical Oncology, Azienda Ospedaliera ASMN, IRCCS, Reggio Emilia, Italy; Division of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori IRCCS, Meldola, Italy; Division of Medical Oncology, University Hospital, Parma, Italy; GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | - Guido Ficarra
- Department of Surgery, Oncology and Gastroenterology, University of Padua, Padua, Italy; Division of Medical Oncology 2, Istituto Oncologico Veneto Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Padua, Italy; Division of Oncology, University Hospital, Ferrara, Italy; Division of Pathology, Modena University Hospital, Modena, Italy; Center for Genome Research, University of Modena and Reggio Emilia, Modena, Italy; Unità Operativa Multidisciplinare di Patologia Mammaria, Azienda Ospedaliera Istituti Ospitalieri di Cremona, Cremona, Italy; Division of Medical Oncology, Ramazzini Hospital, Carpi, Italy; Department of Medical Oncology, Azienda Ospedaliera ASMN, IRCCS, Reggio Emilia, Italy; Division of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori IRCCS, Meldola, Italy; Division of Medical Oncology, University Hospital, Parma, Italy; GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | - Stefania Bettelli
- Department of Surgery, Oncology and Gastroenterology, University of Padua, Padua, Italy; Division of Medical Oncology 2, Istituto Oncologico Veneto Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Padua, Italy; Division of Oncology, University Hospital, Ferrara, Italy; Division of Pathology, Modena University Hospital, Modena, Italy; Center for Genome Research, University of Modena and Reggio Emilia, Modena, Italy; Unità Operativa Multidisciplinare di Patologia Mammaria, Azienda Ospedaliera Istituti Ospitalieri di Cremona, Cremona, Italy; Division of Medical Oncology, Ramazzini Hospital, Carpi, Italy; Department of Medical Oncology, Azienda Ospedaliera ASMN, IRCCS, Reggio Emilia, Italy; Division of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori IRCCS, Meldola, Italy; Division of Medical Oncology, University Hospital, Parma, Italy; GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | - Enrico Tagliafico
- Department of Surgery, Oncology and Gastroenterology, University of Padua, Padua, Italy; Division of Medical Oncology 2, Istituto Oncologico Veneto Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Padua, Italy; Division of Oncology, University Hospital, Ferrara, Italy; Division of Pathology, Modena University Hospital, Modena, Italy; Center for Genome Research, University of Modena and Reggio Emilia, Modena, Italy; Unità Operativa Multidisciplinare di Patologia Mammaria, Azienda Ospedaliera Istituti Ospitalieri di Cremona, Cremona, Italy; Division of Medical Oncology, Ramazzini Hospital, Carpi, Italy; Department of Medical Oncology, Azienda Ospedaliera ASMN, IRCCS, Reggio Emilia, Italy; Division of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori IRCCS, Meldola, Italy; Division of Medical Oncology, University Hospital, Parma, Italy; GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | - Silvio Bicciato
- Department of Surgery, Oncology and Gastroenterology, University of Padua, Padua, Italy; Division of Medical Oncology 2, Istituto Oncologico Veneto Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Padua, Italy; Division of Oncology, University Hospital, Ferrara, Italy; Division of Pathology, Modena University Hospital, Modena, Italy; Center for Genome Research, University of Modena and Reggio Emilia, Modena, Italy; Unità Operativa Multidisciplinare di Patologia Mammaria, Azienda Ospedaliera Istituti Ospitalieri di Cremona, Cremona, Italy; Division of Medical Oncology, Ramazzini Hospital, Carpi, Italy; Department of Medical Oncology, Azienda Ospedaliera ASMN, IRCCS, Reggio Emilia, Italy; Division of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori IRCCS, Meldola, Italy; Division of Medical Oncology, University Hospital, Parma, Italy; GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | - Daniele Giulio Generali
- Department of Surgery, Oncology and Gastroenterology, University of Padua, Padua, Italy; Division of Medical Oncology 2, Istituto Oncologico Veneto Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Padua, Italy; Division of Oncology, University Hospital, Ferrara, Italy; Division of Pathology, Modena University Hospital, Modena, Italy; Center for Genome Research, University of Modena and Reggio Emilia, Modena, Italy; Unità Operativa Multidisciplinare di Patologia Mammaria, Azienda Ospedaliera Istituti Ospitalieri di Cremona, Cremona, Italy; Division of Medical Oncology, Ramazzini Hospital, Carpi, Italy; Department of Medical Oncology, Azienda Ospedaliera ASMN, IRCCS, Reggio Emilia, Italy; Division of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori IRCCS, Meldola, Italy; Division of Medical Oncology, University Hospital, Parma, Italy; GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | - Katia Cagossi
- Department of Surgery, Oncology and Gastroenterology, University of Padua, Padua, Italy; Division of Medical Oncology 2, Istituto Oncologico Veneto Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Padua, Italy; Division of Oncology, University Hospital, Ferrara, Italy; Division of Pathology, Modena University Hospital, Modena, Italy; Center for Genome Research, University of Modena and Reggio Emilia, Modena, Italy; Unità Operativa Multidisciplinare di Patologia Mammaria, Azienda Ospedaliera Istituti Ospitalieri di Cremona, Cremona, Italy; Division of Medical Oncology, Ramazzini Hospital, Carpi, Italy; Department of Medical Oncology, Azienda Ospedaliera ASMN, IRCCS, Reggio Emilia, Italy; Division of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori IRCCS, Meldola, Italy; Division of Medical Oncology, University Hospital, Parma, Italy; GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | - Giancarlo Bisagni
- Department of Surgery, Oncology and Gastroenterology, University of Padua, Padua, Italy; Division of Medical Oncology 2, Istituto Oncologico Veneto Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Padua, Italy; Division of Oncology, University Hospital, Ferrara, Italy; Division of Pathology, Modena University Hospital, Modena, Italy; Center for Genome Research, University of Modena and Reggio Emilia, Modena, Italy; Unità Operativa Multidisciplinare di Patologia Mammaria, Azienda Ospedaliera Istituti Ospitalieri di Cremona, Cremona, Italy; Division of Medical Oncology, Ramazzini Hospital, Carpi, Italy; Department of Medical Oncology, Azienda Ospedaliera ASMN, IRCCS, Reggio Emilia, Italy; Division of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori IRCCS, Meldola, Italy; Division of Medical Oncology, University Hospital, Parma, Italy; GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | - Samanta Sarti
- Department of Surgery, Oncology and Gastroenterology, University of Padua, Padua, Italy; Division of Medical Oncology 2, Istituto Oncologico Veneto Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Padua, Italy; Division of Oncology, University Hospital, Ferrara, Italy; Division of Pathology, Modena University Hospital, Modena, Italy; Center for Genome Research, University of Modena and Reggio Emilia, Modena, Italy; Unità Operativa Multidisciplinare di Patologia Mammaria, Azienda Ospedaliera Istituti Ospitalieri di Cremona, Cremona, Italy; Division of Medical Oncology, Ramazzini Hospital, Carpi, Italy; Department of Medical Oncology, Azienda Ospedaliera ASMN, IRCCS, Reggio Emilia, Italy; Division of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori IRCCS, Meldola, Italy; Division of Medical Oncology, University Hospital, Parma, Italy; GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | - Antonino Musolino
- Department of Surgery, Oncology and Gastroenterology, University of Padua, Padua, Italy; Division of Medical Oncology 2, Istituto Oncologico Veneto Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Padua, Italy; Division of Oncology, University Hospital, Ferrara, Italy; Division of Pathology, Modena University Hospital, Modena, Italy; Center for Genome Research, University of Modena and Reggio Emilia, Modena, Italy; Unità Operativa Multidisciplinare di Patologia Mammaria, Azienda Ospedaliera Istituti Ospitalieri di Cremona, Cremona, Italy; Division of Medical Oncology, Ramazzini Hospital, Carpi, Italy; Department of Medical Oncology, Azienda Ospedaliera ASMN, IRCCS, Reggio Emilia, Italy; Division of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori IRCCS, Meldola, Italy; Division of Medical Oncology, University Hospital, Parma, Italy; GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | - Catherine Ellis
- Department of Surgery, Oncology and Gastroenterology, University of Padua, Padua, Italy; Division of Medical Oncology 2, Istituto Oncologico Veneto Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Padua, Italy; Division of Oncology, University Hospital, Ferrara, Italy; Division of Pathology, Modena University Hospital, Modena, Italy; Center for Genome Research, University of Modena and Reggio Emilia, Modena, Italy; Unità Operativa Multidisciplinare di Patologia Mammaria, Azienda Ospedaliera Istituti Ospitalieri di Cremona, Cremona, Italy; Division of Medical Oncology, Ramazzini Hospital, Carpi, Italy; Department of Medical Oncology, Azienda Ospedaliera ASMN, IRCCS, Reggio Emilia, Italy; Division of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori IRCCS, Meldola, Italy; Division of Medical Oncology, University Hospital, Parma, Italy; GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | - Rocco Crescenzo
- Department of Surgery, Oncology and Gastroenterology, University of Padua, Padua, Italy; Division of Medical Oncology 2, Istituto Oncologico Veneto Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Padua, Italy; Division of Oncology, University Hospital, Ferrara, Italy; Division of Pathology, Modena University Hospital, Modena, Italy; Center for Genome Research, University of Modena and Reggio Emilia, Modena, Italy; Unità Operativa Multidisciplinare di Patologia Mammaria, Azienda Ospedaliera Istituti Ospitalieri di Cremona, Cremona, Italy; Division of Medical Oncology, Ramazzini Hospital, Carpi, Italy; Department of Medical Oncology, Azienda Ospedaliera ASMN, IRCCS, Reggio Emilia, Italy; Division of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori IRCCS, Meldola, Italy; Division of Medical Oncology, University Hospital, Parma, Italy; GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | - PierFranco Conte
- Department of Surgery, Oncology and Gastroenterology, University of Padua, Padua, Italy; Division of Medical Oncology 2, Istituto Oncologico Veneto Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Padua, Italy; Division of Oncology, University Hospital, Ferrara, Italy; Division of Pathology, Modena University Hospital, Modena, Italy; Center for Genome Research, University of Modena and Reggio Emilia, Modena, Italy; Unità Operativa Multidisciplinare di Patologia Mammaria, Azienda Ospedaliera Istituti Ospitalieri di Cremona, Cremona, Italy; Division of Medical Oncology, Ramazzini Hospital, Carpi, Italy; Department of Medical Oncology, Azienda Ospedaliera ASMN, IRCCS, Reggio Emilia, Italy; Division of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori IRCCS, Meldola, Italy; Division of Medical Oncology, University Hospital, Parma, Italy; GlaxoSmithKline, Collegeville, Pennsylvania, USA
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Peano C, Damiano F, Forcato M, Pietrelli A, Palumbo C, Corti G, Siculella L, Fuligni F, Tagliazucchi GM, De Benedetto GE, Bicciato S, De Bellis G, Alifano P. Comparative genomics revealed key molecular targets to rapidly convert a reference rifamycin-producing bacterial strain into an overproducer by genetic engineering. Metab Eng 2014; 26:1-16. [DOI: 10.1016/j.ymben.2014.08.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Revised: 08/08/2014] [Accepted: 08/10/2014] [Indexed: 10/24/2022]
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Lahti L, Schäfer M, Klein HU, Bicciato S, Dugas M. Cancer gene prioritization by integrative analysis of mRNA expression and DNA copy number data: a comparative review. Brief Bioinform 2012; 14:27-35. [PMID: 22441573 PMCID: PMC3548603 DOI: 10.1093/bib/bbs005] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
A variety of genome-wide profiling techniques are available to investigate complementary aspects of genome structure and function. Integrative analysis of heterogeneous data sources can reveal higher level interactions that cannot be detected based on individual observations. A standard integration task in cancer studies is to identify altered genomic regions that induce changes in the expression of the associated genes based on joint analysis of genome-wide gene expression and copy number profiling measurements. In this review, we highlight common approaches to genomic data integration and provide a transparent benchmarking procedure to quantitatively compare method performances in cancer gene prioritization. Algorithms, data sets and benchmarking results are available at http://intcomp.r-forge.r-project.org.
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Affiliation(s)
- Leo Lahti
- Wageningen University, Laboratory of Microbiology, 6703HB Wageningen, Netherlands.
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Comparative genomics and transcriptional profiles of Saccharopolyspora erythraea NRRL 2338 and a classically improved erythromycin over-producing strain. Microb Cell Fact 2012; 11:32. [PMID: 22401291 PMCID: PMC3359211 DOI: 10.1186/1475-2859-11-32] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Accepted: 03/08/2012] [Indexed: 11/10/2022] Open
Abstract
Background The molecular mechanisms altered by the traditional mutation and screening approach during the improvement of antibiotic-producing microorganisms are still poorly understood although this information is essential to design rational strategies for industrial strain improvement. In this study, we applied comparative genomics to identify all genetic changes occurring during the development of an erythromycin overproducer obtained using the traditional mutate-and- screen method. Results Compared with the parental Saccharopolyspora erythraea NRRL 2338, the genome of the overproducing strain presents 117 deletion, 78 insertion and 12 transposition sites, with 71 insertion/deletion sites mapping within coding sequences (CDSs) and generating frame-shift mutations. Single nucleotide variations are present in 144 CDSs. Overall, the genomic variations affect 227 proteins of the overproducing strain and a considerable number of mutations alter genes of key enzymes in the central carbon and nitrogen metabolism and in the biosynthesis of secondary metabolites, resulting in the redirection of common precursors toward erythromycin biosynthesis. Interestingly, several mutations inactivate genes coding for proteins that play fundamental roles in basic transcription and translation machineries including the transcription anti-termination factor NusB and the transcription elongation factor Efp. These mutations, along with those affecting genes coding for pleiotropic or pathway-specific regulators, affect global expression profile as demonstrated by a comparative analysis of the parental and overproducer expression profiles. Genomic data, finally, suggest that the mutate-and-screen process might have been accelerated by mutations in DNA repair genes. Conclusions This study helps to clarify the mechanisms underlying antibiotic overproduction providing valuable information about new possible molecular targets for rationale strain improvement.
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