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Huynh J, Nhat LHT, Bao NLH, Hai HT, Thu DDA, Tram TTB, Dung VTM, Vinh DD, Ngoc NM, Donovan J, Phu NH, Van Thanh D, Thu NTA, Bang ND, Ha DTM, Nghia HDT, Van Tan L, Van LH, Thwaites G, Thuong NTT. The Ability of a 3-Gene Host Signature in Blood to Distinguish Tuberculous Meningitis From Other Brain Infections. J Infect Dis 2024; 230:e268-e278. [PMID: 38169323 PMCID: PMC11326836 DOI: 10.1093/infdis/jiad606] [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: 08/07/2023] [Revised: 12/10/2023] [Accepted: 12/29/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Tuberculous meningitis (TBM) is difficult to diagnose. We investigated whether a 3-gene host response signature in blood can distinguish TBM from other brain infections. METHODS The expression of 3 genes (dual specificity phosphatase 3 [DUSP3], guanylate-binding protein [GBP5], krupple-like factor 2 [KLF2]) was analyzed by RNA sequencing of archived whole blood from 4 cohorts of Vietnamese adults: 281 with TBM, 279 with pulmonary tuberculosis, 50 with other brain infections, and 30 healthy controls. Tuberculosis scores (combined 3-gene expression) were calculated following published methodology and discriminatory performance compared using area under a receiver operator characteristic curve (AUC). RESULTS GBP5 was upregulated in TBM compared to other brain infections (P < .001), with no difference in DUSP3 and KLF2 expression. The diagnostic performance of GBP5 alone (AUC, 0.74; 95% confidence interval [CI], .67-.81) was slightly better than the 3-gene tuberculosis score (AUC, 0.66; 95% CI, .58-.73) in TBM. Both GBP5 expression and tuberculosis score were higher in participants with human immunodeficiency virus (HIV; P < .001), with good diagnostic performance of GBP5 alone (AUC, 0.86; 95% CI, .80-.93). CONCLUSIONS The 3-gene host signature in whole blood has the ability to discriminate TBM from other brain infections, including in individuals with HIV. Validation in large prospective diagnostic study is now required.
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Affiliation(s)
- Julie Huynh
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Oxford University, OxfordUnited Kingdom
| | | | | | - Hoang Thanh Hai
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Do Dang Anh Thu
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | - Vu Thi Mong Dung
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Do Dinh Vinh
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Nghiem My Ngoc
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Joseph Donovan
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Oxford University, OxfordUnited Kingdom
| | - Nguyen Hoan Phu
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- School of Medicine, Vietnam National University of Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Dang Van Thanh
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | - Nguyen Duc Bang
- Pham Ngoc Thach Hospital for Tuberculosis and Lung Disease, Ho Chi Minh City, Vietnam
| | - Dang Thi Minh Ha
- Pham Ngoc Thach Hospital for Tuberculosis and Lung Disease, Ho Chi Minh City, Vietnam
| | - Ho Dang Trung Nghia
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Pham Ngoc Thach University of Medicine, Ho Chi Minh City, Vietnam
- The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Le Van Tan
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Oxford University, OxfordUnited Kingdom
| | - Le Hong Van
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Guy Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Oxford University, OxfordUnited Kingdom
| | - Nguyen Thuy Thuong Thuong
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Oxford University, OxfordUnited Kingdom
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Ribeiro Tomé LM, Dornelles Parise MT, Parise D, de Carvalho Azevedo VA, Brenig B, Badotti F, Góes-Neto A. Pure lignin induces overexpression of cytochrome P450 (CYP) encoding genes and brings insights into the lignocellulose depolymerization by Trametes villosa. Heliyon 2024; 10:e28449. [PMID: 38689961 PMCID: PMC11059554 DOI: 10.1016/j.heliyon.2024.e28449] [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: 01/24/2024] [Revised: 03/16/2024] [Accepted: 03/19/2024] [Indexed: 05/02/2024] Open
Abstract
Trametes villosa is a remarkable white-rot fungus (WRF) with the potential to be applied in lignocellulose conversion to obtain chemical compounds and biofuels. Lignocellulose breakdown by WRF is carried out through the secretion of oxidative and hydrolytic enzymes. Despite the existing knowledge about this process, the complete molecular mechanisms involved in the regulation of this metabolic system have not yet been elucidated. Therefore, in order to understand the genes and metabolic pathways regulated during lignocellulose degradation, the strain T. villosa CCMB561 was cultured in media with different carbon sources (lignin, sugarcane bagasse, and malt extract). Subsequently, biochemical assays and differential gene expression analysis by qPCR and high-throughput RNA sequencing were carried out. Our results revealed the ability of T. villosa CCMB561 to grow on lignin (AL medium) as the unique carbon source. An overexpression of Cytochrome P450 was detected in this medium, which may be associated with the lignin O-demethylation pathway. Clusters of up-regulated CAZymes-encoding genes were identified in lignin and sugarcane bagasse, revealing that T. villosa CCMB561 acts simultaneously in the depolymerization of lignin, cellulose, hemicellulose, and pectin. Furthermore, genes encoding nitroreductases and homogentisate-1,2-dioxygenase that act in the degradation of organic pollutants were up-regulated in the lignin medium. Altogether, these findings provide new insights into the mechanisms of lignocellulose degradation by T. villosa and confirm the ability of this fungal species to be applied in biorefineries and in the bioremediation of organic pollutants.
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Affiliation(s)
- Luiz Marcelo Ribeiro Tomé
- Laboratory of Molecular and Computational Biology of Fungi, Department of Microbiology, Institute of Biological Sciences, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, 31270-901, MG, Brazil
- Graduate Program in Bioinformatics, Institute of Biological Sciences, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, 31270-901, MG, Brazil
| | - Mariana Teixeira Dornelles Parise
- Laboratory of Molecular and Computational Biology of Fungi, Department of Microbiology, Institute of Biological Sciences, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, 31270-901, MG, Brazil
- Graduate Program in Bioinformatics, Institute of Biological Sciences, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, 31270-901, MG, Brazil
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, 31270-901, MG, Brazil
| | - Doglas Parise
- Laboratory of Molecular and Computational Biology of Fungi, Department of Microbiology, Institute of Biological Sciences, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, 31270-901, MG, Brazil
- Graduate Program in Bioinformatics, Institute of Biological Sciences, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, 31270-901, MG, Brazil
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, 31270-901, MG, Brazil
| | - Vasco Ariston de Carvalho Azevedo
- Graduate Program in Bioinformatics, Institute of Biological Sciences, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, 31270-901, MG, Brazil
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, 31270-901, MG, Brazil
| | - Bertram Brenig
- Institute of Veterinary Medicine, Burckhardtweg, University of Göttingen, 37073, Göttingen, Germany
| | - Fernanda Badotti
- Department of Chemistry, Centro Federal de Educação Tecnológica de Minas Gerais, Belo Horizonte, 30421-169, MG, Brazil
| | - Aristóteles Góes-Neto
- Laboratory of Molecular and Computational Biology of Fungi, Department of Microbiology, Institute of Biological Sciences, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, 31270-901, MG, Brazil
- Graduate Program in Bioinformatics, Institute of Biological Sciences, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, 31270-901, MG, Brazil
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Song J, Song Z, Zhang J, Gong Y. Privacy-Preserving Identification of Cancer Subtype-Specific Driver Genes Based on Multigenomics Data with Privatedriver. J Comput Biol 2024; 31:99-116. [PMID: 38271572 DOI: 10.1089/cmb.2023.0115] [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] [Indexed: 01/27/2024] Open
Abstract
Identifying cancer subtype-specific driver genes from a large number of irrelevant passengers is crucial for targeted therapy in cancer treatment. Recently, the rapid accumulation of large-scale cancer genomics data from multiple institutions has presented remarkable opportunities for identification of cancer subtype-specific driver genes. However, the insufficient subtype samples, privacy issues, and heterogenous of aberration events pose great challenges in precisely identifying cancer subtype-specific driver genes. To address this, we introduce privatedriver, the first model for identifying subtype-specific driver genes that integrates genomics data from multiple institutions in a data privacy-preserving collaboration manner. The process of identifying subtype-specific cancer driver genes using privatedriver involves the following two steps: genomics data integration and collaborative training. In the integration process, the aberration events from multiple genomics data sources are combined for each institution using the forward and backward propagation method of NetICS. In the collaborative training process, each institution utilizes the federated learning framework to upload encrypted model parameters instead of raw data of all institutions to train a global model by using the non-negative matrix factorization algorithm. We applied privatedriver on head and neck squamous cell and colon cancer from The Cancer Genome Atlas website and evaluated it with two benchmarks using macro-Fscore. The comparison analysis demonstrates that privatedriver achieves comparable results to centralized learning models and outperforms most other nonprivacy preserving models, all while ensuring the confidentiality of patient information. We also demonstrate that, for varying predicted driver gene distributions in subtype, our model fully considers the heterogeneity of subtype and identifies subtype-specific driver genes corresponding to the given prognosis and therapeutic effect. The success of privatedriver reveals the feasibility and effectiveness of identifying cancer subtype-specific driver genes in a data protection manner, providing new insights for future privacy-preserving driver gene identification studies.
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Affiliation(s)
- Junrong Song
- School of Information; Kunming, P.R. China
- Yunnan Key Laboratory of Service Computing; Yunnan University of Finance and Economics, Kunming, P.R. China
| | - Zhiming Song
- School of Information; Kunming, P.R. China
- Yunnan Key Laboratory of Service Computing; Yunnan University of Finance and Economics, Kunming, P.R. China
| | - Jinpeng Zhang
- School of Information; Kunming, P.R. China
- Yunnan Key Laboratory of Service Computing; Yunnan University of Finance and Economics, Kunming, P.R. China
- The School of Computer Science and Engineering, Yunnan University, Kunming, P.R. China
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Urgessa OE, Woldesemayat AA. OMICs approaches and technologies for understanding low-high feed efficiency traits in chicken: implication to breeding. Anim Biotechnol 2023; 34:4147-4166. [PMID: 36927292 DOI: 10.1080/10495398.2023.2187404] [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] [Indexed: 03/18/2023]
Abstract
In poultry production, there has been a trend of continuous increase in cost of feed ingredients which represents the major proportion of the production costs. Feed costs can be reduced by improving feed efficiency traits which increase the possibility of using various indigestible feed sources and decrease the environmental impact of the enhanced poultry production. Therefore, feed efficiency has been used as one of the most important economic traits of selection in the breeding program of chickens. Recently, many OMICs experimental studies have been designed to characterize biological differences between the high and low feed efficiency chicken phenotypes. Biological complexity cannot be fully captured by main individual OMICs such as genomics, transcriptomics, proteomics and metabolomics. Therefore, researchers have combined multiple assays from the same set of samples to create multi-OMICs datasets. OMICs findings are crucial in improving existing approaches to poultry breeding. The current review aimed to highlight the components of feed efficiency and general OMICs approaches and technologies. Besides, individual and multi-OMICs based understanding of chicken feed efficiency traits and the application of the acquired knowledge in the chicken breeding program were addressed.
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Affiliation(s)
- Olyad Erba Urgessa
- School of Biological Sciences and Biotechnology, College of Natural and Computational Sciences, Haramaya University, Dire Dawa, Ethiopia
- Department of Applied Biology, School of Applied Natural Science, Adama Science and Technology University, Adama, Ethiopia
| | - Adugna Abdi Woldesemayat
- College of Biological and Chemical Engineering, Department of Biotechnology, Genomics and Bioinformatics Research Unit, Addis Ababa Science and Technology University, Addis Ababa, Ethiopia
- College of Agriculture & Environmental Sciences, University of South Africa, Florida Science Campus, 28 Pioneer Ave, Florida Park, Roodepoort, South Africa
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5
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Shen L, Huang H, Li J, Chen W, Yao Y, Hu J, Zhou J, Huang F, Ni C. Exploration of prognosis and immunometabolism landscapes in ER+ breast cancer based on a novel lipid metabolism-related signature. Front Immunol 2023; 14:1199465. [PMID: 37469520 PMCID: PMC10352658 DOI: 10.3389/fimmu.2023.1199465] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 06/19/2023] [Indexed: 07/21/2023] Open
Abstract
Introduction Lipid metabolic reprogramming is gaining attention as a hallmark of cancers. Recent mounting evidence indicates that the malignant behavior of breast cancer (BC) is closely related to lipid metabolism. Here, we focus on the estrogen receptor-positive (ER+) subtype, the most common subgroup of BC, to explore immunometabolism landscapes and prognostic significance according to lipid metabolism-related genes (LMRGs). Methods Samples from The Cancer Genome Atlas (TCGA) database were used as training cohort, and samples from the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC), Gene Expression Omnibus (GEO) datasets and our cohort were applied for external validation. The survival-related LMRG molecular pattern and signature were constructed by unsupervised consensus clustering and least absolute shrinkage and selection operator (LASSO) analysis. A lipid metabolism-related clinicopathologic nomogram was established. Gene enrichment and pathway analysis were performed to explore the underlying mechanism. Immune landscapes, immunotherapy and chemotherapy response were further explored. Moreover, the relationship between gene expression and clinicopathological features was assessed by immunohistochemistry. Results Two LMRG molecular patterns were identified and associated with distinct prognoses and immune cell infiltration. Next, a prognostic signature based on nine survival-related LMRGs was established and validated. The signature was confirmed to be an independent prognostic factor and an optimal nomogram incorporating age and T stage (AUC of 5-year overall survival: 0.778). Pathway enrichment analysis revealed differences in immune activities, lipid biosynthesis and drug metabolism by comparing groups with low- and high-risk scores. Further exploration verified different immune microenvironment profiles, immune checkpoint expression, and sensitivity to immunotherapy and chemotherapy between the two groups. Finally, arachidonate 15-lipoxygenase (ALOX15) was selected as the most prominent differentially expressed gene between the two groups. Its expression was positively related to larger tumor size, more advanced tumor stage and vascular invasion in our cohort (n = 149). Discussion This is the first lipid metabolism-based signature with value for prognosis prediction and immunotherapy or chemotherapy guidance for ER+ BC.
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Affiliation(s)
- Lesang Shen
- Department of Breast Surgery, Second Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Tumor Microenvironment and Immune Therapy of Zhejiang Province, Second Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, China
| | - Huanhuan Huang
- Department of Breast Surgery, Second Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Tumor Microenvironment and Immune Therapy of Zhejiang Province, Second Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, China
| | - Jiaxin Li
- Department of Breast Surgery, Second Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Tumor Microenvironment and Immune Therapy of Zhejiang Province, Second Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, China
| | - Wuzhen Chen
- Department of Breast Surgery, Second Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Tumor Microenvironment and Immune Therapy of Zhejiang Province, Second Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, China
| | - Yao Yao
- Department of Breast Surgery, Second Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Tumor Microenvironment and Immune Therapy of Zhejiang Province, Second Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, China
| | - Jianming Hu
- Department of Breast Surgery, Second Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Tumor Microenvironment and Immune Therapy of Zhejiang Province, Second Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, China
| | - Jun Zhou
- Department of Breast Surgery, Affiliated Hangzhou First People’s Hospital, Zhejiang University, Hangzhou, Zhejiang, China
| | - Fengbo Huang
- Department of Pathology, Second Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, China
| | - Chao Ni
- Department of Breast Surgery, Second Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Tumor Microenvironment and Immune Therapy of Zhejiang Province, Second Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, China
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de Prisco N, Ford C, Elrod ND, Lee W, Tang LC, Huang KL, Lin A, Ji P, Jonnakuti VS, Boyle L, Cabaj M, Botta S, Õunap K, Reinson K, Wojcik MH, Rosenfeld JA, Bi W, Tveten K, Prescott T, Gerstner T, Schroeder A, Fong CT, George-Abraham JK, Buchanan CA, Hanson-Khan A, Bernstein JA, Nella AA, Chung WK, Brandt V, Jovanovic M, Targoff KL, Yalamanchili HK, Wagner EJ, Gennarino VA. Alternative polyadenylation alters protein dosage by switching between intronic and 3'UTR sites. SCIENCE ADVANCES 2023; 9:eade4814. [PMID: 36800428 PMCID: PMC9937581 DOI: 10.1126/sciadv.ade4814] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
Alternative polyadenylation (APA) creates distinct transcripts from the same gene by cleaving the pre-mRNA at poly(A) sites that can lie within the 3' untranslated region (3'UTR), introns, or exons. Most studies focus on APA within the 3'UTR; however, here, we show that CPSF6 insufficiency alters protein levels and causes a developmental syndrome by deregulating APA throughout the transcript. In neonatal humans and zebrafish larvae, CPSF6 insufficiency shifts poly(A) site usage between the 3'UTR and internal sites in a pathway-specific manner. Genes associated with neuronal function undergo mostly intronic APA, reducing their expression, while genes associated with heart and skeletal function mostly undergo 3'UTR APA and are up-regulated. This suggests that, under healthy conditions, cells toggle between internal and 3'UTR APA to modulate protein expression.
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Affiliation(s)
- Nicola de Prisco
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY, USA
| | - Caitlin Ford
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
- Department of Pediatrics, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Nathan D. Elrod
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - Winston Lee
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
- Department Ophthalmology, Columbia University Irving Medical Center, New York, NY, USA
| | - Lauren C. Tang
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Kai-Lieh Huang
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, TX, USA
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Ai Lin
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, WC67+HC Dongcheng, Beijing, China
| | - Ping Ji
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - Venkata S. Jonnakuti
- Department of Pediatrics, Baylor College of Medicine and Texas Children’s Hospital, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, USA
- Program in Quantitative and Computational Biology, Baylor College of Medicine, Houston, TX, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, USA
| | - Lia Boyle
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
- Department of Pediatrics, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Maximilian Cabaj
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Salvatore Botta
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
- Department of Translational Medical Science, University of Campania Luigi Vanvitelli, Caserta, Italy
| | - Katrin Õunap
- Department of Clinical Genetics, Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia
- Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Karit Reinson
- Department of Clinical Genetics, Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia
- Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Monica H. Wojcik
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jill A. Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor Genetics Laboratories, Houston, TX, USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor Genetics Laboratories, Houston, TX, USA
| | - Kristian Tveten
- Department of Medical Genetics, Telemark Hospital Trust, 3710 Skien, Norway
| | - Trine Prescott
- Department of Medical Genetics, Telemark Hospital Trust, 3710 Skien, Norway
| | - Thorsten Gerstner
- Department of Child Neurology and Rehabilitation and Department of Pediatrics, Hospital of Southern Norway, Arendal, Norway
| | - Audrey Schroeder
- Division of Medical Genetics, University of Rochester Medical Center, Rochester, NY, USA
| | - Chin-To Fong
- Department of Pediatrics and of Medicine, University of Rochester Medical Center, Rochester, NY, USA
| | - Jaya K. George-Abraham
- Dell Children’s Medical Group, Austin, TX, USA
- Department of Pediatrics, The University of Texas at Austin Dell Medical School, Austin, TX, USA
| | | | - Andrea Hanson-Khan
- Department of Pediatrics, Division of Medical Genetics, Stanford School of Medicine, Palo Alto, CA, USA
- Department of Genetics, Stanford School of Medicine, Palo Alto, CA, USA
| | - Jonathan A. Bernstein
- Department of Pediatrics, Division of Medical Genetics, Stanford School of Medicine, Palo Alto, CA, USA
| | - Aikaterini A. Nella
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, USA
| | - Wendy K. Chung
- Department of Pediatrics, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Vicky Brandt
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Marko Jovanovic
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Kimara L. Targoff
- Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY, USA
- Department of Pediatrics, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Hari Krishna Yalamanchili
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, USA
- USDA/ARS Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Eric J. Wagner
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, TX, USA
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Vincenzo A. Gennarino
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY, USA
- Department of Pediatrics, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
- Initiative for Columbia Ataxia and Tremor, Columbia University Irving Medical Center, New York, NY, USA
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Riojas AM, Spradling-Reeves KD, Christensen CL, Hall-Ursone S, Cox LA. Cell-type deconvolution of bulk RNA-Seq from kidney using opensource bioinformatic tools. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.13.528258. [PMID: 36824792 PMCID: PMC9949078 DOI: 10.1101/2023.02.13.528258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Traditional bulk RNA-Seq pipelines do not assess cell-type composition within heterogeneous tissues. Therefore, it is difficult to determine whether conflicting findings among samples or datasets are the result of biological differences or technical differences due to variation in sample collections. This report provides a user-friendly, open source method to assess cell-type composition in bulk RNA-Seq datasets for heterogeneous tissues using published single cell (sc)RNA-Seq data as a reference. As an example, we apply the method to analysis of kidney cortex bulk RNA-Seq data from female (N=8) and male (N=9) baboons to assess whether observed transcriptome sex differences are biological or technical, i.e., variation due to ultrasound guided biopsy collections. We found cell-type composition was not statistically different in female versus male transcriptomes based on expression of 274 kidney cell-type specific transcripts, indicating differences in gene expression are not due to sampling differences. This method of cell-type composition analysis is recommended for providing rigor in analysis of bulk RNA-Seq datasets from complex tissues. It is clear that with reduced costs, more analyses will be done using scRNA-Seq; however, the approach described here is relevant for data mining and meta analyses of the thousands of bulk RNA-Seq data archived in the NCBI GEO public database.
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Affiliation(s)
- Angelica M. Riojas
- Center for Precision Medicine, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Kimberly D. Spradling-Reeves
- Section on Molecular Medicine, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | | | - Shannan Hall-Ursone
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Laura A. Cox
- Center for Precision Medicine, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
- Section on Molecular Medicine, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
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8
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Pabón-Mora N, Suárez-Baron H, Madrigal Y, Alzate JF, González F. Expression and Functional Studies of Leaf, Floral, and Fruit Developmental Genes in Non-model Species. Methods Mol Biol 2023; 2686:365-401. [PMID: 37540370 DOI: 10.1007/978-1-0716-3299-4_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
Researchers working on evolutionary developmental plant biology are inclined to choose non-model taxa to address how specific features have been acquired during ontogeny and fixed during phylogeny. In this chapter we describe methods to extract RNA, to assemble de-novo transcriptomes, to isolate orthologous genes within gene families, and to evaluate expression and function of target genes. We have successfully optimized these protocols for non-model plant species including ferns, gymnosperms, and a large assortment of angiosperms. In the latter, we have ranged a large number of families including Aristolochiaceae, Apodanthaceae, Chloranthaceae, Orchidaceae, Papaveraceae, Rubiaceae, Solanaceae, and Tropaeolaceae.
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Affiliation(s)
| | - Harold Suárez-Baron
- Instituto de Biología, Universidad de Antioquia, Medellín, Colombia
- Departamento de Ciencias Naturales y Matemáticas, Pontificia Universidad Javeriana, Cali, Colombia
| | - Yesenia Madrigal
- Instituto de Biología, Universidad de Antioquia, Medellín, Colombia
| | - Juan F Alzate
- Centro Nacional de Secuenciación Genómica-CNSG, Sede de Investigación Universitaria-SIU, Medellín, Antioquia, Colombia
| | - Favio González
- Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Sede Bogotá, Bogotá, Colombia
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9
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Radzikowska U, Baerenfaller K, Cornejo‐Garcia JA, Karaaslan C, Barletta E, Sarac BE, Zhakparov D, Villaseñor A, Eguiluz‐Gracia I, Mayorga C, Sokolowska M, Barbas C, Barber D, Ollert M, Chivato T, Agache I, Escribese MM. Omics technologies in allergy and asthma research: An EAACI position paper. Allergy 2022; 77:2888-2908. [PMID: 35713644 PMCID: PMC9796060 DOI: 10.1111/all.15412] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 05/30/2022] [Accepted: 06/06/2022] [Indexed: 01/27/2023]
Abstract
Allergic diseases and asthma are heterogenous chronic inflammatory conditions with several distinct complex endotypes. Both environmental and genetic factors can influence the development and progression of allergy. Complex pathogenetic pathways observed in allergic disorders present a challenge in patient management and successful targeted treatment strategies. The increasing availability of high-throughput omics technologies, such as genomics, epigenomics, transcriptomics, proteomics, and metabolomics allows studying biochemical systems and pathophysiological processes underlying allergic responses. Additionally, omics techniques present clinical applicability by functional identification and validation of biomarkers. Therefore, finding molecules or patterns characteristic for distinct immune-inflammatory endotypes, can subsequently influence its development, progression, and treatment. There is a great potential to further increase the effectiveness of single omics approaches by integrating them with other omics, and nonomics data. Systems biology aims to simultaneously and longitudinally understand multiple layers of a complex and multifactorial disease, such as allergy, or asthma by integrating several, separated data sets and generating a complete molecular profile of the condition. With the use of sophisticated biostatistics and machine learning techniques, these approaches provide in-depth insight into individual biological systems and will allow efficient and customized healthcare approaches, called precision medicine. In this EAACI Position Paper, the Task Force "Omics technologies in allergic research" broadly reviewed current advances and applicability of omics techniques in allergic diseases and asthma research, with a focus on methodology and data analysis, aiming to provide researchers (basic and clinical) with a desk reference in the field. The potential of omics strategies in understanding disease pathophysiology and key tools to reach unmet needs in allergy precision medicine, such as successful patients' stratification, accurate disease prognosis, and prediction of treatment efficacy and successful prevention measures are highlighted.
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Affiliation(s)
- Urszula Radzikowska
- Swiss Institute of Allergy and Asthma Research (SIAF)University of ZurichDavosSwitzerland,Christine‐Kühne Center for Allergy Research and Education (CK‐CARE)DavosSwitzerland
| | - Katja Baerenfaller
- Swiss Institute of Allergy and Asthma Research (SIAF)University of ZurichDavosSwitzerland,Swiss Institute of Bioinformatics (SIB)DavosSwitzerland
| | - José Antonio Cornejo‐Garcia
- Research LaboratoryIBIMA, ARADyAL Instituto de Salud Carlos III, Regional University Hospital of Málaga, UMAMálagaSpain
| | - Cagatay Karaaslan
- Department of Biology, Molecular Biology SectionFaculty of ScienceHacettepe UniversityAnkaraTurkey
| | - Elena Barletta
- Swiss Institute of Allergy and Asthma Research (SIAF)University of ZurichDavosSwitzerland,Swiss Institute of Bioinformatics (SIB)DavosSwitzerland
| | - Basak Ezgi Sarac
- Department of Biology, Molecular Biology SectionFaculty of ScienceHacettepe UniversityAnkaraTurkey
| | - Damir Zhakparov
- Swiss Institute of Allergy and Asthma Research (SIAF)University of ZurichDavosSwitzerland,Swiss Institute of Bioinformatics (SIB)DavosSwitzerland
| | - Alma Villaseñor
- Centre for Metabolomics and Bioanalysis (CEMBIO)Department of Chemistry and BiochemistryFacultad de FarmaciaUniversidad San Pablo‐CEU, CEU UniversitiesMadridSpain,Institute of Applied Molecular Medicine Nemesio Diaz (IMMAND)Department of Basic Medical SciencesFacultad de MedicinaUniversidad San Pablo CEU, CEU UniversitiesMadridSpain
| | - Ibon Eguiluz‐Gracia
- Allergy UnitHospital Regional Universitario de MálagaMálagaSpain,Allergy Research GroupInstituto de Investigación Biomédica de Málaga‐IBIMAMálagaSpain
| | - Cristobalina Mayorga
- Allergy UnitHospital Regional Universitario de MálagaMálagaSpain,Allergy Research GroupInstituto de Investigación Biomédica de Málaga‐IBIMAMálagaSpain,Andalusian Centre for Nanomedicine and Biotechnology – BIONANDMálagaSpain
| | - Milena Sokolowska
- Swiss Institute of Allergy and Asthma Research (SIAF)University of ZurichDavosSwitzerland,Christine‐Kühne Center for Allergy Research and Education (CK‐CARE)DavosSwitzerland
| | - Coral Barbas
- Centre for Metabolomics and Bioanalysis (CEMBIO)Department of Chemistry and BiochemistryFacultad de FarmaciaUniversidad San Pablo‐CEU, CEU UniversitiesMadridSpain
| | - Domingo Barber
- Institute of Applied Molecular Medicine Nemesio Diaz (IMMAND)Department of Basic Medical SciencesFacultad de MedicinaUniversidad San Pablo CEU, CEU UniversitiesMadridSpain
| | - Markus Ollert
- Department of Infection and ImmunityLuxembourg Institute of HealthyEsch‐sur‐AlzetteLuxembourg,Department of Dermatology and Allergy CenterOdense Research Center for AnaphylaxisOdense University Hospital, University of Southern DenmarkOdenseDenmark
| | - Tomas Chivato
- Institute of Applied Molecular Medicine Nemesio Diaz (IMMAND)Department of Basic Medical SciencesFacultad de MedicinaUniversidad San Pablo CEU, CEU UniversitiesMadridSpain,Department of Clinic Medical SciencesFacultad de MedicinaUniversidad San Pablo CEU, CEU UniversitiesMadridSpain
| | | | - Maria M. Escribese
- Institute of Applied Molecular Medicine Nemesio Diaz (IMMAND)Department of Basic Medical SciencesFacultad de MedicinaUniversidad San Pablo CEU, CEU UniversitiesMadridSpain
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10
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Kocagöz Y, Demirler MC, Eski SE, Güler K, Dokuzluoglu Z, Fuss SH. Disparate progenitor cell populations contribute to maintenance and repair neurogenesis in the zebrafish olfactory epithelium. Cell Tissue Res 2022; 388:331-358. [PMID: 35266039 DOI: 10.1007/s00441-022-03597-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 02/02/2022] [Indexed: 12/25/2022]
Abstract
Olfactory sensory neurons (OSNs) undergo constant turnover under physiological conditions but also regenerate efficiently following tissue injury. Maintenance and repair neurogenesis in the olfactory epithelium (OE) have been attributed to the selective activity of globose (GBCs) and horizontal basal cells (HBCs), respectively. In zebrafish, cells with GBC-like properties are localized to the peripheral margins of the sensory OE and contribute to OSN neurogenesis in the intact OE, while cells that resemble HBCs at the morphological and molecular level are more uniformly distributed. However, the contribution of these cells to the restoration of the injured OE has not been demonstrated. Here, we provide a detailed cellular and molecular analysis of the tissue response to injury and show that a dual progenitor cell system also exists in zebrafish. Zebrafish HBCs respond to the structural damage of the OE and generate a transient population of proliferative neurogenic progenitors that restores OSNs. In contrast, selective ablation of OSNs by axotomy triggers neurogenic GBC proliferation, suggesting that distinct signaling events activate GBC and HBC responses. Molecular analysis of differentially expressed genes in lesioned and regenerating OEs points toward an involvement of the canonical Wnt/β-catenin pathway. Activation of Wnt signaling appears to be sufficient to stimulate mitotic activity, while inhibition significantly reduces, but does not fully eliminate, HBC responses. Zebrafish HBCs are surprisingly active even under physiological conditions with a strong bias toward the zones of constitutive OSN neurogenesis, suggestive of a direct lineage relationship between progenitor cell subtypes.
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Affiliation(s)
- Yigit Kocagöz
- Department of Molecular Biology and Genetics, Center for Life Sciences and Technologies, Bogazici University, Kuzey Park 319, 34342, Bebek - Istanbul, Turkey
| | - Mehmet Can Demirler
- Department of Molecular Biology and Genetics, Center for Life Sciences and Technologies, Bogazici University, Kuzey Park 319, 34342, Bebek - Istanbul, Turkey
| | - Sema Elif Eski
- Department of Molecular Biology and Genetics, Center for Life Sciences and Technologies, Bogazici University, Kuzey Park 319, 34342, Bebek - Istanbul, Turkey
- Institute of Interdisciplinary Research in Human and Molecular Biology, Free University of Brussels, Campus Erasme, 1070, Brussels, Belgium
| | - Kardelen Güler
- Department of Molecular Biology and Genetics, Center for Life Sciences and Technologies, Bogazici University, Kuzey Park 319, 34342, Bebek - Istanbul, Turkey
| | - Zeynep Dokuzluoglu
- Department of Molecular Biology and Genetics, Center for Life Sciences and Technologies, Bogazici University, Kuzey Park 319, 34342, Bebek - Istanbul, Turkey
| | - Stefan H Fuss
- Department of Molecular Biology and Genetics, Center for Life Sciences and Technologies, Bogazici University, Kuzey Park 319, 34342, Bebek - Istanbul, Turkey.
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11
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Thomas SM, Ackert-Bicknell CL, Zuscik MJ, Payne KA. Understanding the Transcriptomic Landscape to Drive New Innovations in Musculoskeletal Regenerative Medicine. Curr Osteoporos Rep 2022; 20:141-152. [PMID: 35156183 DOI: 10.1007/s11914-022-00726-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/18/2022] [Indexed: 11/03/2022]
Abstract
PURPOSE OF REVIEW RNA-sequencing (RNA-seq) is a novel and highly sought-after tool in the field of musculoskeletal regenerative medicine. The technology is being used to better understand pathological processes, as well as elucidate mechanisms governing development and regeneration. It has allowed in-depth characterization of stem cell populations and discovery of molecular mechanisms that regulate stem cell development, maintenance, and differentiation in a way that was not possible with previous technology. This review introduces RNA-seq technology and how it has paved the way for advances in musculoskeletal regenerative medicine. RECENT FINDINGS Recent studies in regenerative medicine have utilized RNA-seq to decipher mechanisms of pathophysiology and identify novel targets for regenerative medicine. The technology has also advanced stem cell biology through in-depth characterization of stem cells, identifying differentiation trajectories and optimizing cell culture conditions. It has also provided new knowledge that has led to improved growth factor use and scaffold design for musculoskeletal regenerative medicine. This article reviews recent studies utilizing RNA-seq in the field of musculoskeletal regenerative medicine. It demonstrates how transcriptomic analysis can be used to provide insights that can aid in formulating a regenerative strategy.
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Affiliation(s)
- Stacey M Thomas
- Colorado Program for Musculoskeletal Research, Department of Orthopedics, University of Colorado Anschutz Medical Campus, Mail Stop 8343, 12800 East 19th Avenue, Aurora, CO, 80045, USA
| | - Cheryl L Ackert-Bicknell
- Colorado Program for Musculoskeletal Research, Department of Orthopedics, University of Colorado Anschutz Medical Campus, Mail Stop 8343, 12800 East 19th Avenue, Aurora, CO, 80045, USA
| | - Michael J Zuscik
- Colorado Program for Musculoskeletal Research, Department of Orthopedics, University of Colorado Anschutz Medical Campus, Mail Stop 8343, 12800 East 19th Avenue, Aurora, CO, 80045, USA
| | - Karin A Payne
- Colorado Program for Musculoskeletal Research, Department of Orthopedics, University of Colorado Anschutz Medical Campus, Mail Stop 8343, 12800 East 19th Avenue, Aurora, CO, 80045, USA.
- Gates Center for Regenerative Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
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12
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Trapotsi MA, Hosseini-Gerami L, Bender A. Computational analyses of mechanism of action (MoA): data, methods and integration. RSC Chem Biol 2022; 3:170-200. [PMID: 35360890 PMCID: PMC8827085 DOI: 10.1039/d1cb00069a] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 12/09/2021] [Indexed: 12/15/2022] Open
Abstract
The elucidation of a compound's Mechanism of Action (MoA) is a challenging task in the drug discovery process, but it is important in order to rationalise phenotypic findings and to anticipate potential side-effects. Bioinformatic approaches, advances in machine learning techniques and the increasing deposition of high-throughput data in public databases have significantly contributed to recent advances in the field, but it is not straightforward to decide which data and methods are most suitable to use in a given case. In this review, we focus on these methods and data and their applications in generating MoA hypotheses for subsequent experimental validation. We discuss compound-specific data such as -omics, cell morphology and bioactivity data, as well as commonly used supplementary prior knowledge such as network and pathway data, and provide information on databases where this data can be accessed. In terms of methodologies, we discuss both well-established methods (connectivity mapping, pathway enrichment) as well as more developing methods (neural networks and multi-omics integration). Finally, we review case studies where the MoA of a compound was successfully suggested from computational analysis by incorporating multiple data modalities and/or methodologies. Our aim for this review is to provide researchers with insights into the benefits and drawbacks of both the data and methods in terms of level of understanding, biases and interpretation - and to highlight future avenues of investigation which we foresee will improve the field of MoA elucidation, including greater public access to -omics data and methodologies which are capable of data integration.
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Affiliation(s)
- Maria-Anna Trapotsi
- Centre for Molecular Informatics, Yusuf Hamied Department of Chemistry, University of Cambridge UK
| | - Layla Hosseini-Gerami
- Centre for Molecular Informatics, Yusuf Hamied Department of Chemistry, University of Cambridge UK
| | - Andreas Bender
- Centre for Molecular Informatics, Yusuf Hamied Department of Chemistry, University of Cambridge UK
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13
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Bodein A, Scott-Boyer MP, Perin O, Lê Cao KA, Droit A. Interpretation of network-based integration from multi-omics longitudinal data. Nucleic Acids Res 2021; 50:e27. [PMID: 34883510 PMCID: PMC8934642 DOI: 10.1093/nar/gkab1200] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 10/19/2021] [Accepted: 11/22/2021] [Indexed: 12/26/2022] Open
Abstract
Multi-omics integration is key to fully understand complex biological processes in an holistic manner. Furthermore, multi-omics combined with new longitudinal experimental design can unreveal dynamic relationships between omics layers and identify key players or interactions in system development or complex phenotypes. However, integration methods have to address various experimental designs and do not guarantee interpretable biological results. The new challenge of multi-omics integration is to solve interpretation and unlock the hidden knowledge within the multi-omics data. In this paper, we go beyond integration and propose a generic approach to face the interpretation problem. From multi-omics longitudinal data, this approach builds and explores hybrid multi-omics networks composed of both inferred and known relationships within and between omics layers. With smart node labelling and propagation analysis, this approach predicts regulation mechanisms and multi-omics functional modules. We applied the method on 3 case studies with various multi-omics designs and identified new multi-layer interactions involved in key biological functions that could not be revealed with single omics analysis. Moreover, we highlighted interplay in the kinetics that could help identify novel biological mechanisms. This method is available as an R package netOmics to readily suit any application.
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Affiliation(s)
- Antoine Bodein
- Molecular Medicine Department, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Marie-Pier Scott-Boyer
- Molecular Medicine Department, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Olivier Perin
- Digital Sciences Department, L'Oréal Advanced Research, Aulnay-sous-bois, France
| | - Kim-Anh Lê Cao
- Melbourne Integrative Genomics, School of Mathematics and Statistics, University of Melbourne, Melbourne, VIC, Australia
| | - Arnaud Droit
- Molecular Medicine Department, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
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14
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Eraslan Z, Papatzikas G, Cazier JB, Khanim FL, Günther UL. Targeting Asparagine and Serine Metabolism in Germinal Centre-Derived B Cells Non-Hodgkin Lymphomas (B-NHL). Cells 2021; 10:cells10102589. [PMID: 34685569 PMCID: PMC8533740 DOI: 10.3390/cells10102589] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/14/2021] [Accepted: 09/16/2021] [Indexed: 11/30/2022] Open
Abstract
BL and DLBCL are subtypes of B-cell lymphomas that arise from germinal centre B lymphocytes. Differentiation between BL and DLBCL is critical and can be challenging, as these two types of cancer share the same morphological, immunophenotypic, and genetic characteristics. In this study, we have examined metabolism in BL and DLBCL lymphomas and found distinctive differences in serine metabolism. We show that BL cells consume significantly more extracellular asparagine than DLBCL cells. Using a tracer-based approach, we find that asparagine regulates the serine uptake and serine synthesis in BL and DLBCL cells. Calculation of Differentially Expressed Genes (DEGs) from RNAseq datasets of BL and DLBCL patients show that BL cancers express the genes involved in serine synthesis at a higher level than DLBCL. Remarkably, combined use of an inhibitor of serine biosynthesis pathway and an anticancer drug asparaginase increases the sensitivity of BL cells to extracellular asparagine deprivation without inducing a change in the sensitivity of DLBCL cells to asparaginase. In summary, our study unravels metabolic differences between BL and DLBCL with diagnostic potential which may also open new avenues for treatment.
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Affiliation(s)
- Zuhal Eraslan
- Institute of Clinical Sciences, University of Birmingham, Birmingham B15 2TT, UK; (Z.E.); (F.L.K.)
| | - Grigorios Papatzikas
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK; (G.P.); (J.-B.C.)
- Centre for Computational Biology, University of Birmingham, Birmingham B15 2TT, UK
| | - Jean-Baptiste Cazier
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK; (G.P.); (J.-B.C.)
- Centre for Computational Biology, University of Birmingham, Birmingham B15 2TT, UK
| | - Farhat L. Khanim
- Institute of Clinical Sciences, University of Birmingham, Birmingham B15 2TT, UK; (Z.E.); (F.L.K.)
| | - Ulrich L. Günther
- Institute for Chemistry and Metabolomics, University of Lübeck, 23562 Lübeck, Germany
- Correspondence:
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15
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Sweeney BA, Tagmazian AA, Ribas CE, Finn RD, Bateman A, Petrov AI. Exploring Non-Coding RNAs in RNAcentral. ACTA ACUST UNITED AC 2021; 71:e104. [PMID: 32846052 DOI: 10.1002/cpbi.104] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Non-coding RNAs are essential for all life and carry out a wide range of functions. Information about these molecules is distributed across dozens of specialized resources. RNAcentral is a database of non-coding RNA sequences that provides a unified access point to non-coding RNA annotations from >40 member databases and helps provide insight into the function of these RNAs. This article describes different ways of accessing the data, including searching the website and retrieving the data programmatically over web APIs and a public database. We also demonstrate an example Galaxy workflow for using RNAcentral for RNA-seq differential expression analysis. RNAcentral is available at https://rnacentral.org. © 2020 The Authors. Basic Protocol 1: Viewing RNAcentral sequence reports Basic Protocol 2: Using RNAcentral text search to explore ncRNA sequences Basic Protocol 3: Using RNAcentral sequence search Basic Protocol 4: Using RNAcentral FTP archive Support Protocol 1: Using web APIs for programmatic data access Support Protocol 2: Using public Postgres database to export large datasets Support Protocol 3: Analyze non-coding RNA in RNA-seq datasets using RNAcentral and Galaxy.
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Affiliation(s)
- Blake A Sweeney
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Arina A Tagmazian
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.,Federal State Budget Scientific Institution Center of Experimental Embryology and Reproductive Biotechnologies, Moscow, Russia
| | - Carlos E Ribas
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Robert D Finn
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Alex Bateman
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Anton I Petrov
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
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16
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Inhibition of the lncRNA Coded within Transglutaminase 2 Gene Impacts Several Relevant Networks in MCF-7 Breast Cancer Cells. Noncoding RNA 2021; 7:ncrna7030049. [PMID: 34449674 PMCID: PMC8395837 DOI: 10.3390/ncrna7030049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/12/2021] [Accepted: 08/13/2021] [Indexed: 12/13/2022] Open
Abstract
Long non-coding RNAs are nucleotide molecules that regulate transcription in numerous cellular processes and are related to the occurrence of many diseases, including cancer. In this regard, we recently discovered a polyadenylated long non-coding RNA (named TG2-lncRNA) encoded within the first intron of the Transglutaminase type 2 gene (TGM2), which is related to tumour proliferation in human cancer cell lines. To better characterize this new biological player, we investigated the effects of its suppression in MCF-7 breast cancer cells, using siRNA treatment and RNA-sequencing. In this way, we found modifications in several networks associated to biological functions relevant for tumorigenesis (apoptosis, chronic inflammation, angiogenesis, immunomodulation, cell mobility, and epithelial–mesenchymal transition) that were originally attributed only to Transglutaminase type 2 protein but that could be regulated also by TG2-lncRNA. Moreover, our experiments strongly suggest the ability of TG2-lncRNA to directly interact with important transcription factors, such as RXRα and TP53, paving the way for several regulatory loops that can potentially influence the phenotypic behaviour of MCF-7 cells. These considerations imply the need to further investigate the relative relevance of the TG2 protein itself and/or other gene products as key regulators in the organization of breast cancer program.
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17
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Lee JH, Hong J, Zhang Z, de la Peña Avalos B, Proietti CJ, Deamicis AR, Guzmán G P, Lam HM, Garcia J, Roudier MP, Sisk AE, De La Rosa R, Vu K, Yang M, Liao Y, Scheirer J, Pechacek D, Yadav P, Rao MK, Zheng S, Johnson-Pais TL, Leach RJ, Elizalde PV, Dray E, Xu K. Regulation of telomere homeostasis and genomic stability in cancer by N 6-adenosine methylation (m 6A). SCIENCE ADVANCES 2021; 7:7/31/eabg7073. [PMID: 34321211 PMCID: PMC8318370 DOI: 10.1126/sciadv.abg7073] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 06/11/2021] [Indexed: 05/04/2023]
Abstract
The role of RNA methylation on N 6-adenosine (m6A) in cancer has been acknowledged, but the underlying mechanisms remain obscure. Here, we identified homeobox containing 1 (HMBOX1) as an authentic target mRNA of m6A machinery, which is highly methylated in malignant cells compared to the normal counterparts and subject to expedited degradation upon the modification. m6A-mediated down-regulation of HMBOX1 causes telomere dysfunction and inactivation of p53 signaling, which leads to chromosome abnormalities and aggressive phenotypes. CRISPR-based, m6A-editing tools further prove that the methyl groups on HMBOX1 per se contribute to the generation of altered cancer genome. In multiple types of human cancers, expression of the RNA methyltransferase METTL3 is negatively correlated with the telomere length but favorably with fractions of altered cancer genome, whereas HMBOX1 mRNA levels show the opposite patterns. Our work suggests that the cancer-driving genomic alterations may potentially be fixed by rectifying particular epitranscriptomic program.
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Affiliation(s)
- Ji Hoon Lee
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Juyeong Hong
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Zhao Zhang
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Bárbara de la Peña Avalos
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
- Mays Cancer Center, UT Health San Antonio MD Anderson, San Antonio, TX 78229, USA
| | - Cecilia J Proietti
- Laboratory of Molecular Mechanisms of Carcinogenesis and Molecular Endocrinology, Instituto de Biología y Medicina Experimental (IBYME), CONICET, Buenos Aires C1428ADN, Argentina
| | - Agustina Roldán Deamicis
- Laboratory of Molecular Mechanisms of Carcinogenesis and Molecular Endocrinology, Instituto de Biología y Medicina Experimental (IBYME), CONICET, Buenos Aires C1428ADN, Argentina
| | - Pablo Guzmán G
- Departamento de Anatomía Patológica (BIOREN), Universidad de La Frontera, Temuco Casilla 54-D, Chile
| | - Hung-Ming Lam
- Department of Urology, University of Washington, Seattle, WA 98195, USA
| | - Jose Garcia
- Department of Urology, University of Washington, Seattle, WA 98195, USA
| | - Martine P Roudier
- Department of Urology, University of Washington, Seattle, WA 98195, USA
| | - Anthony E Sisk
- Department of Pathology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Richard De La Rosa
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Kevin Vu
- Department of Medical Education, Joe R. and Teresa Lozano Long School of Medicine, San Antonio, TX 78229, USA
| | - Mei Yang
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Yiji Liao
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Jessica Scheirer
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Douglas Pechacek
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Pooja Yadav
- Department of Cell Systems and Anatomy, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Manjeet K Rao
- Department of Cell Systems and Anatomy, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Siyuan Zheng
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
- Department of Population Health Sciences, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Teresa L Johnson-Pais
- Department of Urology, University of Texas Health Sciences Center at San Antonio, San Antonio, TX 78229, USA
| | - Robin J Leach
- Mays Cancer Center, UT Health San Antonio MD Anderson, San Antonio, TX 78229, USA
- Department of Cell Systems and Anatomy, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Patricia V Elizalde
- Laboratory of Molecular Mechanisms of Carcinogenesis and Molecular Endocrinology, Instituto de Biología y Medicina Experimental (IBYME), CONICET, Buenos Aires C1428ADN, Argentina
| | - Eloïse Dray
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
- Mays Cancer Center, UT Health San Antonio MD Anderson, San Antonio, TX 78229, USA
| | - Kexin Xu
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA.
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Establishment of bioinformatics pipeline for deciphering the biological complexities of fragmented sperm transcriptome. Anal Biochem 2021; 620:114141. [PMID: 33617829 DOI: 10.1016/j.ab.2021.114141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 01/29/2021] [Accepted: 02/16/2021] [Indexed: 10/22/2022]
Abstract
Despite the development of several tools for the analysis of the transcriptome data, non-availability of a standard pipeline for analyzing the low quality and fragmented mRNA samples pose a major challenge to the computational molecular biologist for effective interpretation of the data. Hence the present study aimed to establish a bioinformatics pipeline for analyzing the biologically fragmented sperm RNA. Sperm transcriptome data (2 x 75 PE sequencing) generated from bulls (n = 8) of high-fertile (n = 4) and low-fertile (n = 4) classified based on the fertility rate (41.52 ± 1.07 vs 36.04 ± 1.04%) were analyzed with different bioinformatics tools for alignment, quantitation, and differential gene expression studies. TopHat2 was effectual compared to HISAT2 and STAR for sperm mRNA due to the higher exonic (6% vs 2%) mapping percentage and quantitating the low expressed genes. TopHat2 also had significantly strong correlation with STAR (0.871, p = 0.05) and HISAT2 (0.933, p = 0.01). TopHat2 and Cufflinks combo quantitated the number of genes higher than the other combinations. Among the tools (Cuffdiff, DESeq, DESeq2, edgeR, and limma) used for the differential gene expression analysis, edgeR and limma identified the largest number of significantly differentially expressed genes (p < 0.05) with biological relevance. The concordance analysis concurred that edgeR had an edge over the other tools. It also identified a higher number (9.5%) of fertility-related genes to be differentially expressed between the two groups. The present study established that TopHat2, Cufflinks, and edgeR as a suitable pipeline for the analysis of fragmented mRNA from bovine spermatozoa.
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Zhao G, Weiner AI, Neupauer KM, de Mello Costa MF, Palashikar G, Adams-Tzivelekidis S, Mangalmurti NS, Vaughan AE. Regeneration of the pulmonary vascular endothelium after viral pneumonia requires COUP-TF2. SCIENCE ADVANCES 2020; 6:6/48/eabc4493. [PMID: 33239293 PMCID: PMC7688336 DOI: 10.1126/sciadv.abc4493] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 10/09/2020] [Indexed: 05/08/2023]
Abstract
Acute respiratory distress syndrome is associated with a robust inflammatory response that damages the vascular endothelium, impairing gas exchange. While restoration of microcapillaries is critical to avoid mortality, therapeutic targeting of this process requires a greater understanding of endothelial repair mechanisms. Here, we demonstrate that lung endothelium possesses substantial regenerative capacity and lineage tracing reveals that native endothelium is the source of vascular repair after influenza injury. Ablation of chicken ovalbumin upstream promoter-transcription factor 2 (COUP-TF2) (Nr2f2), a transcription factor implicated in developmental angiogenesis, reduced endothelial proliferation, exacerbating viral lung injury in vivo. In vitro, COUP-TF2 regulates proliferation and migration through activation of cyclin D1 and neuropilin 1. Upon influenza injury, nuclear factor κB suppresses COUP-TF2, but surviving endothelial cells ultimately reestablish vascular homeostasis dependent on restoration of COUP-TF2. Therefore, stabilization of COUP-TF2 may represent a therapeutic strategy to enhance recovery from pathogens, including H1N1 influenza and SARS-CoV-2.
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Affiliation(s)
- Gan Zhao
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Lung Biology Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Aaron I Weiner
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Lung Biology Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Katherine M Neupauer
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Maria Fernanda de Mello Costa
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Lung Biology Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gargi Palashikar
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Lung Biology Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Stephanie Adams-Tzivelekidis
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Lung Biology Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nilam S Mangalmurti
- Pulmonary, Allergy, and Critical Care Division, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Andrew E Vaughan
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
- Lung Biology Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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Ambrosino L, Colantuono C, Diretto G, Fiore A, Chiusano ML. Bioinformatics Resources for Plant Abiotic Stress Responses: State of the Art and Opportunities in the Fast Evolving -Omics Era. PLANTS 2020; 9:plants9050591. [PMID: 32384671 PMCID: PMC7285221 DOI: 10.3390/plants9050591] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/24/2020] [Accepted: 04/29/2020] [Indexed: 12/13/2022]
Abstract
Abiotic stresses are among the principal limiting factors for productivity in agriculture. In the current era of continuous climate changes, the understanding of the molecular aspects involved in abiotic stress response in plants is a priority. The rise of -omics approaches provides key strategies to promote effective research in the field, facilitating the investigations from reference models to an increasing number of species, tolerant and sensitive genotypes. Integrated multilevel approaches, based on molecular investigations at genomics, transcriptomics, proteomics and metabolomics levels, are now feasible, expanding the opportunities to clarify key molecular aspects involved in responses to abiotic stresses. To this aim, bioinformatics has become fundamental for data production, mining and integration, and necessary for extracting valuable information and for comparative efforts, paving the way to the modeling of the involved processes. We provide here an overview of bioinformatics resources for research on plant abiotic stresses, describing collections from -omics efforts in the field, ranging from raw data to complete databases or platforms, highlighting opportunities and still open challenges in abiotic stress research based on -omics technologies.
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Affiliation(s)
- Luca Ambrosino
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici (Na), Italy; (L.A.); (C.C.)
- Department of Research Infrastructures for Marine Biological Resources (RIMAR), 80121 Naples, Italy
| | - Chiara Colantuono
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici (Na), Italy; (L.A.); (C.C.)
- Department of Research Infrastructures for Marine Biological Resources (RIMAR), 80121 Naples, Italy
| | - Gianfranco Diretto
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), 00123 Rome, Italy; (G.D.); (A.F.)
| | - Alessia Fiore
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), 00123 Rome, Italy; (G.D.); (A.F.)
| | - Maria Luisa Chiusano
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici (Na), Italy; (L.A.); (C.C.)
- Department of Research Infrastructures for Marine Biological Resources (RIMAR), 80121 Naples, Italy
- Correspondence: ; Tel.: +39-081-253-9492
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Alcott CE, Yalamanchili HK, Ji P, van der Heijden ME, Saltzman A, Elrod N, Lin A, Leng M, Bhatt B, Hao S, Wang Q, Saliba A, Tang J, Malovannaya A, Wagner EJ, Liu Z, Zoghbi HY. Partial loss of CFIm25 causes learning deficits and aberrant neuronal alternative polyadenylation. eLife 2020; 9:e50895. [PMID: 32319885 PMCID: PMC7176433 DOI: 10.7554/elife.50895] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 04/05/2020] [Indexed: 12/19/2022] Open
Abstract
We previously showed that NUDT21-spanning copy-number variations (CNVs) are associated with intellectual disability (Gennarino et al., 2015). However, the patients' CNVs also included other genes. To determine if reduced NUDT21 function alone can cause disease, we generated Nudt21+/- mice to mimic NUDT21-deletion patients. We found that although these mice have 50% reduced Nudt21 mRNA, they only have 30% less of its cognate protein, CFIm25. Despite this partial protein-level compensation, the Nudt21+/- mice have learning deficits, cortical hyperexcitability, and misregulated alternative polyadenylation (APA) in their hippocampi. Further, to determine the mediators driving neural dysfunction in humans, we partially inhibited NUDT21 in human stem cell-derived neurons to reduce CFIm25 by 30%. This induced APA and protein level misregulation in hundreds of genes, a number of which cause intellectual disability when mutated. Altogether, these results show that disruption of NUDT21-regulated APA events in the brain can cause intellectual disability.
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Affiliation(s)
- Callison E Alcott
- Program in Developmental Biology, Baylor College of MedicineHoustonUnited States
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s HospitalHoustonUnited States
- Medical Scientist Training Program, Baylor College of MedicineHoustonUnited States
| | - Hari Krishna Yalamanchili
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s HospitalHoustonUnited States
- Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
| | - Ping Ji
- Department of Biochemistry & Molecular Biology, University of Texas Medical BranchGalvestonUnited States
| | - Meike E van der Heijden
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s HospitalHoustonUnited States
- Department of Neuroscience, Baylor College of MedicineHoustonUnited States
| | - Alexander Saltzman
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology Baylor College of MedicineHoustonUnited States
| | - Nathan Elrod
- Department of Biochemistry & Molecular Biology, University of Texas Medical BranchGalvestonUnited States
| | - Ai Lin
- Department of Biochemistry & Molecular Biology, University of Texas Medical BranchGalvestonUnited States
- Department of Etiology and Carcinogenesis, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Mei Leng
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology Baylor College of MedicineHoustonUnited States
| | - Bhoomi Bhatt
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology Baylor College of MedicineHoustonUnited States
| | - Shuang Hao
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s HospitalHoustonUnited States
- Section of Neurology, Department of Pediatrics, Baylor College of MedicineHoustonUnited States
| | - Qi Wang
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s HospitalHoustonUnited States
- Section of Neurology, Department of Pediatrics, Baylor College of MedicineHoustonUnited States
| | - Afaf Saliba
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s HospitalHoustonUnited States
- Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
| | - Jianrong Tang
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s HospitalHoustonUnited States
- Section of Neurology, Department of Pediatrics, Baylor College of MedicineHoustonUnited States
| | - Anna Malovannaya
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology Baylor College of MedicineHoustonUnited States
- Department of Molecular and Cellular Biology, Baylor College of MedicineHoustonUnited States
- Mass Spectrometry Proteomics Core, Baylor College of MedicineHoustonUnited States
- Dan L Duncan Comprehensive Cancer Center, Baylor College of MedicineHoustonUnited States
| | - Eric J Wagner
- Department of Biochemistry & Molecular Biology, University of Texas Medical BranchGalvestonUnited States
| | - Zhandong Liu
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s HospitalHoustonUnited States
- Section of Neurology, Department of Pediatrics, Baylor College of MedicineHoustonUnited States
- Graduate Program in Quantitative and Computational Biosciences, Baylor College of MedicineHoustonUnited States
| | - Huda Y Zoghbi
- Program in Developmental Biology, Baylor College of MedicineHoustonUnited States
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s HospitalHoustonUnited States
- Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
- Department of Neuroscience, Baylor College of MedicineHoustonUnited States
- Department of Pediatrics, Baylor College of MedicineHoustonUnited States
- Howard Hughes Medical Institute, Baylor College of MedicineHoustonUnited States
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De Maio A, Yalamanchili HK, Adamski CJ, Gennarino VA, Liu Z, Qin J, Jung SY, Richman R, Orr H, Zoghbi HY. RBM17 Interacts with U2SURP and CHERP to Regulate Expression and Splicing of RNA-Processing Proteins. Cell Rep 2019; 25:726-736.e7. [PMID: 30332651 PMCID: PMC6292215 DOI: 10.1016/j.celrep.2018.09.041] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 08/07/2018] [Accepted: 09/12/2018] [Indexed: 01/01/2023] Open
Abstract
RNA splicing entails the coordinated interaction of more than 150 proteins in the spliceosome, one of the most complex of the cell’s molecular machines. We previously discovered that the RNA-binding motif protein 17 (RBM17), a component of the spliceosome, is essential for survival and cell maintenance. Here, we find that it interacts with the spliceosomal factors U2SURP and CHERP and that they reciprocally regulate each other’s stability, both in mouse and in human cells. Individual knockdown of each of the three proteins induces overlapping changes in splicing and gene expression of transcripts enriched for RNA-processing factors. Our results elucidate the function of RBM17, U2SURP, and CHERP and link the activity of the spliceosome to the regulation of downstream RNA-binding proteins. These data support the hypothesis that, beyond driving constitutive splicing, spliceosomal factors can regulate alternative splicing of specific targets. De Maio et al. find that the splicing factor RBM17 establishes a physical and functional relation with U2SURP and CHERP. Knockdown of these U2 snRNP-associated spliceosomal components reveals their synergistic activity toward regulation of a given set of transcripts rather than a more predictable transcriptome-wide inhibition of splicing.
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Affiliation(s)
- Antonia De Maio
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA
| | - Hari Krishna Yalamanchili
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Carolyn J Adamski
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA
| | - Vincenzo A Gennarino
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zhandong Liu
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jun Qin
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sung Y Jung
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ronald Richman
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA
| | - Harry Orr
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Huda Y Zoghbi
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA.
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23
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De Vitis C, Corleone G, Salvati V, Ascenzi F, Pallocca M, De Nicola F, Fanciulli M, di Martino S, Bruschini S, Napoli C, Ricci A, Bassi M, Venuta F, Rendina EA, Ciliberto G, Mancini R. B4GALT1 Is a New Candidate to Maintain the Stemness of Lung Cancer Stem Cells. J Clin Med 2019; 8:E1928. [PMID: 31717588 PMCID: PMC6912435 DOI: 10.3390/jcm8111928] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 10/30/2019] [Accepted: 11/05/2019] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND According to the cancer stem cells (CSCs) hypothesis, a population of cancer cells with stem cell properties is responsible for tumor propagation, drug resistance, and disease recurrence. Study of the mechanisms responsible for lung CSCs propagation is expected to provide better understanding of cancer biology and new opportunities for therapy. METHODS The Lung Adenocarcinoma (LUAD) NCI-H460 cell line was grown either as 2D or as 3D cultures. Transcriptomic and genome-wide chromatin accessibility studies of 2D vs. 3D cultures were carried out using RNA-sequencing and Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq), respectively. Reverse transcription polymerase chain reaction (RT-PCR) was also carried out on RNA extracted from primary cultures derived from malignant pleural effusions to validate RNA-seq results. RESULTS RNA-seq and ATAC-seq data disentangled transcriptional and genome accessibility variability of 3D vs. 2D cultures in NCI-H460 cells. The examination of genomic landscape of genes upregulated in 3D vs. 2D cultures led to the identification of 2D cultures led to the identification of Beta-1,4-galactosyltranferase 1 (B4GALT1) as the top candidate. B4GALT1 as the top candidate. B4GALT1 was validated as a stemness factor, since its silencing caused strong inhibition of 3D spheroid formation. CONCLUSION Combined transcriptomic and chromatin accessibility study of 3D vs. 2D LUAD cultures led to the identification of B4GALT1 as a new factor involved in the propagation and maintenance of LUAD CSCs.
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Affiliation(s)
- Claudia De Vitis
- Department of Clinical and Molecular Medicine, Sant’Andrea Hospital, “Sapienza” University of Rome, 00161 Rome, Italy; (C.D.V.); (R.M.)
| | - Giacomo Corleone
- SAFU Laboratory, Department of Research, Advanced Diagnostic, and Technological Innovation, IRCCS “Regina Elena” National Cancer Institute, 00144 Rome, Italy; (G.C.); (M.P.); (F.D.N.); (M.F.)
| | - Valentina Salvati
- Preclinical Models and New Therapeutic Agents Unit, IRCCS-Regina Elena National Cancer Institute, 00144 Rome, Italy;
| | - Francesca Ascenzi
- Tumor Immunology and Immunotherapy Unit, Department of Research, Advanced Diagnostic and Technological Innovation, IRCCS Regina Elena National Cancer Institute, 00144 Rome, Italy;
| | - Matteo Pallocca
- SAFU Laboratory, Department of Research, Advanced Diagnostic, and Technological Innovation, IRCCS “Regina Elena” National Cancer Institute, 00144 Rome, Italy; (G.C.); (M.P.); (F.D.N.); (M.F.)
| | - Francesca De Nicola
- SAFU Laboratory, Department of Research, Advanced Diagnostic, and Technological Innovation, IRCCS “Regina Elena” National Cancer Institute, 00144 Rome, Italy; (G.C.); (M.P.); (F.D.N.); (M.F.)
| | - Maurizio Fanciulli
- SAFU Laboratory, Department of Research, Advanced Diagnostic, and Technological Innovation, IRCCS “Regina Elena” National Cancer Institute, 00144 Rome, Italy; (G.C.); (M.P.); (F.D.N.); (M.F.)
| | - Simona di Martino
- Pathology Unit, IRCSS “Regina Elena” National Cancer Institute, 00144 Rome, Italy;
| | - Sara Bruschini
- Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy;
| | - Christian Napoli
- Department of Medical Surgical Sciences and Translational Medicine, Sant’Andrea Hospital, “Sapienza” University of Rome, 00189 Rome, Italy;
| | - Alberto Ricci
- Department of Clinical and Molecular Medicine, Division of Pneumology, Sapienza University of Rome, Sant’Andrea Hospital, 00189 Rome, Italy;
| | - Massimiliano Bassi
- Department of Thoracic Surgery, University of Rome Sapienza, 00161 Rome, Italy; (M.B.); (F.V.)
| | - Federico Venuta
- Department of Thoracic Surgery, University of Rome Sapienza, 00161 Rome, Italy; (M.B.); (F.V.)
| | - Erino Angelo Rendina
- Department of Thoracic Surgery, Sant’Andrea Hospital, “Sapienza” University of Rome, 00189 Rome, Italy
| | - Gennaro Ciliberto
- Scientific Direction, IRCCS “Regina Elena” National Cancer Institute, 00144 Rome, Italy
| | - Rita Mancini
- Department of Clinical and Molecular Medicine, Sant’Andrea Hospital, “Sapienza” University of Rome, 00161 Rome, Italy; (C.D.V.); (R.M.)
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Genome-wide discovery and characterization of long noncoding RNAs in patients with multiple myeloma. BMC Med Genomics 2019; 12:135. [PMID: 31619233 PMCID: PMC6794882 DOI: 10.1186/s12920-019-0577-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 08/30/2019] [Indexed: 12/12/2022] Open
Abstract
Background Long noncoding RNAs (lncRNAs) are involved in a wide range of biological processes in tumorigenesis. However, the role of lncRNA expression in the biology, prognosis, and molecular classification of human multiple myeloma (MM) remains unclear, especially the biological functions of the vast majority of lncRNAs. Recently, lncRNAs have been identified in neoplastic hematologic disorders. Evidence has accumulated on the molecular mechanisms of action of lncRNAs, providing insight into their functional roles in tumorigenesis. This study aimed to characterize potential lncRNAs in patients with MM. Methods In this study, the whole-transcriptome strand-specific RNA sequencing of samples from three newly diagnosed patients with MM was performed. The whole transcriptome, including lncRNAs, microRNAs, and mRNAs, was analyzed. Using these data, MM lncRNAs were systematically analyzed, and the lncRNAs involved in the occurrence of MM were identified. Results The results revealed that MM lncRNAs had distinctive characteristics different from those of other malignant tumors. Further, the functions of a set of lncRNAs preferentially expressed in MM were verified, and several lncRNAs were identified as competing endogenous RNAs. More importantly, the aberrant expression of certain lncRNAs, including maternally expressed gene3, colon cancer–associated transcript1, and coiled-coil domain-containing 26, as well as some novel lncRNAs involved in the occurrence of MM was established. Further, lncRNAs were related to some microRNAs, regulated each other, and participated in MM development. Conclusions Genome-wide screening and functional analysis enabled the identification of a set of lncRNAs involved in the occurrence of MM. The interaction exists among microRNAs and lncRNAs.
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Bioinformatics for Marine Products: An Overview of Resources, Bottlenecks, and Perspectives. Mar Drugs 2019; 17:md17100576. [PMID: 31614509 PMCID: PMC6835618 DOI: 10.3390/md17100576] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/01/2019] [Accepted: 10/02/2019] [Indexed: 12/13/2022] Open
Abstract
The sea represents a major source of biodiversity. It exhibits many different ecosystems in a huge variety of environmental conditions where marine organisms have evolved with extensive diversification of structures and functions, making the marine environment a treasure trove of molecules with potential for biotechnological applications and innovation in many different areas. Rapid progress of the omics sciences has revealed novel opportunities to advance the knowledge of biological systems, paving the way for an unprecedented revolution in the field and expanding marine research from model organisms to an increasing number of marine species. Multi-level approaches based on molecular investigations at genomic, metagenomic, transcriptomic, metatranscriptomic, proteomic, and metabolomic levels are essential to discover marine resources and further explore key molecular processes involved in their production and action. As a consequence, omics approaches, accompanied by the associated bioinformatic resources and computational tools for molecular analyses and modeling, are boosting the rapid advancement of biotechnologies. In this review, we provide an overview of the most relevant bioinformatic resources and major approaches, highlighting perspectives and bottlenecks for an appropriate exploitation of these opportunities for biotechnology applications from marine resources.
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Kohen R, Barlev J, Hornung G, Stelzer G, Feldmesser E, Kogan K, Safran M, Leshkowitz D. UTAP: User-friendly Transcriptome Analysis Pipeline. BMC Bioinformatics 2019; 20:154. [PMID: 30909881 PMCID: PMC6434621 DOI: 10.1186/s12859-019-2728-2] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Accepted: 03/13/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND RNA-Seq technology is routinely used to characterize the transcriptome, and to detect gene expression differences among cell types, genotypes and conditions. Advances in short-read sequencing instruments such as Illumina Next-Seq have yielded easy-to-operate machines, with high throughput, at a lower price per base. However, processing this data requires bioinformatics expertise to tailor and execute specific solutions for each type of library preparation. RESULTS In order to enable fast and user-friendly data analysis, we developed an intuitive and scalable transcriptome pipeline that executes the full process, starting from cDNA sequences derived by RNA-Seq [Nat Rev Genet 10:57-63, 2009] and bulk MARS-Seq [Science 343:776-779, 2014] and ending with sets of differentially expressed genes. Output files are placed in structured folders, and results summaries are provided in rich and comprehensive reports, containing dozens of plots, tables and links. CONCLUSION Our User-friendly Transcriptome Analysis Pipeline (UTAP) is an open source, web-based intuitive platform available to the biomedical research community, enabling researchers to efficiently and accurately analyse transcriptome sequence data.
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Affiliation(s)
- Refael Kohen
- Bioinformatics Unit, Department of Life Sciences Core Facilities, Weizmann Institute of Science, 76100, Rehovot, Israel.
| | - Jonathan Barlev
- The Mantoux Bioinformatics institute of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Department of Life Sciences Core Facilities, Weizmann Institute of Science, 76100, Rehovot, Israel
| | - Gil Hornung
- The Mantoux Bioinformatics institute of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Department of Life Sciences Core Facilities, Weizmann Institute of Science, 76100, Rehovot, Israel
| | - Gil Stelzer
- Bioinformatics Unit, Department of Life Sciences Core Facilities, Weizmann Institute of Science, 76100, Rehovot, Israel
| | - Ester Feldmesser
- Bioinformatics Unit, Department of Life Sciences Core Facilities, Weizmann Institute of Science, 76100, Rehovot, Israel
| | - Kiril Kogan
- Bioinformatics Unit, Department of Life Sciences Core Facilities, Weizmann Institute of Science, 76100, Rehovot, Israel
| | - Marilyn Safran
- Bioinformatics Unit, Department of Life Sciences Core Facilities, Weizmann Institute of Science, 76100, Rehovot, Israel
| | - Dena Leshkowitz
- Bioinformatics Unit, Department of Life Sciences Core Facilities, Weizmann Institute of Science, 76100, Rehovot, Israel.
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Ather SH, Awe OI, Butler TJ, Denka T, Semick SA, Tang W, Busby B. SeqAcademy: an educational pipeline for RNA-Seq and anchor-Seq analysis. F1000Res 2018; 7:ISCB Comm J-628. [PMID: 33014338 PMCID: PMC7525341.3 DOI: 10.12688/f1000research.14880.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/07/2019] [Indexed: 03/30/2024] Open
Abstract
Quantification of gene expression and characterization of gene transcript structures are central problems in molecular biology. RNA sequencing (RNA-Seq) and chromatin immunoprecipitation sequencing (anchor-Seq) are important methods, but can be cumbersome and difficult for beginners to learn. To teach interested students and scientists how to analyze RNA-Seq and anchor-Seq data, we present a start-to-finish tutorial for analyzing RNA-Seq and anchor-Seq data: SeqAcademy ( source code: https://github.com/NCBI-Hackathons/seqacademy, webpage: http://www.seqacademy.org/). This user-friendly pipeline, fully written in markdown language, emphasizes the use of publicly available RNA-Seq and anchor-Seq data and strings together popular tools that bridge that gap between raw sequencing reads and biological insight. We demonstrate practical and conceptual considerations for various RNA-Seq and anchor-Seq analysis steps with a biological use case - a previously published yeast experiment. This work complements existing sophisticated RNA-Seq and anchor-Seq pipelines designed for advanced users by gently introducing the critical components of RNA-Seq and anchor-Seq analysis to the novice bioinformatician. In conclusion, this well-documented pipeline will introduce state-of-the-art RNA-Seq and anchor-Seq analysis tools to beginning bioinformaticians and help facilitate the analysis of the burgeoning amounts of public RNA-Seq and anchor-Seq data.
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Affiliation(s)
- Syed Hussain Ather
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Olaitan Igbagbo Awe
- National Center for Biotechnology Information, U.S. National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Thomas J Butler
- National Institute on Aging , National Institutes of Health, Baltimore , MD, 21224, USA
| | - Tamiru Denka
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, 20894, USA
| | | | - Wanhu Tang
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Ben Busby
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, 20894, USA
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Ather SH, Awe OI, Butler TJ, Denka T, Semick SA, Tang W, Busby B. SeqAcademy: an educational pipeline for RNA-Seq and ChIP-Seq analysis. F1000Res 2018; 7:ISCB Comm J-628. [PMID: 33014338 PMCID: PMC7525341 DOI: 10.12688/f1000research.14880.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/18/2018] [Indexed: 03/30/2024] Open
Abstract
Quantification of gene expression and characterization of gene transcript structures are central problems in molecular biology. RNA sequencing (RNA-Seq) and chromatin immunoprecipitation sequencing (ChIP-Seq) are important methods, but can be cumbersome and difficult for beginners to learn. To teach interested students and scientists how to analyze RNA-Seq and ChIP-Seq data, we present a start-to-finish tutorial for analyzing RNA-Seq and ChIP-Seq data: SeqAcademy ( source code: https://github.com/NCBI-Hackathons/seqacademy, webpage: http://www.seqacademy.org/). This user-friendly pipeline, fully written in Jupyter Notebook, emphasizes the use of publicly available RNA-Seq and ChIP-Seq data and strings together popular tools that bridge that gap between raw sequencing reads and biological insight. We demonstrate practical and conceptual considerations for various RNA-Seq and ChIP-Seq analysis steps with a biological use case - a previously published yeast experiment. This work complements existing sophisticated RNA-Seq and ChIP-Seq pipelines designed for advanced users by gently introducing the critical components of RNA-Seq and ChIP-Seq analysis to the novice bioinformatician. In conclusion, this well-documented pipeline will introduce state-of-the-art RNA-Seq and ChIP-Seq analysis tools to beginning bioinformaticians and help facilitate the analysis of the burgeoning amounts of public RNA-Seq and ChIP-Seq data.
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Affiliation(s)
- Syed Hussain Ather
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Olaitan Igbagbo Awe
- National Center for Biotechnology Information, U.S. National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Thomas J. Butler
- National Institute on Aging , National Institutes of Health, Baltimore , MD, 21224, USA
| | - Tamiru Denka
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, 20894, USA
| | | | - Wanhu Tang
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Ben Busby
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, 20894, USA
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Ather SH, Awe OI, Butler TJ, Denka T, Semick SA, Tang W, Busby B. SeqAcademy: an educational pipeline for RNA-Seq and ChIP-Seq analysis. F1000Res 2018; 7:ISCB Comm J-628. [PMID: 33014338 PMCID: PMC7525341 DOI: 10.12688/f1000research.14880.4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/16/2020] [Indexed: 12/02/2022] Open
Abstract
Quantification of gene expression and characterization of gene transcript structures are central problems in molecular biology. RNA sequencing (RNA-Seq) and chromatin immunoprecipitation sequencing (ChIP-Seq) are important methods, but can be cumbersome and difficult for beginners to learn. To teach interested students and scientists how to analyze RNA-Seq and ChIP-Seq data, we present a start-to-finish tutorial for analyzing RNA-Seq and ChIP-Seq data: SeqAcademy ( source code: https://github.com/NCBI-Hackathons/seqacademy, webpage: http://www.seqacademy.org/). This user-friendly pipeline, fully written in markdown language, emphasizes the use of publicly available RNA-Seq and ChIP-Seq data and strings together popular tools that bridge that gap between raw sequencing reads and biological insight. We demonstrate practical and conceptual considerations for various RNA-Seq and ChIP-Seq analysis steps with a biological use case - a previously published yeast experiment. This work complements existing sophisticated RNA-Seq and ChIP-Seq pipelines designed for advanced users by gently introducing the critical components of RNA-Seq and ChIP-Seq analysis to the novice bioinformatician. In conclusion, this well-documented pipeline will introduce state-of-the-art RNA-Seq and ChIP-Seq analysis tools to beginning bioinformaticians and help facilitate the analysis of the burgeoning amounts of public RNA-Seq and ChIP-Seq data.
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Affiliation(s)
- Syed Hussain Ather
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Olaitan Igbagbo Awe
- National Center for Biotechnology Information, U.S. National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Thomas J Butler
- National Institute on Aging , National Institutes of Health, Baltimore , MD, 21224, USA
| | - Tamiru Denka
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, 20894, USA
| | | | - Wanhu Tang
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Ben Busby
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, 20894, USA
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Ather SH, Awe OI, Butler TJ, Denka T, Semick SA, Tang W, Busby B. SeqAcademy: an educational pipeline for RNA-Seq and ChIP-Seq analysis. F1000Res 2018; 7:ISCB Comm J-628. [PMID: 33014338 PMCID: PMC7525341.2 DOI: 10.12688/f1000research.14880.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/28/2018] [Indexed: 03/30/2024] Open
Abstract
Quantification of gene expression and characterization of gene transcript structures are central problems in molecular biology. RNA sequencing (RNA-Seq) and chromatin immunoprecipitation sequencing (ChIP-Seq) are important methods, but can be cumbersome and difficult for beginners to learn. To teach interested students and scientists how to analyze RNA-Seq and ChIP-Seq data, we present a start-to-finish tutorial for analyzing RNA-Seq and ChIP-Seq data: SeqAcademy ( source code: https://github.com/NCBI-Hackathons/seqacademy, webpage: http://www.seqacademy.org/). This user-friendly pipeline, fully written in Jupyter Notebook, emphasizes the use of publicly available RNA-Seq and ChIP-Seq data and strings together popular tools that bridge that gap between raw sequencing reads and biological insight. We demonstrate practical and conceptual considerations for various RNA-Seq and ChIP-Seq analysis steps with a biological use case - a previously published yeast experiment. This work complements existing sophisticated RNA-Seq and ChIP-Seq pipelines designed for advanced users by gently introducing the critical components of RNA-Seq and ChIP-Seq analysis to the novice bioinformatician. In conclusion, this well-documented pipeline will introduce state-of-the-art RNA-Seq and ChIP-Seq analysis tools to beginning bioinformaticians and help facilitate the analysis of the burgeoning amounts of public RNA-Seq and ChIP-Seq data.
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Affiliation(s)
- Syed Hussain Ather
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Olaitan Igbagbo Awe
- National Center for Biotechnology Information, U.S. National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Thomas J Butler
- National Institute on Aging , National Institutes of Health, Baltimore , MD, 21224, USA
| | - Tamiru Denka
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, 20894, USA
| | | | - Wanhu Tang
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Ben Busby
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, 20894, USA
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Pohodich AE, Yalamanchili H, Raman AT, Wan YW, Gundry M, Hao S, Jin H, Tang J, Liu Z, Zoghbi HY. Forniceal deep brain stimulation induces gene expression and splicing changes that promote neurogenesis and plasticity. eLife 2018; 7:34031. [PMID: 29570050 PMCID: PMC5906096 DOI: 10.7554/elife.34031] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 03/22/2018] [Indexed: 12/12/2022] Open
Abstract
Clinical trials are currently underway to assess the efficacy of forniceal deep brain stimulation (DBS) for improvement of memory in Alzheimer's patients, and forniceal DBS has been shown to improve learning and memory in a mouse model of Rett syndrome (RTT), an intellectual disability disorder caused by loss-of-function mutations in MECP2. The mechanism of DBS benefits has been elusive, however, so we assessed changes in gene expression, splice isoforms, DNA methylation, and proteome following acute forniceal DBS in wild-type mice and mice lacking Mecp2. We found that DBS upregulates genes involved in synaptic function, cell survival, and neurogenesis and normalized expression of ~25% of the genes altered in Mecp2-null mice. Moreover, DBS induced expression of 17-24% of the genes downregulated in other intellectual disability mouse models and in post-mortem human brain tissue from patients with Major Depressive Disorder, suggesting forniceal DBS could benefit individuals with a variety of neuropsychiatric disorders.
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Affiliation(s)
- Amy E Pohodich
- Department of Neuroscience, Baylor College of Medicine, Houston, United States.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, United States
| | - Hari Yalamanchili
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, United States.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
| | - Ayush T Raman
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, United States.,Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, United States
| | - Ying-Wooi Wan
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, United States.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
| | - Michael Gundry
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
| | - Shuang Hao
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, United States.,Section of Neurology, Department of Pediatrics, Baylor College of Medicine, Houston, United States
| | - Haijing Jin
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, United States.,Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, United States
| | - Jianrong Tang
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, United States.,Section of Neurology, Department of Pediatrics, Baylor College of Medicine, Houston, United States
| | - Zhandong Liu
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, United States.,Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, United States.,Section of Neurology, Department of Pediatrics, Baylor College of Medicine, Houston, United States
| | - Huda Y Zoghbi
- Department of Neuroscience, Baylor College of Medicine, Houston, United States.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, United States.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States.,Howard Hughes Medical Institute, Baylor College of Medicine, Houston, United States
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