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Ma H, Kennard A, Mattson N, Khan AS. Characterization of Sf9 cell clones with differential susceptibilities to Sf-rhabdovirus X +3.7 and Sf-rhabdovirus X - replication. Virology 2024; 594:110038. [PMID: 38471199 DOI: 10.1016/j.virol.2024.110038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 02/16/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024]
Abstract
Our laboratory previously discovered a novel rhabdovirus in the Spodoptera frugiperda Sf9 insect cell line that was designated as Sf-rhabdovirus. Using limiting dilution, this cell line was found to be a mixed population of cells infected by Sf-rhabdovirus variants containing either the full length X accessory gene with a 3.7 kb internal duplication (designated as Sf-rhabdovirus X+3.7) or lacking the duplication and part of the X gene (designated as Sf-rhabdovirus X-), and cells that were negative for Sf-rhabdovirus. In this paper, we found that the Sf-rhabdovirus negative cell clones had sub-populations with different susceptibilities to the replication of Sf-rhabdovirus X+3.7 and X- variants: cell clone Sf9-13F12 was more sensitive to replication by both virus variants compared to Sf9-3003; moreover, Sf9-3003 showed more resistance to X+3.7 replication than to X- replication. RNA-Seq analysis indicated significant differentially expressed genes in the Sf9-13F12 and Sf9-3003 cell clones further supporting that distinct sub-populations of virus-negative cells co-exist in the parent Sf9 cell line.
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Affiliation(s)
- Hailun Ma
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - Andrea Kennard
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - Nicholas Mattson
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - Arifa S Khan
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, 20993, USA.
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2
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Verble KM, Keaveny EC, Rahman SR, Jenny MJ, Dillon ME, Lozier JD. A rapid return to normal: temporal gene expression patterns following cold exposure in the bumble bee Bombus impatiens. J Exp Biol 2024; 227:jeb247040. [PMID: 38629177 DOI: 10.1242/jeb.247040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 04/02/2024] [Indexed: 05/01/2024]
Abstract
Bumble bees are common in cooler climates and many species likely experience periodic exposure to very cold temperatures, but little is known about the temporal dynamics of cold response mechanisms following chill exposure, especially how persistent effects of cold exposure may facilitate tolerance of future events. To investigate molecular processes involved in the temporal response by bumble bees to acute cold exposure, we compared mRNA transcript abundance in Bombus impatiens workers exposed to 0°C for 75 min (inducing chill coma) and control bees maintained at a constant ambient temperature (28°C). We sequenced the 3' end of mRNA transcripts (TagSeq) to quantify gene expression in thoracic tissue of bees at several time points (0, 10, 30, 120 and 720 min) following cold exposure. Significant differences from control bees were only detectable within 30 min after the treatment, with most occurring at the 10 min recovery time point. Genes associated with gluconeogenesis and glycolysis were most notably upregulated, while genes related to lipid and purine metabolism were downregulated. The observed patterns of expression indicate a rapid recovery after chill coma, suggesting an acute differential transcriptional response during recovery from chill coma and return to baseline expression levels within an hour, with no long-term gene expression markers of this cold exposure. Our work highlights the functions and pathways important for acute cold recovery, provides an estimated time frame for recovery from cold exposure in bumble bees, and suggests that cold hardening may be less important for these heterothermic insects.
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Affiliation(s)
- Kelton M Verble
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Ellen C Keaveny
- Department of Zoology & Physiology and Program in Ecology and Evolution, University of Wyoming, Laramie, WY 82072, USA
| | | | - Matthew J Jenny
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Michael E Dillon
- Department of Zoology & Physiology and Program in Ecology and Evolution, University of Wyoming, Laramie, WY 82072, USA
| | - Jeffrey D Lozier
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
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3
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Juaiti M, Feng Y, Tang Y, Liang B, Zha L, Yu Z. Integrated bioinformatics analysis and experimental animal models identify a robust biomarker and its correlation with the immune microenvironment in pulmonary arterial hypertension. Heliyon 2024; 10:e29587. [PMID: 38660271 PMCID: PMC11040037 DOI: 10.1016/j.heliyon.2024.e29587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/09/2024] [Accepted: 04/10/2024] [Indexed: 04/26/2024] Open
Abstract
Background Pulmonary arterial hypertension (PAH) represents a substantial global risk to human health. This study aims to identify diagnostic biomarkers for PAH and assess their association with the immune microenvironment through the utilization of sophisticated bioinformatics techniques. Methods Based on two microarray datasets, differentially expressed genes (DEGs) were detected, and hub genes underwent a sequence of machine learning analyses. After pathways associated with PAH were assessed by gene enrichment analysis, the identified genes were validated using external datasets and confirmed in a monocrotaline (MCT)-induced rat model. In addition, three algorithms were employed to estimate the proportions of various immune cell types, and the link between hub genes and immune cells was substantiated. Results Using SVM, LASSO, and WGCNA, we identified seven hub genes, including (BPIFA1, HBA2, HBB, LOC441081, PI15, S100A9, and WIF1), of which only BPIFA1 remained stable in the external datasets and was validated in an MCT-induced rat model. Furthermore, the results of the functional enrichment analysis established a link between PAH and both metabolism and the immune system. Correlation assessment showed that BPIFA1 expression in the MCP-counter algorithm was negatively associated with various immune cell types, positively correlated with macrophages in the ssGSEA algorithm, and correlated with M1 and M2 macrophages in the CIBERSORT algorithm. Conclusion BPIFA1 serves as a modulator of PAH, with the potential to impact the immune microenvironment and disease progression, possibly through its regulatory influence on both M1 and M2 macrophages.
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Affiliation(s)
- Mukamengjiang Juaiti
- Department of Cardiology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P.R. China
| | - Yilu Feng
- Department of Cardiology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P.R. China
| | - Yiyang Tang
- Department of Cardiology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P.R. China
| | - Benhui Liang
- Department of Cardiology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P.R. China
| | - Lihuang Zha
- Department of Cardiology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P.R. China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P.R. China
| | - Zaixin Yu
- Department of Cardiology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P.R. China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P.R. China
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Lee WG, Asuelime GE, Asuelime-Smith MBT, Chen SY, Kim ES. Differential RNA Expression Between Metastatic and Primary Neuroblastoma Cells. J Surg Res 2024; 298:240-250. [PMID: 38631173 DOI: 10.1016/j.jss.2024.03.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 02/01/2024] [Accepted: 03/21/2024] [Indexed: 04/19/2024]
Abstract
INTRODUCTION Neuroblastoma (NB) is the most common extra-cranial malignancy in children. Poor survival in high-risk NB is attributed to recurrent metastatic disease. To better study metastatic disease, we used a novel mouse model to investigate differential gene expression between primary tumor cells and metastatic cells. We hypothesized that metastatic NB cells have a different gene expression profile from primary tumor cells and cultured cells. METHODS Using three human NB cell lines (NGP, CHLA255, and SH-SY5Y), orthotopic xenografts were established in immunodeficient nod/scid gamma mice via subcapsular renal injection. Mice were sacrificed and NB cells were isolated from the primary tumor and from sites of metastasis (bone marrow, liver). RNA sequencing, gene set analysis, and pathway analysis were performed to identify differentially expressed genes and molecular pathways in the metastatic cells compared to primary tumor cells. RESULTS There were 266 differentially expressed genes in metastatic tumor cells (bone marrow and liver combined) compared to primary tumor cells. The top upregulated gene was KCNK1 and the top downregulated genes were PDE7B and NEBL. Top upregulated pathways in the metastatic cells were involved in ion transport, cell signaling, and cell proliferation. Top downregulated pathways were involved in DNA synthesis, transcription, and cellular metabolism. CONCLUSIONS In metastatic NB cells, our study identified the upregulation of biologic processes involved in cell cycle regulation, cell proliferation, migration, and invasion. Ongoing studies aim to validate downstream translation of these genomic alterations, as well as target these pathways to more effectively suppress and inhibit recurrent metastatic disease in NB.
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Affiliation(s)
- William G Lee
- Division of Pediatric Surgery, Children's Hospital Los Angeles, Los Angeles, California; Division of Pediatric Surgery, Cedars-Sinai Medical Center, Los Angeles, California
| | - Grace E Asuelime
- Division of Pediatric Surgery, Children's Hospital Los Angeles, Los Angeles, California
| | | | - Stephanie Y Chen
- Division of Pediatric Surgery, Children's Hospital Los Angeles, Los Angeles, California; Division of Pediatric Surgery, Cedars-Sinai Medical Center, Los Angeles, California
| | - Eugene S Kim
- Division of Pediatric Surgery, Children's Hospital Los Angeles, Los Angeles, California; Division of Pediatric Surgery, Cedars-Sinai Medical Center, Los Angeles, California; Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, California.
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Saizonou H, Impoinvil LM, Derilus D, Omoke D, Okeyo S, Dada N, Corredor C, Mulder N, Lenhart A, Ochomo E, Djogbénou LS. Transcriptomic analysis of Anopheles gambiae from Benin reveals overexpression of salivary and cuticular proteins associated with cross-resistance to pyrethroids and organophosphates. BMC Genomics 2024; 25:348. [PMID: 38582836 PMCID: PMC10998338 DOI: 10.1186/s12864-024-10261-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 03/27/2024] [Indexed: 04/08/2024] Open
Abstract
BACKGROUND Insecticide resistance (IR) is one of the major threats to malaria vector control programs in endemic countries. However, the mechanisms underlying IR are poorly understood. Thus, investigating gene expression patterns related to IR can offer important insights into the molecular basis of IR in mosquitoes. In this study, RNA-Seq was used to characterize gene expression in Anopheles gambiae surviving exposure to pyrethroids (deltamethrin, alphacypermethrin) and an organophosphate (pirimiphos-methyl). RESULTS Larvae of An. gambiae s.s. collected from Bassila and Djougou in Benin were reared to adulthood and phenotyped for IR using a modified CDC intensity bottle bioassay. The results showed that mosquitoes from Djougou were more resistant to pyrethroids (5X deltamethrin: 51.7% mortality; 2X alphacypermethrin: 47.4%) than Bassila (1X deltamethrin: 70.7%; 1X alphacypermethrin: 77.7%), while the latter were more resistant to pirimiphos-methyl (1.5X: 48.3% in Bassila and 1X: 21.5% in Djougou). RNA-seq was then conducted on resistant mosquitoes, non-exposed mosquitoes from the same locations and the laboratory-susceptible An. gambiae s.s. Kisumu strain. The results showed overexpression of detoxification genes, including cytochrome P450s (CYP12F2, CYP12F3, CYP4H15, CYP4H17, CYP6Z3, CYP9K1, CYP4G16, and CYP4D17), carboxylesterase genes (COEJHE5E, COE22933) and glutathione S-transferases (GSTE2 and GSTMS3) in all three resistant mosquito groups analyzed. Genes encoding cuticular proteins (CPR130, CPR10, CPR15, CPR16, CPR127, CPAP3-C, CPAP3-B, and CPR76) were also overexpressed in all the resistant groups, indicating their potential role in cross resistance in An. gambiae. Salivary gland protein genes related to 'salivary cysteine-rich peptide' and 'salivary secreted mucin 3' were also over-expressed and shared across all resistant groups. CONCLUSION Our results suggest that in addition to metabolic enzymes, cuticular and salivary gland proteins could play an important role in cross-resistance to multiple classes of insecticides in Benin. These genes warrant further investigation to validate their functional role in An. gambiae resistance to insecticides.
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Affiliation(s)
- Helga Saizonou
- Tropical Infectious Diseases Research Centre (TIDRC), University of Abomey-Calavi (UAC), Abomey-Calavi, Benin.
| | - Lucy Mackenzie Impoinvil
- Entomology Branch, Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Dieunel Derilus
- Entomology Branch, Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Diana Omoke
- Kenya Medical Research Institute (KEMRI), Centre for Global Health Research (CGHR), Kisumu, Kenya
| | - Stephen Okeyo
- Kenya Medical Research Institute (KEMRI), Centre for Global Health Research (CGHR), Kisumu, Kenya
| | - Nsa Dada
- Tropical Infectious Diseases Research Centre (TIDRC), University of Abomey-Calavi (UAC), Abomey-Calavi, Benin
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Claudia Corredor
- Entomology Branch, Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Nicola Mulder
- Human, Heredity, and Health in Africa H3ABionet network, Cape Town, South Africa
| | - Audrey Lenhart
- Entomology Branch, Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Eric Ochomo
- Kenya Medical Research Institute (KEMRI), Centre for Global Health Research (CGHR), Kisumu, Kenya
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Luc S Djogbénou
- Tropical Infectious Diseases Research Centre (TIDRC), University of Abomey-Calavi (UAC), Abomey-Calavi, Benin.
- Regional Institute of Public Health (IRSP), Ouidah, Benin.
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, UK.
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Lobo-Alves SC, Oliveira LAD, Kretzschmar GC, Valengo AE, Rosati R. Long noncoding RNA expression in acute lymphoblastic leukemia: A systematic review. Crit Rev Oncol Hematol 2024; 196:104290. [PMID: 38341118 DOI: 10.1016/j.critrevonc.2024.104290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 01/03/2024] [Accepted: 02/05/2024] [Indexed: 02/12/2024] Open
Abstract
Long noncoding RNAs (lncRNAs), as gene expression modulators, are potential players in Acute Lymphoblastic Leukemia (ALL) pathogenesis. We systematically explored current literature on lncRNA expression in ALL to identify lncRNAs consistently reported as differentially expressed (DE) either in ALL versus controls or between ALL subtypes. By comparing articles that provided global expression data for DE lncRNAs in the ETV6::RUNX1-positive ALL subtype, we identified four DE lncRNAs in three independent studies (two versus other subtypes and one versus controls), showing concordant expression of LINC01013, CRNDE and lnc-KLF7-1. Additionally, LINC01503 was consistently downregulated on ALL versus controls. Within RT-qPCR studies, twelve lncRNA were DE in more than one source. Thus, several lncRNAs were supported as DE in ALL by multiple sources, highlighting their potential role as candidate biomarkers or therapeutic targets. Finally, as lncRNA annotation is rapidly expanding, standardization of reporting and nomenclature is urgently needed to improve data verifiability and compilation.
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Affiliation(s)
- Sara Cristina Lobo-Alves
- Instituto de Pesquisa Pelé Pequeno Príncipe, Av. Silva Jardim, 1632 - Água Verde, Curitiba, PR 80250-060, Brazil; Faculdades Pequeno Príncipe, Av Iguaçu, 333, Rebouças, Curitiba, PR 80230-020, Brazil; National Science and Technology Institute for Children's Cancer Biology and Pediatric Oncology - INCT BioOncoPed, Porto Alegre, RS 90035-003, Brazil.
| | - Liana Alves de Oliveira
- Instituto de Pesquisa Pelé Pequeno Príncipe, Av. Silva Jardim, 1632 - Água Verde, Curitiba, PR 80250-060, Brazil; National Science and Technology Institute for Children's Cancer Biology and Pediatric Oncology - INCT BioOncoPed, Porto Alegre, RS 90035-003, Brazil.
| | - Gabriela Canalli Kretzschmar
- Instituto de Pesquisa Pelé Pequeno Príncipe, Av. Silva Jardim, 1632 - Água Verde, Curitiba, PR 80250-060, Brazil; Faculdades Pequeno Príncipe, Av Iguaçu, 333, Rebouças, Curitiba, PR 80230-020, Brazil; National Science and Technology Institute for Children's Cancer Biology and Pediatric Oncology - INCT BioOncoPed, Porto Alegre, RS 90035-003, Brazil.
| | - Andressa Eloisa Valengo
- Instituto de Pesquisa Pelé Pequeno Príncipe, Av. Silva Jardim, 1632 - Água Verde, Curitiba, PR 80250-060, Brazil; Faculdades Pequeno Príncipe, Av Iguaçu, 333, Rebouças, Curitiba, PR 80230-020, Brazil
| | - Roberto Rosati
- Instituto de Pesquisa Pelé Pequeno Príncipe, Av. Silva Jardim, 1632 - Água Verde, Curitiba, PR 80250-060, Brazil; Faculdades Pequeno Príncipe, Av Iguaçu, 333, Rebouças, Curitiba, PR 80230-020, Brazil; National Science and Technology Institute for Children's Cancer Biology and Pediatric Oncology - INCT BioOncoPed, Porto Alegre, RS 90035-003, Brazil.
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Sabalette KB, Campo VA, Sotelo-Silveira JR, Smircich P, De Gaudenzi JG. RNA-seq data exploration after trypanosome RNA-binding protein UBP1 expression is altered by CRISPR-Cas9 gene editing and overexpression. Data Brief 2024; 53:110156. [PMID: 38389957 PMCID: PMC10881420 DOI: 10.1016/j.dib.2024.110156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/24/2024] Open
Abstract
Previous studies have shown that overexpression of the Trypanosoma cruzi U-rich RNA-binding protein 1 (TcUBP1) in insect-dwelling epimastigotes results in a gene expression pattern resembling that of the infective form of the pathogen. Here, we used CRISPR-Cas9-induced edition of TcUBP1 and full-length protein overexpression in epimastigote cells to monitor transcriptomic changes during the epimastigote-to-metacyclic trypomastigote stage transition of T. cruzi. This dataset includes the bioinformatics analysis of three different RNA-seq samples, each with three biological replicates, showing differential mRNA abundances. The current transcriptome report has the potential to shed light on the quantitative variances in the expression of significant up- or down-regulated mRNAs as a consequence of the levels of the UBP1 protein. Raw data files were deposited at the NCBI Sequence Read Archive - SRA at http://ncbi.nlm.nih.gov/Traces/sra/sra.cgi with accession numbers PRJNA907231 and PRJNA949967.
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Affiliation(s)
- Karina B Sabalette
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín - Consejo Nacional de Investigaciones Científicas y Técnicas, 1650 General San Martín, Prov. de Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, 1650 General San Martín, Prov. de Buenos Aires, Argentina
| | - Vanina A Campo
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín - Consejo Nacional de Investigaciones Científicas y Técnicas, 1650 General San Martín, Prov. de Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, 1650 General San Martín, Prov. de Buenos Aires, Argentina
| | - José R Sotelo-Silveira
- Instituto de Investigaciones Biológicas Clemente Estable, Av. Italia 3318, Montevideo, CP 11600, Uruguay
- Instituto de Biología, School of Sciences, Universidad de la República, Montevideo, Uruguay
| | - Pablo Smircich
- Instituto de Investigaciones Biológicas Clemente Estable, Av. Italia 3318, Montevideo, CP 11600, Uruguay
- Instituto de Biología, School of Sciences, Universidad de la República, Montevideo, Uruguay
| | - Javier G De Gaudenzi
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín - Consejo Nacional de Investigaciones Científicas y Técnicas, 1650 General San Martín, Prov. de Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, 1650 General San Martín, Prov. de Buenos Aires, Argentina
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Bugaj AM, Kunath N, Saasen VL, Fernandez-Berrocal MS, Vankova A, Sætrom P, Bjørås M, Ye J. Dissecting gene expression networks in the developing hippocampus through the lens of NEIL3 depletion. Prog Neurobiol 2024; 235:102599. [PMID: 38522610 DOI: 10.1016/j.pneurobio.2024.102599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/09/2024] [Accepted: 03/19/2024] [Indexed: 03/26/2024]
Abstract
Gene regulation in the hippocampus is fundamental for its development, synaptic plasticity, memory formation, and adaptability. Comparisons of gene expression among different developmental stages, distinct cell types, and specific experimental conditions have identified differentially expressed genes contributing to the organization and functionality of hippocampal circuits. The NEIL3 DNA glycosylase, one of the DNA repair enzymes, plays an important role in hippocampal maturation and neuron functionality by shaping transcription. While differential gene expression (DGE) analysis has identified key genes involved, broader gene expression patterns crucial for high-order hippocampal functions remain uncharted. By utilizing the weighted gene co-expression network analysis (WGCNA), we mapped gene expression networks in immature (p8-neonatal) and mature (3 m-adult) hippocampal circuits in wild-type and NEIL3-deficient mice. Our study unveiled intricate gene network structures underlying hippocampal maturation, delineated modules of co-expressed genes, and pinpointed highly interconnected hub genes specific to the maturity of hippocampal subregions. We investigated variations within distinct gene network modules following NEIL3 depletion, uncovering NEIL3-targeted hub genes that influence module connectivity and specificity. By integrating WGCNA with DGE, we delve deeper into the NEIL3-dependent molecular intricacies of hippocampal maturation. This study provides a comprehensive systems-level analysis for assessing the potential correlation between gene connectivity and functional connectivity within the hippocampal network, thus shaping hippocampal function throughout development.
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Affiliation(s)
- Anna M Bugaj
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), Trondheim 7491, Norway
| | - Nicolas Kunath
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), Trondheim 7491, Norway; Department of Neuromedicine and Movement Science, Norwegian University of Science and Technology (NTNU), Trondheim 7491, Norway; Department of Neurology, University Hospital of Trondheim, Trondheim 7491, Norway
| | - Vidar Langseth Saasen
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), Trondheim 7491, Norway
| | - Marion S Fernandez-Berrocal
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), Trondheim 7491, Norway
| | - Ana Vankova
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), Trondheim 7491, Norway
| | - Pål Sætrom
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), Trondheim 7491, Norway
| | - Magnar Bjørås
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), Trondheim 7491, Norway; Department of Microbiology, Oslo University Hospital, University of Oslo, Oslo 0424, Norway; Centre for Embryology and Healthy Development, University of Oslo, Oslo 0373, Norway.
| | - Jing Ye
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), Trondheim 7491, Norway.
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Blumenkamp P, Pfister M, Diedrich S, Brinkrolf K, Jaenicke S, Goesmann A. Curare and GenExVis: a versatile toolkit for analyzing and visualizing RNA-Seq data. BMC Bioinformatics 2024; 25:138. [PMID: 38553675 PMCID: PMC10979593 DOI: 10.1186/s12859-024-05761-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 03/25/2024] [Indexed: 04/02/2024] Open
Abstract
Even though high-throughput transcriptome sequencing is routinely performed in many laboratories, computational analysis of such data remains a cumbersome process often executed manually, hence error-prone and lacking reproducibility. For corresponding data processing, we introduce Curare, an easy-to-use yet versatile workflow builder for analyzing high-throughput RNA-Seq data focusing on differential gene expression experiments. Data analysis with Curare is customizable and subdivided into preprocessing, quality control, mapping, and downstream analysis stages, providing multiple options for each step while ensuring the reproducibility of the workflow. For a fast and straightforward exploration and visualization of differential gene expression results, we provide the gene expression visualizer software GenExVis. GenExVis can create various charts and tables from simple gene expression tables and DESeq2 results without the requirement to upload data or install software packages. In combination, Curare and GenExVis provide a comprehensive software environment that supports the entire data analysis process, from the initial handling of raw RNA-Seq data to the final DGE analyses and result visualizations, thereby significantly easing data processing and subsequent interpretation.
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Affiliation(s)
- Patrick Blumenkamp
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, 35392, Giessen, Germany.
| | - Max Pfister
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, 35392, Giessen, Germany
| | - Sonja Diedrich
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, 35392, Giessen, Germany
| | - Karina Brinkrolf
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, 35392, Giessen, Germany
| | - Sebastian Jaenicke
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, 35392, Giessen, Germany
| | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, 35392, Giessen, Germany
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Thirunavukkarasu MK, Ramesh P, Karuppasamy R, Veerappapillai S. Transcriptome profiling and metabolic pathway analysis towards reliable biomarker discovery in early-stage lung cancer. J Appl Genet 2024:10.1007/s13353-024-00847-2. [PMID: 38443694 DOI: 10.1007/s13353-024-00847-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 02/21/2024] [Accepted: 02/22/2024] [Indexed: 03/07/2024]
Abstract
Earlier diagnosis of lung cancer is crucial for reducing mortality and morbidity in high-risk patients. Liquid biopsy is a critical technique for detecting the cancer earlier and tracking the treatment outcomes. However, noninvasive biomarkers are desperately needed due to the lack of therapeutic sensitivity and early-stage diagnosis. Therefore, we have utilized transcriptomic profiling of early-stage lung cancer patients to discover promising biomarkers and their associated metabolic functions. Initially, PCA highlights the diversity level of gene expression in three stages of lung cancer samples. We have identified two major clusters consisting of highly variant genes among the three stages. Further, a total of 7742, 6611, and 643 genes were identified as DGE for stages I-III respectively. Topological analysis of the protein-protein interaction network resulted in seven candidate biomarkers such as JUN, LYN, PTK2, UBC, HSP90AA1, TP53, and UBB cumulatively for the three stages of lung cancers. Gene enrichment and KEGG pathway analyses aid in the comprehension of pathway mechanisms and regulation of identified hub genes in lung cancer. Importantly, the medial survival rates up to ~ 70 months were identified for hub genes during the Kaplan-Meier survival analysis. Moreover, the hub genes displayed the significance of risk factors during gene expression analysis using TIMER2.0 analysis. Therefore, we have reason that these biomarkers may serve as a prospective targeting candidate with higher treatment efficacy in early-stage lung cancer patients.
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Affiliation(s)
| | - Priyanka Ramesh
- Bioinformatics Core, College of Agriculture, Agriculture Research and Graduate Education, Purdue University, West Lafayette, IN, 47907, USA
| | - Ramanathan Karuppasamy
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, 632014, Tamil Nadu, India
| | - Shanthi Veerappapillai
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, 632014, Tamil Nadu, India.
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Panzade KP, Tribhuvan KU, Pawar DV, Jasrotia RS, Gaikwad K, Dalal M, Kumar RR, Singh MP, Awasthi OP, Padaria JC. Discovering the regulators of heat stress tolerance in Ziziphus nummularia (Burm.f) wight and walk.-arn. Physiol Mol Biol Plants 2024; 30:497-511. [PMID: 38633271 PMCID: PMC11018567 DOI: 10.1007/s12298-024-01431-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 12/14/2023] [Accepted: 03/01/2024] [Indexed: 04/19/2024]
Abstract
Ziziphus nummularia an elite heat-stress tolerant shrub, grows in arid regions of desert. However, its molecular mechanism responsible for heat stress tolerance is unexplored. Therefore, we analysed whole transcriptome of Jaisalmer (heat tolerant) and Godhra (heat sensitive) genotypes of Z. nummularia to understand its molecular mechanism responsible for heat stress tolerance. De novo assembly of 16,22,25,052 clean reads yielded 276,029 transcripts. A total of 208,506 unigenes were identified which contains 4290 and 1043 differentially expressed genes (DEG) in TGO (treated Godhra at 42 °C) vs. CGO (control Godhra) and TJR (treated Jaisalmer at 42 °C) vs. CJR (control Jaisalmer), respectively. A total of 987 (67 highly enriched) and 754 (34 highly enriched) pathways were obsorved in CGO vs. TGO and CJR vs. TJR, respectively. Antioxidant pathways and TFs like Homeobox, HBP, ARR, PHD, GRAS, CPP, and E2FA were uniquely observed in Godhra genotype and SET domains were uniquely observed in Jaisalmer genotype. Further transposable elements were highly up-regulated in Godhra genotype but no activation in Jaisalmer genotype. A total of 43,093 and 39,278 simple sequence repeats were identified in the Godhra and Jaisalmer genotypes, respectively. A total of 10 DEGs linked to heat stress were validated in both genotypes for their expression under different heat stresses using quantitative real-time PCR. Comparing expression patterns of the selected DEGs identified ClpB1 as a potential candidate gene for heat tolerance in Z. nummularia. Here we present first characterized transcriptome of Z. nummularia in response to heat stress for the identification and characterization of heat stress-responsive genes. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-024-01431-y.
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Affiliation(s)
- Kishor Prabhakar Panzade
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012 Delhi India
- PG School, Indian Agricultural Research Institute, New Delhi, 110 012 Delhi India
| | - Kishor U. Tribhuvan
- ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, Jharkhand 834 003 India
| | - Deepak V. Pawar
- ICAR- Directorate of Weed Research, Maharajpur, Jabalpur, Madhya Pradesh 482004 India
| | - Rahul Singh Jasrotia
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012 Delhi India
- University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Dr., San Antonio, TX 78229 USA
| | - Kishor Gaikwad
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012 Delhi India
- PG School, Indian Agricultural Research Institute, New Delhi, 110 012 Delhi India
| | - Monika Dalal
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012 Delhi India
- PG School, Indian Agricultural Research Institute, New Delhi, 110 012 Delhi India
| | - Ranjeet Ranjan Kumar
- Division of Biochemistry, ICAR–Indian Agricultural Research Institute, New Delhi, 110 012 Delhi India
- PG School, Indian Agricultural Research Institute, New Delhi, 110 012 Delhi India
| | - Madan Pal Singh
- Division of Plant Physiology, ICAR-Indian Agrcultural Research Institute, New Delhi, 110 012 Delhi India
- PG School, Indian Agricultural Research Institute, New Delhi, 110 012 Delhi India
| | - Om Prakash Awasthi
- Division of Horticulture, ICAR-Indian Agrcultural Research Institute, New Delhi, 110 012 Delhi India
- PG School, Indian Agricultural Research Institute, New Delhi, 110 012 Delhi India
| | - Jasdeep Chatrath Padaria
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012 Delhi India
- PG School, Indian Agricultural Research Institute, New Delhi, 110 012 Delhi India
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12
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Kälin C, Piombo E, Bourras S, Brantestam AK, Dubey M, Elfstrand M, Karlsson M. Transcriptomic analysis identifies candidate genes for Aphanomyces root rot disease resistance in pea. BMC Plant Biol 2024; 24:144. [PMID: 38413860 PMCID: PMC10900555 DOI: 10.1186/s12870-024-04817-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 02/12/2024] [Indexed: 02/29/2024]
Abstract
BACKGROUND Aphanomyces euteiches is a soil-borne oomycete that causes root rot in pea and other legume species. Symptoms of Aphanomyces root rot (ARR) include root discoloration and wilting, leading to significant yield losses in pea production. Resistance to ARR is known to be polygenic but the roles of single genes in the pea immune response are still poorly understood. This study uses transcriptomics to elucidate the immune response of two pea genotypes varying in their levels of resistance to A. euteiches. RESULTS In this study, we inoculated roots of the pea (P. sativum L.) genotypes 'Linnea' (susceptible) and 'PI180693' (resistant) with two different A. euteiches strains varying in levels of virulence. The roots were harvested at 6 h post-inoculation (hpi), 20 hpi and 48 hpi, followed by differential gene expression analysis. Our results showed a time- and genotype-dependent immune response towards A. euteiches infection, involving several WRKY and MYB-like transcription factors, along with genes associated with jasmonic acid (JA) and abscisic acid (ABA) signaling. By cross-referencing with genes segregating with partial resistance to ARR, we identified 39 candidate disease resistance genes at the later stage of infection. Among the genes solely upregulated in the resistant genotype 'PI180693', Psat7g091800.1 was polymorphic between the pea genotypes and encoded a Leucine-rich repeat receptor-like kinase reminiscent of the Arabidopsis thaliana FLAGELLIN-SENSITIVE 2 receptor. CONCLUSIONS This study provides new insights into the gene expression dynamics controlling the immune response of resistant and susceptible pea genotypes to A. euteiches infection. We present a set of 39 candidate disease resistance genes for ARR in pea, including the putative immune receptor Psat7g091800.1, for future functional validation.
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Affiliation(s)
- Carol Kälin
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
| | - Edoardo Piombo
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Salim Bourras
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | | | - Mukesh Dubey
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Malin Elfstrand
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Magnus Karlsson
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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13
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Castillejo-López C, Bárcenas-Walls JR, Cavalli M, Larsson A, Wadelius C. A regulatory element associated to NAFLD in the promoter of DIO1 controls LDL-C, HDL-C and triglycerides in hepatic cells. Lipids Health Dis 2024; 23:48. [PMID: 38365720 PMCID: PMC10870585 DOI: 10.1186/s12944-024-02029-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 01/22/2024] [Indexed: 02/18/2024] Open
Abstract
BACKGROUND Genome-wide association studies (GWAS) have identified genetic variants linked to fat metabolism and related traits, but rarely pinpoint causative variants. This limitation arises from GWAS not considering functional implications of noncoding variants that can affect transcription factor binding and potentially regulate gene expression. The aim of this study is to investigate a candidate noncoding functional variant within a genetic locus flagged by a GWAS SNP associated with non-alcoholic fatty liver disease (NAFLD), a condition characterized by liver fat accumulation in non-alcohol consumers. METHODS CRISPR-Cas9 gene editing in HepG2 cells was used to modify the regulatory element containing the candidate functional variant linked to NAFLD. Global gene expression in mutant cells was assessed through RT-qPCR and targeted transcriptomics. A phenotypic assay measured lipid droplet accumulation in the CRISPR-Cas9 mutants. RESULTS The candidate functional variant, rs2294510, closely linked to the NAFLD-associated GWAS SNP rs11206226, resided in a regulatory element within the DIO1 gene's promoter region. Altering this element resulted in changes in transcription factor binding sites and differential expression of candidate target genes like DIO1, TMEM59, DHCR24, and LDLRAD1, potentially influencing the NAFLD phenotype. Mutant HepG2 cells exhibited increased lipid accumulation, a hallmark of NAFLD, along with reduced LDL-C, HDL-C and elevated triglycerides. CONCLUSIONS This comprehensive approach, that combines genome editing, transcriptomics, and phenotypic assays identified the DIO1 promoter region as a potential enhancer. Its activity could regulate multiple genes involved in the NAFLD phenotype or contribute to defining a polygenic risk score for enhanced risk assessment in NAFLD patients.
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Affiliation(s)
- Casimiro Castillejo-López
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, 751 08 , Uppsala, Sweden, Box 815, Husargatan 3, BMC
| | - José Ramón Bárcenas-Walls
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, 751 08 , Uppsala, Sweden, Box 815, Husargatan 3, BMC
| | - Marco Cavalli
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, 751 08 , Uppsala, Sweden, Box 815, Husargatan 3, BMC
| | - Anders Larsson
- Department of Medical Sciences, Clinical Chemistry, Uppsala University Hospital, 751 85, Uppsala, Sweden
| | - Claes Wadelius
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, 751 08 , Uppsala, Sweden, Box 815, Husargatan 3, BMC.
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Sadeesh EM, Lahamge MS, Malik A, Ampadi AN. Differential Expression of Nuclear-Encoded Mitochondrial Protein Genes of ATP Synthase Across Different Tissues of Female Buffalo. Mol Biotechnol 2024:10.1007/s12033-024-01085-x. [PMID: 38305843 DOI: 10.1007/s12033-024-01085-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 01/22/2024] [Indexed: 02/03/2024]
Abstract
The physiological well-being of buffaloes, encompassing phenotypic traits, reproductive health, and productivity, depends on their energy status. Mitochondria, the architects of energy production, orchestrate a nuanced interplay between nuclear and mitochondrial domains. Oxidative phosphorylation complexes and associated proteins wield significant influence over metabolic functions, energy synthesis, and organelle dynamics, often linked to tissue-specific pathologies. The unexplored role of ATP synthase in buffalo tissues prompted a hypothesis: in-depth exploration of nuclear-derived mitochondrial genes, notably ATP synthase, reveals distinctive tissue-specific diversity. RNA extraction and sequencing of buffalo tissues (kidney, heart, brain, and ovary) enabled precise quantification of nuclear-derived mitochondrial protein gene expression. The analysis unveiled 24 ATP synthase transcript variants, each with unique tissue-specific patterns. Kidney, brain, and heart exhibited elevated gene expression compared to ovaries, with 10, 8, and 19 up-regulated genes, respectively. The kidney showed 3 and 12 down-regulated genes compared to the brain and heart. The heart-brain comparison highlighted ten highly expressed genes in ATP synthase functions. Gene ontology and pathway analyses revealed enriched functions linked to ATP synthesis and oxidative phosphorylation, offering a comprehensive understanding of energy production in buffalo tissues. This analysis enhances understanding of tissue-specific gene expression, emphasizing the influence of energy demands. Revealing intricate links between mitochondrial gene expression and tissue specialization in buffaloes, it provides nuanced insights into tissue-specific expression of nuclear-encoded mitochondrial protein genes, notably ATP synthase, advancing the comprehension of buffalo tissue biology.
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Affiliation(s)
- E M Sadeesh
- Laboratory of Mitochondrial Biology of Farm Animals, Animal Biochemistry Division, ICAR- National Dairy Research Institute, Karnal, Haryana, 132001, India.
| | - Madhuri S Lahamge
- Laboratory of Mitochondrial Biology of Farm Animals, Animal Biochemistry Division, ICAR- National Dairy Research Institute, Karnal, Haryana, 132001, India
| | - Anuj Malik
- Laboratory of Mitochondrial Biology of Farm Animals, Animal Biochemistry Division, ICAR- National Dairy Research Institute, Karnal, Haryana, 132001, India
| | - A N Ampadi
- Laboratory of Mitochondrial Biology of Farm Animals, Animal Biochemistry Division, ICAR- National Dairy Research Institute, Karnal, Haryana, 132001, India
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15
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Kuttiyarthu Veetil N, Cedraz de Oliveira H, Gomez-Samblas M, Divín D, Melepat B, Voukali E, Świderská Z, Krajzingrová T, Těšický M, Jung F, Beneš V, Madsen O, Vinkler M. Peripheral inflammation-induced changes in songbird brain gene expression: 3' mRNA transcriptomic approach. Dev Comp Immunol 2024; 151:105106. [PMID: 38013114 DOI: 10.1016/j.dci.2023.105106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 11/03/2023] [Accepted: 11/21/2023] [Indexed: 11/29/2023]
Abstract
Species-specific neural inflammation can be induced by profound immune signalling from periphery to brain. Recent advances in transcriptomics offer cost-effective approaches to study this regulation. In a population of captive zebra finch (Taeniopygia guttata), we compare the differential gene expression patterns in lipopolysaccharide (LPS)-triggered peripheral inflammation revealed by RNA-seq and QuantSeq. The RNA-seq approach identified more differentially expressed genes but failed to detect any inflammatory markers. In contrast, QuantSeq results identified specific expression changes in the genes regulating inflammation. Next, we adopted QuantSeq to relate peripheral and brain transcriptomes. We identified subtle changes in the brain gene expression during the peripheral inflammation (e.g. up-regulation in AVD-like and ACOD1 expression) and detected co-structure between the peripheral and brain inflammation. Our results suggest benefits of the 3'end transcriptomics for association studies between peripheral and neural inflammation in genetically heterogeneous models and identify potential targets for the future brain research in birds.
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Affiliation(s)
- Nithya Kuttiyarthu Veetil
- Charles University, Faculty of Science, Department of Zoology, Viničná 7, 128 43, Prague, Czech Republic.
| | - Haniel Cedraz de Oliveira
- Wageningen University and Research, Department of Animal Sciences, Animal Breeding and Genomics, Droevendaalsesteeg 1, 6708PB, Wageningen, the Netherlands; Federal University of Viçosa, Viçosa, MG, 36570-900, Brazil.
| | - Mercedes Gomez-Samblas
- Charles University, Faculty of Science, Department of Zoology, Viničná 7, 128 43, Prague, Czech Republic; Granada University, Science faculty, Department of Parasitology, CP:18071, Granada, Granada, Spain.
| | - Daniel Divín
- Charles University, Faculty of Science, Department of Zoology, Viničná 7, 128 43, Prague, Czech Republic.
| | - Balraj Melepat
- Charles University, Faculty of Science, Department of Zoology, Viničná 7, 128 43, Prague, Czech Republic.
| | - Eleni Voukali
- Charles University, Faculty of Science, Department of Zoology, Viničná 7, 128 43, Prague, Czech Republic.
| | - Zuzana Świderská
- Charles University, Faculty of Science, Department of Zoology, Viničná 7, 128 43, Prague, Czech Republic.
| | - Tereza Krajzingrová
- Charles University, Faculty of Science, Department of Zoology, Viničná 7, 128 43, Prague, Czech Republic.
| | - Martin Těšický
- Charles University, Faculty of Science, Department of Zoology, Viničná 7, 128 43, Prague, Czech Republic.
| | - Ferris Jung
- EMBL, Genomics Core Facility, Meyerhofstraße 1, 69117, Heidelberg, Germany.
| | - Vladimír Beneš
- EMBL, Genomics Core Facility, Meyerhofstraße 1, 69117, Heidelberg, Germany.
| | - Ole Madsen
- Wageningen University and Research, Department of Animal Sciences, Animal Breeding and Genomics, Droevendaalsesteeg 1, 6708PB, Wageningen, the Netherlands.
| | - Michal Vinkler
- Charles University, Faculty of Science, Department of Zoology, Viničná 7, 128 43, Prague, Czech Republic.
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16
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Hyde CJ, Ventura T. CrustyBase v.2.0: new features and enhanced utilities to support open science. BMC Genomics 2024; 25:121. [PMID: 38281926 PMCID: PMC10823621 DOI: 10.1186/s12864-024-10033-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 01/20/2024] [Indexed: 01/30/2024] Open
Abstract
BACKGROUND Transcriptomes present a rich, multi-dimensional subset of genomics data. They provide broad insights into genetic sequence, and more significantly gene expression, across biological samples. This technology is frequently employed for describing the genetic response to experimental conditions and has created vast libraries of datasets which shed light on gene function across different tissues, diseases, diets and developmental stages in many species. However, public accessibility of these data is impeded by a lack of suitable software interfaces and databases with which to locate and analyse them. BODY: Here we present an update on the status of CrustyBase.org, an online resource for analysing and sharing crustacean transcriptome datasets. Since its release in October 2020, the resource has provided many thousands of transcriptome sequences and expression profiles to its users and received 19 new dataset imports from researchers across the globe. In this article we discuss user analytics which point towards the utilization of this resource. The architecture of the application has proven robust with over 99.5% uptime and effective reporting of bugs through both user engagement and the error logging mechanism. We also introduce several new features that have been developed as part of a new release of CrustyBase.org. Two significant features are described in detail, which allow users to navigate through transcripts directly by submission of transcript identifiers, and then more broadly by searching for encoded protein domains by keyword. The latter is a novel and experimental feature, and grants users the ability to curate gene families from any dataset hosted on CrustyBase in a matter of minutes. We present case studies to demonstrate the utility of these features. CONCLUSION Community engagement with this resource has been very positive, and we hope that improvements to the service will further enable the research of users of the platform. Web-based platforms such as CrustyBase have many potential applications across life science domains, including the health sector, which are yet to be realised. This leads to a wider discussion around the role of web-based resources in facilitating an open and collaborative research community.
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Affiliation(s)
- Cameron J Hyde
- Queensland Cyber Infrastructure Foundation, The University of Queensland, Level 5 Axon Building, St. Lucia, QLD, 4072, Australia
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, QLD, 4556, Australia
| | - Tomer Ventura
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, QLD, 4556, Australia.
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Goodheart JA, Rio RA, Taraporevala NF, Fiorenza RA, Barnes SR, Morrill K, Jacob MAC, Whitesel C, Masterson P, Batzel GO, Johnston HT, Ramirez MD, Katz PS, Lyons DC. A chromosome-level genome for the nudibranch gastropod Berghia stephanieae helps parse clade-specific gene expression in novel and conserved phenotypes. BMC Biol 2024; 22:9. [PMID: 38233809 PMCID: PMC10795318 DOI: 10.1186/s12915-024-01814-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 01/03/2024] [Indexed: 01/19/2024] Open
Abstract
BACKGROUND How novel phenotypes originate from conserved genes, processes, and tissues remains a major question in biology. Research that sets out to answer this question often focuses on the conserved genes and processes involved, an approach that explicitly excludes the impact of genetic elements that may be classified as clade-specific, even though many of these genes are known to be important for many novel, or clade-restricted, phenotypes. This is especially true for understudied phyla such as mollusks, where limited genomic and functional biology resources for members of this phylum have long hindered assessments of genetic homology and function. To address this gap, we constructed a chromosome-level genome for the gastropod Berghia stephanieae (Valdés, 2005) to investigate the expression of clade-specific genes across both novel and conserved tissue types in this species. RESULTS The final assembled and filtered Berghia genome is comparable to other high-quality mollusk genomes in terms of size (1.05 Gb) and number of predicted genes (24,960 genes) and is highly contiguous. The proportion of upregulated, clade-specific genes varied across tissues, but with no clear trend between the proportion of clade-specific genes and the novelty of the tissue. However, more complex tissue like the brain had the highest total number of upregulated, clade-specific genes, though the ratio of upregulated clade-specific genes to the total number of upregulated genes was low. CONCLUSIONS Our results, when combined with previous research on the impact of novel genes on phenotypic evolution, highlight the fact that the complexity of the novel tissue or behavior, the type of novelty, and the developmental timing of evolutionary modifications will all influence how novel and conserved genes interact to generate diversity.
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Affiliation(s)
- Jessica A Goodheart
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA.
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
| | - Robin A Rio
- Bioengineering Department, Stanford University, Stanford, CA, USA
| | - Neville F Taraporevala
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
- Department of Wildland Resources, Utah State University, Logan, UT, USA
| | - Rose A Fiorenza
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Seth R Barnes
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Kevin Morrill
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Mark Allan C Jacob
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Carl Whitesel
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Park Masterson
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Grant O Batzel
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Hereroa T Johnston
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - M Desmond Ramirez
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, USA
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
| | - Paul S Katz
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, USA
| | - Deirdre C Lyons
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
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18
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Cao C, Maska B, Malik MA, Tagett R, Kaigler D. Immunomodulatory differences between mesenchymal stem cells from different oral tissues. Heliyon 2024; 10:e23317. [PMID: 38192855 PMCID: PMC10771986 DOI: 10.1016/j.heliyon.2023.e23317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 11/24/2023] [Accepted: 11/30/2023] [Indexed: 01/10/2024] Open
Abstract
Mesenchymal stem cells (MSCs) have recently been identified as having potentially therapeutic immunomodulatory properties. MSCs isolated from different oral tissues have similar morphology and immunophenotypes, however, direct comparisons of their gene expression and immunomodulatory properties have not been conducted. We isolated alveolar bone-derived MSCs (aBMSCs), dental pulp stem cells (DPSCs) and gingiva-derived MSCs (GMSCs) from the same patients and compared their immunophenotypes and transcriptomes. Additionally, we compared their production of soluble immunomodulatory cytokines as well as their immunoregulatory properties in coculture with THP-1 human monocytic cells. RNA sequencing revealed distinct gene expression in DPSCs while aBMSCs and GMSCs had less differentially expressed genes. DPSCs also had significantly less secretion of osteopontin compared to aBMSCs and GMSCs. Finally, DPSCs did not exhibit an immunosuppresive effect on THP-1 cells to the same degree as aBMSCs and GMSCs. These findings demonstrate that MSCs from different oral tissues have distinct transcriptomes and immunoregulatory properties.
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Affiliation(s)
- Chen Cao
- Department of Periodontics and Oral Medicine, School of Dentistry, University of Michigan, Ann Arbor, MI, USA
| | - Bartosz Maska
- Department of Periodontics and Oral Medicine, School of Dentistry, University of Michigan, Ann Arbor, MI, USA
| | - Malika A. Malik
- Department of Periodontics and Oral Medicine, School of Dentistry, University of Michigan, Ann Arbor, MI, USA
| | - Rebecca Tagett
- Bioinformatics Core, Medical School, University of Michigan, Ann Arbor, MI, USA
| | - Darnell Kaigler
- Department of Periodontics and Oral Medicine, School of Dentistry, University of Michigan, Ann Arbor, MI, USA
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19
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Yévenes M, Gallardo-Escárate C, Gajardo G. Epigenetic variation mediated by lncRNAs accounts for adaptive genomic differentiation of the endemic blue mussel Mytiluschilensis. Heliyon 2024; 10:e23695. [PMID: 38205306 PMCID: PMC10776947 DOI: 10.1016/j.heliyon.2023.e23695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 12/09/2023] [Indexed: 01/12/2024] Open
Abstract
Epigenetic variation affects gene expression without altering the underlying DNA sequence of genes controlling ecologically relevant phenotypes through different mechanisms, one of which is long non-coding RNAs (lncRNAs). This study identified and evaluated the gene expression of lncRNAs in the gill and mantle tissues of Mytilus chilensis individuals from two ecologically different sites: Cochamó (41°S) and Yaldad (43°S), southern Chile, both impacted by climatic-related conditions and by mussel farming given their use as seedbeds. Sequences identified as lncRNAs exhibited tissue-specific differences, mapping to 3.54 % of the gill transcriptome and 1.96 % of the mantle transcriptome, representing an average of 2.76 % of the whole transcriptome. Using a high fold change value (≥|100|), we identified 43 and 47 differentially expressed lncRNAs (DE-lncRNAs) in the gill and mantle tissue of individuals sampled from Cochamó and 21 and 17 in the gill and mantle tissue of individuals sampled from Yaldad. Location-specific DE-lncRNAs were also detected in Cochamó (65) and Yaldad (94) samples. Via analysis of the differential expression of neighboring protein-coding genes, we identified enriched GO terms related to metabolic, genetic, and environmental information processing and immune system functions, reflecting how the impact of local ecological conditions may influence the M. chilensis (epi)genome expression. These DE-lncRNAs represent complementary biomarkers to DNA sequence variation for maintaining adaptive differences and phenotypic plasticity to cope with natural and human-driven perturbations.
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Affiliation(s)
- Marco Yévenes
- Laboratorio de Genética, Acuicultura y Biodiversidad, Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, Osorno, Chile
| | - Cristian Gallardo-Escárate
- Centro Interdisciplinario para la Investigación en Acuicultura, Universidad de Concepción, Concepción, Chile
| | - Gonzalo Gajardo
- Laboratorio de Genética, Acuicultura y Biodiversidad, Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, Osorno, Chile
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20
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Crombé A, Bertolo F, Vanhersecke L, Guegan JP, Bessede A, Perret R, Le Loarer F, Chaire V, Coindre JM, Lucchesi C, Italiano A. Deciphering the correlation between metabolic activity through 18F-FDG-PET/CT and immune landscape in soft-tissue sarcomas: an insight from the NEOSARCOMICS study. Biomark Res 2024; 12:3. [PMID: 38185642 PMCID: PMC10773028 DOI: 10.1186/s40364-023-00552-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 12/19/2023] [Indexed: 01/09/2024] Open
Abstract
Metabolic elevation in soft-tissue sarcomas (STS), as documented with 18F-Fluorodeoxyglucose positron emission tomography (18F-FDG-PET/CT) has been linked with cell proliferation, higher grade, and lower survivals. However, the recent diagnostic innovations (CINSARC gene-expression signature and tertiary lymphoid structure [TLS]) and therapeutic innovations (immune checkpoint inhibitors [ICIs]) for STS patients underscore the need to re-assess the role of 18F-FDG-PET/CT. Thus, in this correspondence, our objective was to investigate the correlations between STS metabolism as assessed by nuclear imaging, and the immune landscape as estimated by transcriptomics analysis, immunohistochemistry panels, and TLS assessment. Based on a prospective cohort of 85 adult patients with high-grade STS recruited in the NEOSARCOMICS trial (NCT02789384), we identified 3 metabolic groups according to 18F-FDG-PET/CT metrics (metabolic-low [60%], -intermediate [15.3%] and high [24.7%]). We found that T-cells CD8 pathway was significantly enriched in metabolic-high STS. Conversely, several pathways involved in antitumor immune response, cell differentiation and cell cycle, were downregulated in extreme metabolic-low STS. Next, multiplex immunofluorescence showed that densities of CD8+, CD14+, CD45+, CD68+, and c-MAF cells were significantly higher in the metabolic-high group compared to the metabolic-low group. Lastly, no association was found between metabolic group and TLS status. Overall, these results suggest that (i) rapidly proliferating and metabolically active STS can instigate a more robust immune response, thereby attracting immune cells such as T cells and macrophages, and (ii) metabolic activity and TLS could independently influence immune responses.
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Affiliation(s)
- Amandine Crombé
- Department of Oncologic Imaging, Comprehensive Cancer Center, Institut Bergonié, Bordeaux, F-33076, France.
- Department of Musculoskeletal Imaging, Pellegrin University Hospital, Bordeaux, F-33000, France.
- SARCOTARGET Team, Bordeaux Institute of Oncology (BRIC) INSERM U1312, Bordeaux, F-33076, France.
| | - Frédéric Bertolo
- Department of Bioinformatics, Comprehensive Cancer Center, Institut Bergonié, Bordeaux, F-33076, France
| | - Lucile Vanhersecke
- Department of Pathology, Comprehensive Cancer Center, Institut Bergonié, Bordeaux, F-33076, France
| | | | | | - Raul Perret
- Department of Pathology, Comprehensive Cancer Center, Institut Bergonié, Bordeaux, F-33076, France
| | - François Le Loarer
- SARCOTARGET Team, Bordeaux Institute of Oncology (BRIC) INSERM U1312, Bordeaux, F-33076, France
- Department of Pathology, Comprehensive Cancer Center, Institut Bergonié, Bordeaux, F-33076, France
| | - Vanessa Chaire
- SARCOTARGET Team, Bordeaux Institute of Oncology (BRIC) INSERM U1312, Bordeaux, F-33076, France
- Department of Pathology, Comprehensive Cancer Center, Institut Bergonié, Bordeaux, F-33076, France
| | - Jean-Michel Coindre
- SARCOTARGET Team, Bordeaux Institute of Oncology (BRIC) INSERM U1312, Bordeaux, F-33076, France
- Department of Pathology, Comprehensive Cancer Center, Institut Bergonié, Bordeaux, F-33076, France
| | - Carlo Lucchesi
- Department of Bioinformatics, Comprehensive Cancer Center, Institut Bergonié, Bordeaux, F-33076, France
| | - Antoine Italiano
- SARCOTARGET Team, Bordeaux Institute of Oncology (BRIC) INSERM U1312, Bordeaux, F-33076, France
- Department of Medical Oncology, Comprehensive Cancer Center, Institut Bergonié, Bordeaux, F-33076, France
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21
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Saeedi P, Eslami G, Tohidfar M, Jafari-Nodushan A, Vakili M. Differential gene expression (DGE) analysis in persons with a history of giardiasis. AMB Express 2024; 14:1. [PMID: 38170269 PMCID: PMC10764694 DOI: 10.1186/s13568-023-01657-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 12/17/2023] [Indexed: 01/05/2024] Open
Abstract
Giardiasis, which is caused by Giardia duodenalis, has clinical symptoms such as steatorrhea and can be very dangerous in children. In addition, some documents reported that this parasite is present inside the tissue of patients with cancer. In this study, we analyzed the gene expression profiles of some main genes important to apoptosis and anti-apoptosis in humans.Expression profile arrays of Genomic Spatial Event (GSE) 113666, GSE113667, and GSE113679 obtained from Gene Expression Omnibus were used for meta-analysis using R commands. Cytoscape and STRING databases used the protein-protein Interaction network. Then, the Kyoto Encyclopedia of Genes and Genomes and Gene Ontology analysis was performed. Similar genes in Homo sapiens were identified using Basic Local Alignment Search Tool analysis. The validation was performed on eight people using real-time Polymerase chain reaction. In addition to the candidate genes, the gene expression of some other genes, including Serine/Threonine Kinase 1 (AKT1), Cyclin Dependent Kinase Inhibitor 2A (CDKN2A), Kirsten Rat Sarcoma (KRAS), and Phosphatidylinositol-4,5-Bisphosphate 3-Kinase Catalytic Subunit Alpha (PIK3CA) were also examined. Analysis of the expression of serum amyloid A1 (SAA1), Regenerating Islet-Derived 3 Gamma (REG3G), and REG3A genes did not show any difference between the two groups of healthy and diseased people. Examining the mean expression of the four genes AKT1, CDKN2A, KRAS, and PIK3CA showed that three genes of AKT1, CDKN2A, and KRAS had increased expression in people with a history of giardiasis compared to healthy people. We showed that the gene expression pattern differs in apoptosis and anti-apoptosis signaling in people with a history of giardiasis. Giardia duodenalis seems to induce post-non-infectious symptoms with stimulation of human gene expression.
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Affiliation(s)
- Parnia Saeedi
- Department of Medical Parasitology and Mycology, School of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Gilda Eslami
- Department of Medical Parasitology and Mycology, School of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran.
| | - Masoud Tohidfar
- Department of Cell & Molecular Biology, Faculty of Life Sciences & Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - AbbasAli Jafari-Nodushan
- Department of Medical Parasitology and Mycology, School of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Mahmood Vakili
- Department of Community and Preventive Medicine, Health Monitoring Research Center, School of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
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22
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Chaturvedi A, Som A. Inference of Dynamic Growth Regulatory Network in Cancer Using High-Throughput Transcriptomic Data. Methods Mol Biol 2024; 2719:51-77. [PMID: 37803112 DOI: 10.1007/978-1-0716-3461-5_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/08/2023]
Abstract
Growth is regulated by gene expression variation at different developmental stages of biological processes such as cell differentiation, disease progression, or drug response. In cancer, a stage-specific regulatory model constructed to infer the dynamic expression changes in genes contributing to tissue growth or proliferation is referred as a dynamic growth regulatory network (dGRN). Over the past decade, gene expression data has been widely used for reconstructing dGRN by computing correlations between the differentially expressed genes (DEGs). A wide variety of pipelines are available to construct the GRNs using DEGs and the choice of a particular method or tool depends on the nature of the study. In this protocol, we have outlined a step-by-step guide for the analysis of DEGs using RNA-Seq data, beginning from data acquisition, pre-processing, mapping to reference genome, and construction of a correlation-based co-expression network to further downstream analysis. We have also outlined the steps for the inclusion of publicly available interaction/regulation information into the dGRN followed by relevant topological inferences. This tutorial has been designed in a way that early researchers can refer to for an easy and comprehensive glimpse of methodologies used in the inference of dGRN using transcriptomics data.
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Affiliation(s)
- Aparna Chaturvedi
- Centre of Bioinformatics, Institute of Interdisciplinary Studies, University of Allahabad, Prayagraj, India
| | - Anup Som
- Centre of Bioinformatics, Institute of Interdisciplinary Studies, University of Allahabad, Prayagraj, India
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23
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Gornostaeva AN, Bobyleva PI, Andreeva ER, Gogiya BS, Buravkova LB. Alteration of PBMC transcriptome profile after interaction with multipotent mesenchymal stromal cells under "physiological" hypoxia. Immunobiology 2024; 229:152766. [PMID: 38091798 DOI: 10.1016/j.imbio.2023.152766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/17/2023] [Accepted: 11/22/2023] [Indexed: 01/21/2024]
Abstract
Multipotent mesenchymal stromal cells (MSCs) have demonstrated a pronounced immunosuppressive activity, the manifestation of which depends on the microenvironmental factors, including O2 level. Here we examined the effects of MSCs on transcriptomic profile of allogeneic phytohemagglutinin-stimulated peripheral blood mononuclear cells (PBMCs) after interaction at ambient (20%) or "physiological" hypoxia (5%) O2. As revealed with microarray analysis, PBMC transcriptome at 20% O2 was more affected, which was manifested as differential expression of more than 300 genes, whereas under 5% O2 220 genes were changed. Most of genes at 20% O2 were downregulated, while at hypoxia most of genes were upregulated. Altered gene patterns were only partly overlapped at different O2 levels. A set of altered genes at hypoxia only was of particular interest. According to Gene Ontology a part of above genes was responsible for adhesion, cell communication, and immune response. At both oxygen concentrations, MSCs demonstrated effective immunosuppression manifested as attenuation of T cell activation and proliferation as well as anti-inflammatory shift of cytokine profile. Thus, MSC-mediated immunosuppression is executed with greater efficacy at a "physiological" hypoxia, since the same result has been achieved through a change in the expression of a fewer genes in target PBMCs.
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Affiliation(s)
- A N Gornostaeva
- Cell Physiology Laboratory, Institute of Biomedical Problems, Russian Academy of Sciences, Khoroshevskoye shosse 76a, 123007 Moscow, Russia.
| | - P I Bobyleva
- Cell Physiology Laboratory, Institute of Biomedical Problems, Russian Academy of Sciences, Khoroshevskoye shosse 76a, 123007 Moscow, Russia
| | - E R Andreeva
- Cell Physiology Laboratory, Institute of Biomedical Problems, Russian Academy of Sciences, Khoroshevskoye shosse 76a, 123007 Moscow, Russia
| | - B Sh Gogiya
- Department of Herniology and Plastic Surgery, A. V. Vishnevsky Institute of Surgery, Bolshaya Serpukhovskaya Str, 27, 117997 Moscow, Russia
| | - L B Buravkova
- Cell Physiology Laboratory, Institute of Biomedical Problems, Russian Academy of Sciences, Khoroshevskoye shosse 76a, 123007 Moscow, Russia
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24
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Mirbagheri VS, Alishahi A, Ahmadian G, Petroudi SHH, Ojagh SM, Romanazzi G. Recent findings in molecular reactions of E. coli as exposed to alkylated, nano- and ordinary chitosans. Int J Biol Macromol 2023; 253:127006. [PMID: 37734522 DOI: 10.1016/j.ijbiomac.2023.127006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 09/12/2023] [Accepted: 09/18/2023] [Indexed: 09/23/2023]
Abstract
The antibacterial effects of chitosan have been widely studied, but the underlying molecular mechanisms are not fully understood. We investigated the molecular responses of Escherichia coli MG1655 cell, a model gram-negative bacterium, upon exposure to chitosan (Cs), alkylated Cs (AlkCs), and chitosan nanoparticles (CsNPs). Nine target genes involved in relevant signaling pathways (ompF, ompC, ompA, mrcA, mrcB, mgtA, glnA, kdpA, lptA) were selected for analysis. A significant reduction in the expression of mrcA, mgtA, glnA, and lptA genes was observed in the cells treated with Cs. Those treated with Cs, AlkCs, and CsNPs revealed an increase in ompF gene expression, but the expression level was lower in the cells treated with AlkCs and CsNPs compared to Cs. This increase in porin expression suggests compromised membrane integrity and disrupted nutrient transport. In addition, the changes in the expression of mgtA, kdpA, and glnA are related to different effects on membrane permeability. The higher expression in the genes mrcA and mrcB is associated with morphological changes of cells treated with AlkCs and CsNPs. These findings contribute to our understanding of the molecular mechanisms underlying chitosan-induced stress responses and provide insights for the development of safer antimicrobial compounds in the future.
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Affiliation(s)
- Vasighe Sadat Mirbagheri
- Faculty of Fisheries and Environment Science, Gorgan University of Agriculture Science and Natural Resources, Gorgan, Iran
| | - Alireza Alishahi
- Faculty of Fisheries and Environment Science, Gorgan University of Agriculture Science and Natural Resources, Gorgan, Iran.
| | - Gholamreza Ahmadian
- Department of Industrial Environmental and Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran.
| | - Seyyed Hamidreza Hashemi Petroudi
- Genetics and Agricultural Biotechnology Institute of Tabarestan (GABIT), Sari Agricultural Sciences and Natural Resources University, PO Box 578, Sari, Iran
| | - Seyed Mahdi Ojagh
- Faculty of Fisheries and Environment Science, Gorgan University of Agriculture Science and Natural Resources, Gorgan, Iran
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25
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Chakkingal Bhaskaran B, Meyermans R, Gorssen W, Maes GE, Buyse J, Janssens S, Buys N. The forgotten variable? Does the euthanasia method and sample storage condition influence an organisms transcriptome - a gene expression analysis on multiple tissues in pigs. BMC Genomics 2023; 24:769. [PMID: 38093185 PMCID: PMC10720124 DOI: 10.1186/s12864-023-09794-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 11/08/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND Transcriptomic studies often require collection of fresh tissues post euthanasia. The chosen euthanasia method might have the potential to induce variations in gene expressions that are unlinked with the experimental design. The present study compared the suitability of 'nitrogen gas in foam' (ANOXIA) in comparison to a non-barbiturate anaesthetic, T-61® (T61), for euthanizing piglets used in transcriptome research. Further, the effect of common tissue storage conditions, RNAlater™ (RL) and snap freezing in liquid nitrogen (LN2), on gene expression profiles were also analysed. RESULTS On comparison of the 3'mRNA-Seq data generated from pituitary, hypothalamus, liver and lung tissues, no significant differential expression in the protein coding genes were detected between the euthanasia methods. This implies that the nitrogen anoxia method could be a suitable alternative for euthanasia of piglets used in transcriptomic research. However, small nuclear RNAs (snRNAs) that constitute the eukaryotic spliceosomal machinery were found to be significantly higher (log2fold change ≥ 2.0, and adjusted p value ≤ 0.1) in pituitary samples collected using ANOXIA. Non-protein coding genes like snRNAs that play an important role in pre-mRNA splicing can subsequently modify gene expression. Storage in RL was found to be superior in preserving RNA compared to LN2 storage, as evidenced by the significantly higher RIN values in representative samples. However, storage in RL as opposed to LN2, also influenced differential gene expression in multiple tissues, perhaps as a result of its inability to inhibit biological activity during storage. Hence such external sources of variations should be carefully considered before arriving at research conclusions. CONCLUSIONS Source of biological variations like euthanasia method and storage condition can confound research findings. Even if we are unable to prevent the effect of these external factors, it will be useful to identify the impact of these variables on the parameter under observation and thereby prevent misinterpretation of our results.
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Affiliation(s)
- B Chakkingal Bhaskaran
- Department of Biosystems, Centre for Animal Breeding and Genetics, KU Leuven, Kasteelpark Arenberg 30, Box 2472, Leuven, 3001, Belgium.
| | - R Meyermans
- Department of Biosystems, Centre for Animal Breeding and Genetics, KU Leuven, Kasteelpark Arenberg 30, Box 2472, Leuven, 3001, Belgium
| | - W Gorssen
- Department of Biosystems, Centre for Animal Breeding and Genetics, KU Leuven, Kasteelpark Arenberg 30, Box 2472, Leuven, 3001, Belgium
| | - G E Maes
- Centre for Human Genetics, Genomics Core, UZ-KU Leuven, Leuven, Belgium
| | - J Buyse
- Department of Biosystems, Laboratory of Livestock Physiology, KU Leuven, Kasteelpark Arenberg 30, Box 2472, Leuven, 3001, Belgium
| | - S Janssens
- Department of Biosystems, Centre for Animal Breeding and Genetics, KU Leuven, Kasteelpark Arenberg 30, Box 2472, Leuven, 3001, Belgium
| | - N Buys
- Department of Biosystems, Centre for Animal Breeding and Genetics, KU Leuven, Kasteelpark Arenberg 30, Box 2472, Leuven, 3001, Belgium.
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Kumar R, Malik MZ, Thanaraj TA, Bagabir SA, Haque S, Tambuwala M, Haider S. A computational biology approach to identify potential protein biomarkers and drug targets for sporadic amyotrophic lateral sclerosis. Cell Signal 2023; 112:110915. [PMID: 37838312 DOI: 10.1016/j.cellsig.2023.110915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 09/25/2023] [Accepted: 10/04/2023] [Indexed: 10/16/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease caused by the loss of upper and lower motor neurons. The sporadic ALS (sALS) is a multigenic disorder and the complex mechanisms underlying its onset are still not fully delineated. Despite the recent scientific advancements, certain aspects of ALS pathogenic targets need to be yet clarified. The aim of the presented study is to identify potential genetic biomarkers and drug targets for sALS, by analysing gene expression profiles, presented in the publicly available GSE68605 dataset, of motor neurons cells obtained from sALS patients. We used different computational approaches including differential expression analysis, protein network mapping, candidate protein biomarker (CPB) identification, elucidation of the role of functional modules, and molecular docking analysis. The resultant top ten up- and downregulated genes were further used to construct protein-protein interaction network (PPIN). The PPIN analysis resulted in identifying four CPBs (namely RIOK2, AKT1, CTNNB1, and TNF) that commonly overlapped with one another in network parameters (degree, bottleneck and maximum neighbourhood component). The RIOK2 protein emerged as a potential mediator of top five functional modules that are associated with RNA binding, lipoprotein particle receptor binding in pre-ribosome, and interferon, cytokine-mediated signaling pathway. Furthermore, molecular docking analysis revealed that cyclosporine exhibited the highest binding affinity (-8.6 kJ/mol) with RIOK2, and surpassed the FDA-approved ALS drugs, such as riluzole and edaravone. This suggested that cyclosporine may serve as a promising candidate for targeting RIOK2 downregulation observed in sALS patients. In order to validate our computational results, it is suggested that in vitro and in vivo studies may be conducted in future to provide a more detailed understanding of ALS diagnosis, prognosis, and therapeutic intervention.
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Affiliation(s)
- Rupesh Kumar
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, Sec-62, Uttar Pradesh, India.
| | - Md Zubbair Malik
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Dasman, P.O. Box 1180, Kuwait city 15462, Kuwait.
| | - Thangavel Alphonse Thanaraj
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Dasman, P.O. Box 1180, Kuwait city 15462, Kuwait.
| | - Sali Abubaker Bagabir
- Genetics Unit, Department of Medical Laboratory Technology Faculty of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia.
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan 45142, Saudi Arabia; Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, Lebanon; Centre of Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman, United Arab Emirates.
| | - Murtaza Tambuwala
- Lincoln Medical School, University of Lincoln, Brayford Pool Campus, Lincoln LN6 7TS, UK.
| | - Shazia Haider
- Department of Biosciences, Jamia Millia University, New Delhi 110025, India.
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27
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Chen QL, Qiao F, Lu WT, Shi HL, Zhou CX. [Bioinformatics analysis of primary biliary cholangitis key genes and molecular mechanisms]. Zhonghua Gan Zang Bing Za Zhi 2023; 31:1209-1216. [PMID: 38238956 DOI: 10.3760/cma.j.cn501113-20220315-00110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
Objective: To extract the differentially expressed key genes of primary biliary cholangitis (PBC) using bioinformatics methods, so as to provide information for further study into the mechanism. Methods: The GSE119600 dataset was downloaded from the GEO database to obtain differentially expressed genes. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed for differentially expressed genes. Protein-protein interaction (PPI) network reconstruction, Cytoscape software visualization, and core gene screening were performed. The area under the receiver operating characteristic curve (ROC AUC) was used to assess the diagnostic effectiveness of genes and plot the pROC software package. The x-Cell software was used to calculate the enrichment score of 34 immune cells in each sample. Finally, four key genes (PSMA4, PSMA1, PSMB1, and PSMA3) were selected. Blood samples were analyzed using the qPCR method. Results:: A total of 373 immune-related differentially expressed genes were identified. Eight genes (PSMC6, PSMB2, PSMB1, PSMA3, PSMA4, PSMA1, PSMD7, and PSMB5) were screened from the 178 nodes and 596 edges as hub genes of the PPI network, which were significantly related to amino acid metabolism, hematopoietic stem cell differentiation, cell cycle, and immune processes. PSMA4, PSMA1, PSMB1, and PSMA3 were defined as immunological biomarkers for PBC with an AUC value of the ROC curve > 0.7. Immunoinfiltrating cell analysis showed that the proportion of eosinophils was significantly higher in PBC patients compared to the control group, whereas the proportion of CD4+ memory T cells, plasma cells, Th2 cells, and cDC cells was significantly lower in PBC patients than the control group. Plasma cells were associated with all four immunological biomarkers. Seven PBC patients and seven healthy subjects were selected for peripheral blood qPCR validation, which demonstrates that PSMB1, PSMA3, PSMA1, and PSMA4 levels were significantly lower in PBC patients than healthy subjects, with a statistically significant difference. Conclusion:: Bioinformatics screened eight key genes, of which four were key immunological markers and may serve as a basis for clinical diagnosis and mechanism exploration.
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Affiliation(s)
- Q L Chen
- Jiangsu Hospital of Traditional Chinese Medicine, Affiliated Hospital of Nanjing University of Traditional Chinese Medicine, Nanjing 210007, China
| | - F Qiao
- Jiangsu Hospital of Traditional Chinese Medicine, Affiliated Hospital of Nanjing University of Traditional Chinese Medicine, Nanjing 210007, China
| | - W T Lu
- Jiangsu Hospital of Traditional Chinese Medicine, Affiliated Hospital of Nanjing University of Traditional Chinese Medicine, Nanjing 210007, China
| | - H L Shi
- Jiangsu Hospital of Traditional Chinese Medicine, Affiliated Hospital of Nanjing University of Traditional Chinese Medicine, Nanjing 210007, China
| | - C X Zhou
- Nanjing University of Traditional Chinese Medicine, Nanjing 210023, China
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28
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Vinkel J, Rib L, Buil A, Hedetoft M, Hyldegaard O. Key pathways and genes that are altered during treatment with hyperbaric oxygen in patients with sepsis due to necrotizing soft tissue infection (HBOmic study). Eur J Med Res 2023; 28:507. [PMID: 37946314 PMCID: PMC10636866 DOI: 10.1186/s40001-023-01466-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 10/21/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND For decades, the basic treatment strategies of necrotizing soft tissue infections (NSTI) have remained unchanged, primarily relying on aggressive surgical removal of infected tissue, broad-spectrum antibiotics, and supportive intensive care. One treatment strategy that has been proposed as an adjunctive measure to improve patient outcomes is hyperbaric oxygen (HBO2) treatment. HBO2 treatment has been linked to several immune modulatory effects; however, investigating these effects is complicated due to the disease's acute life-threatening nature, metabolic and cell homeostasis dependent variability in treatment effects, and heterogeneity with respect to both patient characteristics and involved pathogens. To embrace this complexity, we aimed to explore the underlying biological mechanisms of HBO2 treatment in patients with NSTI on the gene expression level. METHODS We conducted an observational cohort study on prospective collected data, including 85 patients admitted to the intensive care unit (ICU) for NSTI. All patients were treated with one or two HBO2 treatments and had one blood sample taken before and after the intervention. Total RNAs from blood samples were extracted and mRNA purified with rRNA depletion, followed by whole-transcriptome RNA sequencing with a targeted sequencing depth of 20 million reads. A model for differentially expressed genes (DEGs) was fitted, and the functional aspects of the obtained set of genes was predicted with GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of genes and Genomes) enrichment analyses. All analyses were corrected for multiple testing with FDR. RESULTS After sequential steps of quality control, a final of 160 biological replicates were included in the present study. We found 394 protein coding genes that were significantly DEGs between the two conditions with FDR < 0.01, of which 205 were upregulated and 189 were downregulated. The enrichment analysis of these DEGs revealed 20 GO terms in biological processes and 12 KEGG pathways that were significantly overrepresented in the upregulated DEGs, of which the term; "adaptive immune response" (GO:0002250) (FDR = 9.88E-13) and "T cell receptor signaling pathway" (hsa04660) (FDR = 1.20E-07) were the most significant. Among the downregulated DEGs two biological processes were significantly enriched, of which the GO term "apoptotic process" (GO:0006915) was the most significant (FDR = 0.001), followed by "Positive regulation of T helper 1 cell cytokine production" (GO:2000556), and "NF-kappa B signaling pathway" (hsa04064) was the only KEGG pathway that was significantly overrepresented (FDR = 0.001). CONCLUSIONS When one or two sessions of HBO2 treatment were administered to patients with a dysregulated immune response and systemic inflammation due to NSTI, the important genes that were regulated during the intervention were involved in activation of T helper cells and downregulation of the disease-induced highly inflammatory pathway NF-κB, which was associated with a decrease in the mRNA level of pro-inflammatory factors. TRIAL REGISTRATION Biological material was collected during the INFECT study, registered at ClinicalTrials.gov (NCT01790698).
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Affiliation(s)
- Julie Vinkel
- Department of Anesthesiology, Copenhagen University Hospital, Rigshospitalet, Inge Lehmanns Vej 6, 2100, Copenhagen, Denmark.
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark.
| | - Leonor Rib
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Alfonso Buil
- Institute for Biological Psychiatry, Mental Health Centre Sct. Hans, Roskilde, Denmark
| | - Morten Hedetoft
- Department of Anesthesiology, Copenhagen University Hospital, Rigshospitalet, Inge Lehmanns Vej 6, 2100, Copenhagen, Denmark
- Department of Anesthesiology, Zealand University Hospital, Køge, Denmark
| | - Ole Hyldegaard
- Department of Anesthesiology, Copenhagen University Hospital, Rigshospitalet, Inge Lehmanns Vej 6, 2100, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
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Liu X, Gao J, Zhang P, Shi T, Yan B, Azra MN, Baloch WA, Wang P, Gao H. De novo transcriptional analysis of the response to starvation stress in the white ridgetail prawn, Exopalaemon carinicauda. Genomics 2023; 115:110746. [PMID: 37977333 DOI: 10.1016/j.ygeno.2023.110746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 10/27/2023] [Accepted: 11/14/2023] [Indexed: 11/19/2023]
Abstract
To study the mechanism of the biomolecular response in Exopalaemon carinicauda to starvation stress, we subjected muscle tissue RNA samples from four stress points, including 0 d(control group), 10 d, 20 d, and 30 d, to starvation stress on white ridgetail prawn with a body weight of 1.41 + 0.42 g, aquaculture water temperature of 23-25 °C, salinity of 26, dissolved oxygen ≥5 mg/L, and pH 8-8.5, Then performed de novo transcriptome assembly and gene expression analysis using BGISEQ-500 with a tag-based digital gene expression (DGE) system. By de novo assembling at the four times, we obtained 28,167, 21,115, 24,497, and 27,080 reads, respectively. The results showed that the stress at 10 d led to no significant difference in the expressed genes, while the stress at 20 d and 30 d showed a significant increase (or decrease) in the expression of 97 (276) and 143 (410) genes, respectively, which were involved in 8 different metabolic pathways. In addition, we detected 2647 unigene transcription factors. Eleven upregulated and sixteen downregulated genes from the different starvation stress groups were choose to verify the reliability of the transcriptome data, and the results showed that the expression trends of these genes were consistent with the results shown by the transcriptome. The analysis of the experimental data and our discussion of the response mechanism of white ridgetail prawn under starvation stress provides a foundation for further screening of the key genes of starvation stress and may help to elucidate their functions.
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Affiliation(s)
- Xue Liu
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222005, China; Marine Resource Development institute of Jiangsu (Lianyungang), Jiangsu Lianyungang, 222005, China
| | - Jiayi Gao
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222005, China; Marine Resource Development institute of Jiangsu (Lianyungang), Jiangsu Lianyungang, 222005, China
| | - Pei Zhang
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222005, China; Marine Resource Development institute of Jiangsu (Lianyungang), Jiangsu Lianyungang, 222005, China
| | - Tingting Shi
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222005, China; Marine Resource Development institute of Jiangsu (Lianyungang), Jiangsu Lianyungang, 222005, China
| | - Binlun Yan
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222005, China; Marine Resource Development institute of Jiangsu (Lianyungang), Jiangsu Lianyungang, 222005, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Lianyungang, Jiangsu 222005, China; The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, Jiangsu 210014, China
| | - Mohamad Nor Azra
- Institute of Climate Adaptation and Marine Biotechnology, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia.
| | - Wazir Ali Baloch
- Department of Freshwater Biology and Fisheries, University of Sindh, Jamshoro 76080, Pakistan.
| | - Panpan Wang
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222005, China; Marine Resource Development institute of Jiangsu (Lianyungang), Jiangsu Lianyungang, 222005, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Lianyungang, Jiangsu 222005, China; The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, Jiangsu 210014, China
| | - Huan Gao
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222005, China; Marine Resource Development institute of Jiangsu (Lianyungang), Jiangsu Lianyungang, 222005, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Lianyungang, Jiangsu 222005, China; The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, Jiangsu 210014, China.
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Massri AJ, Fitzpatrick M, Cunny H, Li JL, Harry GJ. Differential gene expression profiling implicates altered network development in rat postnatal day 4 cortex following 4-Methylimidazole (4-MeI) induced maternal seizures. Neurotoxicol Teratol 2023; 100:107301. [PMID: 37783441 PMCID: PMC10843020 DOI: 10.1016/j.ntt.2023.107301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/31/2023] [Accepted: 09/19/2023] [Indexed: 10/04/2023]
Abstract
Compromised maternal health leading to maternal seizures can have adverse effects on the healthy development of offspring. This may be the result of inflammation, hypoxia-ischemia, and altered GABA signaling. The current study examined cortical tissue from F2b (2nd litter of the 2nd generation) postnatal day 4 (PND4) offspring of female Harlan SD rats chronically exposed to the seizuregenic compound, 4-Methylimidazole (0, 750, or 2500 ppm 4-MeI). Maternal seizures were evident only at 2500 ppm 4-MeI. GABA related gene expression as examined by qRT-PCR and whole genome microarray showed no indication of disrupted GABA or glutamatergic signaling. Canonical pathway hierarchical clustering and multi-omics combinatory genomic (CNet) plots of differentially expressed genes (DEG) showed alterations in genes associated with regulatory processes of cell development including neuronal differentiation and synaptogenesis. Functional enrichment analysis showed a similarity of cellular processes across the two exposure groups however, the genes comprising each cluster were primarily unique rather than shared and often showed different directionality. A dose-related induction of cytokine signaling was indicated however, pathways associated with individual cytokine signaling were not elevated, suggesting an alternative involvement of cytokine signaling. Pathways related to growth process and cell signaling showed a negative activation supporting an interpretation of disruption or delay in developmental processes at the 2500 ppm 4-MeI exposure level with maternal seizures. Thus, while GABA signaling was not altered as has been observed with maternal seizures, the pattern of DEG suggested a potential for alteration in neuronal network formation.
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Affiliation(s)
- Abdull J Massri
- Integrative Bioinformatics, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Mackenzie Fitzpatrick
- Mechanistic Toxicology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Helen Cunny
- Office of the Scientific Director, Division of Translational Toxicology, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Jian-Liang Li
- Integrative Bioinformatics, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - G Jean Harry
- Mechanistic Toxicology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA.
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Zariñán T, Espinal-Enriquez J, De Anda-Jáuregui G, Lira-Albarrán S, Hernández-Montes G, Gutiérrez-Sagal R, Rebollar-Vega RG, Bousfield GR, Butnev VY, Hernández-Lemus E, Ulloa-Aguirre A. Differential effects of follicle-stimulating hormone glycoforms on the transcriptome profile of cultured rat granulosa cells as disclosed by RNA-seq. bioRxiv 2023:2023.10.18.562995. [PMID: 37905087 PMCID: PMC10614937 DOI: 10.1101/2023.10.18.562995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
It has been documented that variations in glycosylation on glycoprotein hormones, confer distinctly different biological features to the corresponding glycoforms when multiple in vitro biochemical readings are analyzed. We here applied next generation RNA sequencing to explore changes in the transcriptome of rat granulosa cells exposed for 0, 6, and 12 h to 100 ng/ml of four highly purified follicle-stimulating hormone (FSH) glycoforms, each exhibiting different glycosylation patterns: human pituitary FSH18/21 and equine FSH (eqFSH) (hypo-glycosylated), and human FSH24 and chinese-hamster ovary cell-derived human recombinant FSH (recFSH) (fully-glycosylated). Total RNA from triplicate incubations was prepared from FSH glycoform-exposed cultured granulosa cells obtained from DES-pretreated immature female rats, and RNA libraries were sequenced in a HighSeq 2500 sequencer (2 × 125 bp paired-end format, 10-15 × 106 reads/sample). The computational workflow focused on investigating differences among the four FSH glycoforms at three levels: gene expression, enriched biological processes, and perturbed pathways. Among the top 200 differentially expressed genes, only 4 (0.6%) were shared by all 4 glycoforms at 6 h, whereas 118 genes (40%) were shared at 12 h. Follicle-stimulating hormone glycocoforms stimulated different patterns of exclusive and associated up regulated biological processes in a glycoform and time-dependent fashion with more shared biological processes after 12 h of exposure and fewer treatment-specific ones, except for recFSH, which exhibited stronger responses with more specifically associated processes at this time. Similar results were found for down-regulated processes, with a greater number of processes at 6 h or 12 h, depending on the particular glycoform. In general, there were fewer downregulated than upregulated processes at both 6 h and 12 h, with FSH18/21 exhibiting the largest number of down-regulated associated processes at 6 h while eqFSH exhibited the greatest number at 12 h. Signaling cascades, largely linked to cAMP-PKA, MAPK, and PI3/AKT pathways were detected as differentially activated by the glycoforms, with each glycoform exhibiting its own molecular signature. These data extend previous observations demonstrating glycosylation-dependent differential regulation of gene expression and intracellular signaling pathways triggered by FSH in granulosa cells. The results also suggest the importance of individual FSH glycoform glycosylation for the conformation of the ligand-receptor complex and induced signalling pathways.
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Affiliation(s)
- Teresa Zariñán
- Red de Apoyo a la Investigación, Universidad Nacional Autónoma de México (UNAM)-Instituto Nacional de Ciencias Médicas y Nutrición SZ, 14080, Mexico City, Mexico
| | | | | | - Saúl Lira-Albarrán
- Department of Reproductive Biology, Instituto Nacional de Ciencias Médicas y Nutrición SZ, Mexico City, 14080, Mexico
| | - Georgina Hernández-Montes
- Red de Apoyo a la Investigación, Universidad Nacional Autónoma de México (UNAM)-Instituto Nacional de Ciencias Médicas y Nutrición SZ, 14080, Mexico City, Mexico
| | - Rubén Gutiérrez-Sagal
- Red de Apoyo a la Investigación, Universidad Nacional Autónoma de México (UNAM)-Instituto Nacional de Ciencias Médicas y Nutrición SZ, 14080, Mexico City, Mexico
| | - Rosa G. Rebollar-Vega
- Red de Apoyo a la Investigación, Universidad Nacional Autónoma de México (UNAM)-Instituto Nacional de Ciencias Médicas y Nutrición SZ, 14080, Mexico City, Mexico
| | - George R. Bousfield
- Department of Biological Sciences, Wichita State University, Wichita Kansas, 67260, USA
| | - Viktor Y. Butnev
- Department of Biological Sciences, Wichita State University, Wichita Kansas, 67260, USA
| | | | - Alfredo Ulloa-Aguirre
- Red de Apoyo a la Investigación, Universidad Nacional Autónoma de México (UNAM)-Instituto Nacional de Ciencias Médicas y Nutrición SZ, 14080, Mexico City, Mexico
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Cai S, Huang S, Zhang W, Xiao H, Yu D, Zhong X, Tao P, Luo Y. Integrated bioinformatic analysis reveals NOS2 as a novel ferroptosis-related biomarker for pre-eclampsia. BMC Pregnancy Childbirth 2023; 23:719. [PMID: 37817070 PMCID: PMC10563238 DOI: 10.1186/s12884-023-06051-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 10/05/2023] [Indexed: 10/12/2023] Open
Abstract
BACKGROUND Pre-eclampsia (PE) is a common condition in pregnancy; however, methods for early diagnosis and effective treatment options are lacking. Ferroptosis is a newly identified iron-dependent cell death pathway. The aim of this study was to investigate the role of ferroptosis-related genes in PE, the underlying mechanism, and their potential diagnostic value using a bioinformatics approach. METHODS We downloaded the GSE48424 and GSE98224 datasets from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) between PE and healthy pregnancy samples were identified in the GSE48424 dataset and subjected to weighted gene co-expression network analysis; the most relevant modules were intersected with known ferroptosis-related genes to distinctly identify the role of ferroptosis in PE. We further searched transcription factors and microRNAs that are predicted to regulate these ferroptosis-related genes, and patients in the GSE48424 dataset were divided into two groups according to high or low expression of the key ferroptosis-related genes associated with PE. To obtain robust key ferroptosis-related genes in PE, we validated their expression levels in the external dataset GSE98224. Finally, the reverse transcription-quantitative polymerase chain reaction (RT-qPCR) assay was utilized to access the expression of these genes in the PE and normal blood samples. RESULTS Six ferroptosis-related genes involved in PE were obtained by overlapping 3661 genes most associated with PE, 565 DEGs between PE and normal samples, and 259 known ferroptosis-related genes. Among these genes, patients with PE displaying lower expression levels of NOS2 and higher expression levels of PTGS2 had a higher ferroptosis potential index. The expression pattern of NOS2 was consistent in the GSE48424 and GSE98224 datasets. RT-qPCR data confirmed that NOS2 expression was more significantly elevated in patients with PE than in those with a normal pregnancy. CONCLUSIONS Our study explored the diagnostic value of ferroptosis-related genes in PE, and identified NOS2 as the key gene linking ferroptosis and PE, suggesting a new candidate biomarker for early PE diagnosis.
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Affiliation(s)
- Shuangming Cai
- Medical Intensive Care Unit, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China
| | - Shan Huang
- Medical Intensive Care Unit, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China
| | - Wenni Zhang
- Medical Intensive Care Unit, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China
| | - Huanshun Xiao
- Medical Intensive Care Unit, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China
| | - Danfeng Yu
- Medical Intensive Care Unit, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China
| | - Xuan Zhong
- Medical Intensive Care Unit, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China
| | - Pei Tao
- Medical Intensive Care Unit, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China
| | - Yiping Luo
- Medical Intensive Care Unit, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China.
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Joon HK, Thalor A, Gupta D. Machine learning analysis of lung squamous cell carcinoma gene expression datasets reveals novel prognostic signatures. Comput Biol Med 2023; 165:107430. [PMID: 37703712 DOI: 10.1016/j.compbiomed.2023.107430] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/06/2023] [Accepted: 08/28/2023] [Indexed: 09/15/2023]
Abstract
BACKGROUND Lung squamous cell carcinoma (LUSC) patients are often diagnosed at an advanced stage and have poor prognoses. Thus, identifying novel biomarkers for the LUSC is of utmost importance. METHODS Multiple datasets from the NCBI-GEO repository were obtained and merged to construct the complete dataset. We also constructed a subset from this complete dataset with only known cancer driver genes. Further, machine learning classifiers were employed to obtain the best features from both datasets. Simultaneously, we perform differential gene expression analysis. Furthermore, survival and enrichment analyses were performed. RESULTS The kNN classifier performed comparatively better on the complete and driver datasets' top 40 and 50 gene features, respectively. Out of these 90 gene features, 35 were found to be differentially regulated. Lasso-penalized Cox regression further reduced the number of genes to eight. The median risk score of these eight genes significantly stratified the patients, and low-risk patients have significantly better overall survival. We validated the robust performance of these eight genes on the TCGA dataset. Pathway enrichment analysis identified that these genes are associated with cell cycle, cell proliferation, and migration. CONCLUSION This study demonstrates that an integrated approach involving machine learning and system biology may effectively identify novel biomarkers for LUSC.
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Affiliation(s)
- Hemant Kumar Joon
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India; Regional Centre for Biotechnology, Faridabad, 121001, Haryana, India
| | - Anamika Thalor
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Dinesh Gupta
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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Brink DP, Mierke F, Norbeck J, Siewers V, Andlid T. Expanding the genetic toolbox of Rhodotorula toruloides by identification and validation of six novel promoters induced or repressed under nitrogen starvation. Microb Cell Fact 2023; 22:160. [PMID: 37598166 PMCID: PMC10440040 DOI: 10.1186/s12934-023-02175-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 08/09/2023] [Indexed: 08/21/2023] Open
Abstract
BACKGROUND The non-conventional yeast Rhodotorula toruloides is an emerging host organism in biotechnology by merit of its natural capacity to accumulate high levels of carotenoids and intracellular storage lipids from a variety of carbon sources. While the number of genetic engineering strategies that employ R. toruloides is increasing, the lack of genetic tools available for modification of this yeast is still limiting strain development. For instance, several strong, constitutive R. toruloides promoters have been characterized, but to date, only five inducible promoters have been identified. Although nitrogen-limited cultivation conditions are commonly used to induce lipid accumulation in this yeast, no promoters regulated by nitrogen starvation have been described for R. toruloides. RESULTS In this study, we used a combination of genomics and transcriptomics methods to identify novel R. toruloides promoter sequences that are either inducible or repressible by nitrogen starvation. RNA sequencing was used to assess gene expression in the recently isolated strain R. toruloides BOT-A2 during exponential growth and during nitrogen starvation, when cultivated with either glucose or xylose as the carbon source. The genome of BOT-A2 was sequenced using a combination of long- and short-read sequencing and annotated with support of the RNAseq data. Differential expression analysis was used to identify genes with a |log2 fold change|≥ 2 when comparing their expression during nitrogen depletion to that during exponential growth. The promoter regions from 16 of these genes were evaluated for their ability to drive the expression of a fluorescent reporter gene. Three promoters that were clearly upregulated under nitrogen starvation and three that were downregulated were selected and further characterized. One promoter, derived from gene RTBOTA2_003877, was found to function like an on-off switch, as it was only upregulated under full nitrogen depletion and downregulated in the presence of the nitrogen source. CONCLUSIONS Six new R. toruloides promoters that were either upregulated or downregulated under nitrogen-starvation were identified. These substantially contribute to the available promoters when engineering this organism and are foreseen to be particularly useful for future engineering strategies requiring specific regulation of target genes in accordance with nitrogen availability.
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Affiliation(s)
- Daniel P Brink
- Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
- Applied Microbiology, Department of Chemistry, Lund University, Lund, Sweden
| | - Friederike Mierke
- Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
- Food and Nutrition Science, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Joakim Norbeck
- Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Verena Siewers
- Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden.
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.
| | - Thomas Andlid
- Food and Nutrition Science, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
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Bhalla N, Franzén L, Scheynius A, Papadogiannakis N, Hansson SR, Lager S, Ståhl PL. Spatial transcriptomics of human placentas reveal distinct RNA patterns associated with morphology and preeclampsia. Placenta 2023; 139:213-216. [PMID: 37481829 DOI: 10.1016/j.placenta.2023.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 02/26/2023] [Accepted: 07/04/2023] [Indexed: 07/25/2023]
Abstract
Spatial transcriptomics (ST) maps RNA level patterns within a tissue. This technology has not been previously applied to human placental tissue. We demonstrate analysis of human placental samples with ST. Unsupervised clustering revealed that distinct RNA patterns were found corresponding to different morphological structures. Additionally, when focusing upon terminal villi and hemoglobin associated structures, RNA levels differed between placentas from full term healthy pregnancies and those complicated by preeclampsia. The results from this study can provide a benchmark for future ST studies in placenta.
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Affiliation(s)
- Nayanika Bhalla
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Lovisa Franzén
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Annika Scheynius
- Department of Clinical Science and Education, Karolinska Institutet, Sachs' Children and Youth Hospital, Södersjukhuset, Stockholm, Sweden
| | - Nikos Papadogiannakis
- Department of Laboratory Medicine, Division of Pathology, Karolinska Institutet, Stockholm, Sweden; Department of Pathology, Karolinska University Hospital, Stockholm, Sweden
| | - Stefan R Hansson
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Susanne Lager
- Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden.
| | - Patrik L Ståhl
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
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Namgial T, Singh AK, Singh NP, Francis A, Chattopadhyay D, Voloudakis A, Chakraborty S. Differential expression of genes during recovery of Nicotiana tabacum from tomato leaf curl Gujarat virus infection. Planta 2023; 258:37. [PMID: 37405593 PMCID: PMC10322791 DOI: 10.1007/s00425-023-04182-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 06/10/2023] [Indexed: 07/06/2023]
Abstract
MAIN CONCLUSION Nicotiana tabacum exhibits recovery response towards tomato leaf curl Gujarat virus. Transcriptome analysis revealed the differential expression of defense-related genes. Genes encoding for cysteine protease inhibitor, hormonal- and stress-related to DNA repair mechanism are found to be involved in the recovery process. Elucidating the role of host factors in response to viral infection is crucial in understanding the plant host-virus interaction. Begomovirus, a genus in the family Geminiviridae, is reported throughout the globe and is known to cause serious crop diseases. Tomato leaf curl Gujarat virus (ToLCGV) infection in Nicotiana tabacum resulted in initial symptom expression followed by a quick recovery in the systemic leaves. Transcriptome analysis using next-generation sequencing (NGS) revealed a large number of differentially expressed genes both in symptomatic as well as recovered leaves when compared to mock-inoculated plants. The virus infected N. tabacum results in alteration of various metabolic pathways, phytohormone signaling pathway, defense related protein, protease inhibitor, and DNA repair pathway. RT-qPCR results indicated that Germin-like protein subfamily T member 2 (NtGLPST), Cysteine protease inhibitor 1-like (NtCPI), Thaumatin-like protein (NtTLP), Kirola-like (NtKL), and Ethylene-responsive transcription factor ERF109-like (NtERTFL) were down-regulated in symptomatic leaves when compared to recovered leaves of ToLCGV-infected plants. In contrast, the Auxin-responsive protein SAUR71-like (NtARPSL) was found to be differentially down-regulated in recovered leaves when compared to symptomatic leaves and the mock-inoculated plants. Lastly, Histone 2X protein like (NtHH2L) gene was found to be down-regulated, whereas Uncharacterized (NtUNCD) was up-regulated in both symptomatic as well as recovered leaves compared to the mock-inoculated plants. Taken together, the present study suggests potential roles of the differentially expressed genes that might govern tobacco's susceptibility and/or recovery response towards ToLCGV infection.
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Affiliation(s)
- T Namgial
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Athens, 11855, Greece
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - A K Singh
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - N P Singh
- Laboratory of Plant Molecular Biology, National Institute of Plant Genome Research, New Delhi, 110067, India
| | - A Francis
- Laboratory of Plant Molecular Biology, National Institute of Plant Genome Research, New Delhi, 110067, India
| | - D Chattopadhyay
- Laboratory of Plant Molecular Biology, National Institute of Plant Genome Research, New Delhi, 110067, India
| | - A Voloudakis
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Athens, 11855, Greece.
| | - S Chakraborty
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
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Becerro-Recio D, Serrat J, López-García M, Torres-Valle M, Colina F, Fernández IM, González-Miguel J, Siles-Lucas M. Study of the cross-talk between Fasciola hepatica juveniles and the intestinal epithelial cells of the host by transcriptomics in an in vitro model. Vet Parasitol 2023; 320:109981. [PMID: 37450963 DOI: 10.1016/j.vetpar.2023.109981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 07/18/2023]
Abstract
Fasciolosis is a globally widespread trematodiasis with a major economic and veterinary impact. Therefore, this disease is responsible for millions of dollars in losses to the livestock industry, and also constitutes an emerging human health problem in endemic areas. The ubiquitous nature of Fasciola hepatica, the main causative agent, is one of the key factors for the success of fasciolosis. Accordingly, this parasite is able to subsist in a wide variety of ecosystems and hosts, thanks to the development of a plethora of strategies for adaption and immune evasion. Fasciolosis comprises a growing concern due to its high prevalence rates, together with the emergence of strains of the parasite resistant to the treatment of choice (triclabendazole). These facts highlight the importance of developing novel control measures which allow for an effective protection against the disease before F. hepatica settles in a niche inaccessible to the immune system. However, knowledge about the initial phases of the infection, including the migration mechanisms of the parasite and the early innate host response, is still scarce. Recently, our group developed an in vitro host-parasite interaction model that allowed the early events to be unveiled after the first contact between the both actors. This occurs shortly upon ingestion of F. hepatica metacercariae and the emergence of the newly excysted juveniles (FhNEJ) in the host duodenum. Here, we present a transcriptomic analysis of such model using an approach based on RNA sequencing (RNA-Seq), which reveals changes in gene expression related to proteolysis and uptake of metabolites in FhNEJ. Additionally, contact with the parasite triggered changes in host intestinal cells related to pseudogenes expression and host defence mechanisms, including immune response, among others. In sum, these results provide a better understanding of the early stages of fasciolosis at molecular level, and a pool of targets that could be used in future therapeutic strategies against the disease.
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Affiliation(s)
- David Becerro-Recio
- Laboratory of Helminth Parasites of Zoonotic Importance (ATENEA), Institute of Natural Resources and Agrobiology of Salamanca (IRNASA-CSIC), 37008 Salamanca, Spain
| | - Judit Serrat
- Laboratory of Helminth Parasites of Zoonotic Importance (ATENEA), Institute of Natural Resources and Agrobiology of Salamanca (IRNASA-CSIC), 37008 Salamanca, Spain
| | - Marta López-García
- Laboratory of Helminth Parasites of Zoonotic Importance (ATENEA), Institute of Natural Resources and Agrobiology of Salamanca (IRNASA-CSIC), 37008 Salamanca, Spain
| | - María Torres-Valle
- Laboratory of Helminth Parasites of Zoonotic Importance (ATENEA), Institute of Natural Resources and Agrobiology of Salamanca (IRNASA-CSIC), 37008 Salamanca, Spain
| | - Francisco Colina
- Institute of Plant Molecular Biology, Centre for Biology, Academy of Sciences of the Czech Republic (ASCR), České Budějovice, Czechia
| | - Iván M Fernández
- Plant-Microorganism Interactions Unit, Institute of Natural Resources and Agrobiology of Salamanca (IRNASA-CSIC), 37008 Salamanca, Spain
| | - Javier González-Miguel
- Laboratory of Helminth Parasites of Zoonotic Importance (ATENEA), Institute of Natural Resources and Agrobiology of Salamanca (IRNASA-CSIC), 37008 Salamanca, Spain
| | - Mar Siles-Lucas
- Laboratory of Helminth Parasites of Zoonotic Importance (ATENEA), Institute of Natural Resources and Agrobiology of Salamanca (IRNASA-CSIC), 37008 Salamanca, Spain.
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Padula G, Garces GR, Fernández ME, Vercellini R, Arias DO, García PP, Giovambattista G. Preliminary transcriptomic analysis of peripheral blood from German Shepherd dogs with degenerative joint disease for the identification of diagnostic biomarkers. Gene 2023; 872:147455. [PMID: 37254296 DOI: 10.1016/j.gene.2023.147455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 04/08/2023] [Accepted: 04/25/2023] [Indexed: 06/01/2023]
Abstract
OBJECTIVE Degenerative joint disease (DJD) includes a group of disorders characterised by the deterioration of the articular cartilage. In this study, we investigated the transcriptomic profile of peripheral blood in German Shepherd dogs with DJD to identify putative diagnostic biomarkers. METHODS Differential gene expression (DGE) and gene ontology (GO) analyses of the bulk RNA-seq experiment were performed in a cohort of 12 adult dogs (five cases and seven controls, classified by clinical and radiographic analyses). RESULTS Radiographs of cases revealed severe signs of progressive DJD. Two up-regulated (LOC106559672 and THBS4) and one down-regulated (LOC106559235) differentially expressed genes (adjusted p value < 0.05) were identified. The DGE with log2 fold change < -1.5 and > 1.5 and non-adjusted p < 0.01 were selected for GO analysis. No significant enrichment terms were observed in the selected threshold. CONCLUSION The gene-encoding protein THBS4 is correlated with DJD severity and long noncoding RNA LOC106559235 is probably involved in the DJD process. The THBS4 gene should be considered a good biomarker for DJD in dogs. Future studies using independent cohorts will be necessary to validate the present results.
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Affiliation(s)
- Gisel Padula
- IGEVET - Instituto de Genética Veterinaria "Ing. Fernando Noel Dulout" (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias UNLP, 60 y 118 S/N, 1900 La Plata, Argentina; Facultad de Ciencias Naturales y Museo UNLP, 60 y 122, 1900 La Plata, Argentina
| | - Gabriela Rudd Garces
- IGEVET - Instituto de Genética Veterinaria "Ing. Fernando Noel Dulout" (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias UNLP, 60 y 118 S/N, 1900 La Plata, Argentina
| | - María Elena Fernández
- IGEVET - Instituto de Genética Veterinaria "Ing. Fernando Noel Dulout" (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias UNLP, 60 y 118 S/N, 1900 La Plata, Argentina
| | - Rosario Vercellini
- Servicio de Radiología, Facultad de Ciencias Veterinarias UNLP, 60 y 118 S/N, 1900 La Plata, Argentina
| | - Daniel Osvaldo Arias
- Servicio de Radiología, Facultad de Ciencias Veterinarias UNLP, 60 y 118 S/N, 1900 La Plata, Argentina
| | - Pilar Peral García
- IGEVET - Instituto de Genética Veterinaria "Ing. Fernando Noel Dulout" (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias UNLP, 60 y 118 S/N, 1900 La Plata, Argentina
| | - Guillermo Giovambattista
- IGEVET - Instituto de Genética Veterinaria "Ing. Fernando Noel Dulout" (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias UNLP, 60 y 118 S/N, 1900 La Plata, Argentina.
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Ma S, Hu H, Zhang H, Ma F, Gao Z, Li X. Physiological response and transcriptome analyses of leguminous Indigofera bungeana Walp. to drought stress. PeerJ 2023; 11:e15440. [PMID: 37334133 PMCID: PMC10276564 DOI: 10.7717/peerj.15440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 04/28/2023] [Indexed: 06/20/2023] Open
Abstract
Objective Indigofera bungeana is a shrub with high quality protein that has been widely utilized for forage grass in the semi-arid regions of China. This study aimed to enrich the currently available knowledge and clarify the detailed drought stress regulatory mechanisms in I. bungeana, and provide a theoretical foundation for the cultivation and resistance breeding of forage crops. Methods This study evaluates the response mechanism to drought stress by exploiting multiple parameters and transcriptomic analyses of a 1-year-old seedlings of I. bungeana in a pot experiment. Results Drought stress significantly caused physiological changes in I. bungeana. The antioxidant enzyme activities and osmoregulation substance content of I. bungeana showed an increase under drought. Moreover, 3,978 and 6,923 differentially expressed genes were approved by transcriptome in leaves and roots. The transcription factors, hormone signal transduction, carbohydrate metabolism of regulatory network were observed to have increased. In both tissues, genes related to plant hormone signaling transduction pathway might play a more pivotal role in drought tolerance. Transcription factors families like basic helix-loop-helix (bHLH), vian myeloblastosis viral oncogene homolog (MYB), basic leucine zipper (bZIP) and the metabolic pathway related-genes like serine/threonine-phosphatase 2C (PP2C), SNF1-related protein kinase 2 (SnRK2), indole-3-acetic acid (IAA), auxin (AUX28), small auxin up-regulated rna (SAUR), sucrose synthase (SUS), sucrosecarriers (SUC) were highlighted for future research about drought stress resistance in Indigofera bungeana. Conclusion Our study posited I. bungeana mainly participate in various physiological and metabolic activities to response severe drought stress, by regulating the expression of the related genes in hormone signal transduction. These findings, which may be valuable for drought resistance breeding, and to clarify the drought stress regulatory mechanisms of I. bungeana and other plants.
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Affiliation(s)
- Shuang Ma
- College of Forestry and Prataculture, Ningxia University, Yinchuan, Ningxia, China
| | - Haiying Hu
- College of Forestry and Prataculture, Ningxia University, Yinchuan, Ningxia, China
- Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration of North-Western China, Ningxia University, Yinchuan, Ningxia, China
| | - Hao Zhang
- College of Forestry and Prataculture, Ningxia University, Yinchuan, Ningxia, China
| | - Fenghua Ma
- College of Forestry and Prataculture, Ningxia University, Yinchuan, Ningxia, China
| | - Zhihao Gao
- College of Forestry and Prataculture, Ningxia University, Yinchuan, Ningxia, China
| | - Xueying Li
- College of Forestry and Prataculture, Ningxia University, Yinchuan, Ningxia, China
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Dai Y, Zhang Y, Sun W, Chen Y, Wang X, Xin T, Wan B, Xia B, Zhong L, Zou Z. The metabolism and detoxification effects of lead exposure on Aleurolyphus ovatus (Acari: Acaridae) via transcriptome analysis. Chemosphere 2023; 333:138886. [PMID: 37164204 DOI: 10.1016/j.chemosphere.2023.138886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/01/2023] [Accepted: 05/06/2023] [Indexed: 05/12/2023]
Abstract
Aleurolyphus ovatus Troupeau is one of the most predominant species of the Acaridae family worldwide. Recent reports have demonstrated that the accumulation of lead in stored grains and dietary items exceeds the required standards. However, the molecular mechanism of heavy metal stress on mites has not been reported. To understand the mechanism underlying the heavy metal response of A. ovatus, comparative transcriptome analysis was performed in this study using an Illumina high throughput mRNA sequencing (RNA-seq) platform. A. ovatus was fed on artificial diets containing two different concentrations of lead, namely, a low concentration of 12.5 mg/kg (LAO) and a high concentration of 100 mg/kg (HAO), while the mites in the control (NAO) group were not exposed to lead. A total of 44,362 unigenes, with an average length of 1547 bp, were identified. Of these, 996 unigenes were successfully annotated in seven functional databases. The number of differentially expressed genes (DEGs) in A. ovatus under different lead concentrations was compared. In NAO versus LAO group, including 310 up-regulated and 1580 down-regulated DEGs. In NAO versus HAO group, including 3928 up-regulated and 1761 down-regulated DEGs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment indicated that detoxification enzyme genes were significantly expressed in pathways, such as cytochrome P450 foreign body metabolism, glutathione metabolism and drug metabolism-cytochrome pathway. The results of gene annotation and quantitative real-time PCR showed that high concentration of lead significantly stimulated the expression of metabolic detoxification enzyme genes such as glutathione S transferase (GST) and superoxide dismutase (SOD), while low concentration inhibited their expression. This study will provide a basis for the molecular mechanism of A. ovatus in response to heavy metal lead stimulation in stored grain.
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Affiliation(s)
- Yi Dai
- School of Life Science, Nanchang University, Nanchang, 330031, China
| | - Yu Zhang
- School of Life Science, Nanchang University, Nanchang, 330031, China
| | - Wenxuan Sun
- School of Life Science, Nanchang University, Nanchang, 330031, China
| | - Yajuan Chen
- School of Life Science, Nanchang University, Nanchang, 330031, China
| | - Xi Wang
- School of Life Science, Nanchang University, Nanchang, 330031, China; Development & Service Center for Agriculture and Rural Industry of Jiangxi Province, Nanchang, 330096, China
| | - Tianrong Xin
- School of Life Science, Nanchang University, Nanchang, 330031, China
| | - Bin Wan
- School of Life Science, Nanchang University, Nanchang, 330031, China
| | - Bin Xia
- School of Life Science, Nanchang University, Nanchang, 330031, China
| | - Ling Zhong
- Development & Service Center for Agriculture and Rural Industry of Jiangxi Province, Nanchang, 330096, China
| | - Zhiwen Zou
- School of Life Science, Nanchang University, Nanchang, 330031, China; Jiangxi Provincial Key Laboratory of Interdisciplinary Science, Nanchang University, Nanchang, 330031, China.
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Marrella MA, Biase FH. Robust identification of regulatory variants (eQTLs) using a differential expression framework developed for RNA-sequencing. J Anim Sci Biotechnol 2023; 14:62. [PMID: 37143150 PMCID: PMC10161580 DOI: 10.1186/s40104-023-00861-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 03/05/2023] [Indexed: 05/06/2023] Open
Abstract
BACKGROUND A gap currently exists between genetic variants and the underlying cell and tissue biology of a trait, and expression quantitative trait loci (eQTL) studies provide important information to help close that gap. However, two concerns that arise with eQTL analyses using RNA-sequencing data are normalization of data across samples and the data not following a normal distribution. Multiple pipelines have been suggested to address this. For instance, the most recent analysis of the human and farm Genotype-Tissue Expression (GTEx) project proposes using trimmed means of M-values (TMM) to normalize the data followed by an inverse normal transformation. RESULTS In this study, we reasoned that eQTL analysis could be carried out using the same framework used for differential gene expression (DGE), which uses a negative binomial model, a statistical test feasible for count data. Using the GTEx framework, we identified 35 significant eQTLs (P < 5 × 10-8) following the ANOVA model and 39 significant eQTLs (P < 5 × 10-8) following the additive model. Using a differential gene expression framework, we identified 930 and six significant eQTLs (P < 5 × 10-8) following an analytical framework equivalent to the ANOVA and additive model, respectively. When we compared the two approaches, there was no overlap of significant eQTLs between the two frameworks. Because we defined specific contrasts, we identified trans eQTLs that more closely resembled what we expect from genetic variants showing complete dominance between alleles. Yet, these were not identified by the GTEx framework. CONCLUSIONS Our results show that transforming RNA-sequencing data to fit a normal distribution prior to eQTL analysis is not required when the DGE framework is employed. Our proposed approach detected biologically relevant variants that otherwise would not have been identified due to data transformation to fit a normal distribution.
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Affiliation(s)
- Mackenzie A Marrella
- School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Fernando H Biase
- School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA.
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Bhattarai R, Liu H, Siddique KHM, Yan G. Transcriptomic profiling of near-isogenic lines reveals candidate genes for a significant locus conferring metribuzin resistance in wheat. BMC Plant Biol 2023; 23:237. [PMID: 37142987 PMCID: PMC10161546 DOI: 10.1186/s12870-023-04166-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 03/13/2023] [Indexed: 05/06/2023]
Abstract
BACKGROUND Weeds reduce wheat yields in dryland farming systems. Herbicides such as metribuzin are commonly used to control weeds. However, wheat has a narrow safety margin against metribuzin. Standing crops such as wheat with weeds in the same field can also be killed by the same dose of metribuzin. Therefore, it is important to identify metribuzin resistance genes and understand the resistance mechanism in wheat for sustainable crop production. A previous study identified a significant metribuzin resistance wheat QTL, Qsns.uwa.4 A.2, explaining 69% of the phenotypic variance for metribuzin resistance. RESULTS Two NIL pairs with the most contrasting performance in the metribuzin treatment and different in genetic backgrounds were compared using RNA sequence analysis, identifying nine candidate genes underlying Qsns.uwa.4 A.2 responsible for metribuzin resistance. Quantitative RT-qPCR further validated the candidate genes, with TraesCS4A03G1099000 (nitrate excretion transporter), TraesCS4A03G1181300 (aspartyl protease), and TraesCS4A03G0741300 (glycine-rich proteins) identified as key factors for metribuzin resistance. CONCLUSION Identified markers and key candidate genes can be used for selecting metribuzin resistance in wheat.
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Affiliation(s)
- Rudra Bhattarai
- UWA School of Agriculture and Environment, The University of Western Australia, 6009, Perth, WA, Australia
- The UWA Institute of Agriculture, The University of Western Australia, 6009, Perth, WA, Australia
| | - Hui Liu
- UWA School of Agriculture and Environment, The University of Western Australia, 6009, Perth, WA, Australia.
- The UWA Institute of Agriculture, The University of Western Australia, 6009, Perth, WA, Australia.
| | - Kadambot H M Siddique
- UWA School of Agriculture and Environment, The University of Western Australia, 6009, Perth, WA, Australia
- The UWA Institute of Agriculture, The University of Western Australia, 6009, Perth, WA, Australia
| | - Guijun Yan
- UWA School of Agriculture and Environment, The University of Western Australia, 6009, Perth, WA, Australia
- The UWA Institute of Agriculture, The University of Western Australia, 6009, Perth, WA, Australia
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Chen W, Zhou W, Li Q, Mao X. Sex differences in gene expression and alternative splicing in the Chinese horseshoe bat. PeerJ 2023; 11:e15231. [PMID: 37123006 PMCID: PMC10135408 DOI: 10.7717/peerj.15231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 03/24/2023] [Indexed: 05/02/2023] Open
Abstract
Sexually dimorphic traits are common in sexually reproducing organisms and can be encoded by differential gene regulation between males and females. Although alternative splicing is common mechanism in generating transcriptional diversity, its role in generating sex differences relative to differential gene expression is less clear. Here, we investigate the relative roles of differential gene expression and alternative splicing between male and female the horseshoe bat species, Rhinolophus sinicus. Horseshoe bats are an excellent model to study acoustic differences between sexes. Using RNA-seq analyses of two somatic tissues (brain and liver) from males and females of the same population, we identified 3,471 and 2,208 differentially expressed genes between the sexes (DEGs) in the brain and liver, respectively. DEGs were enriched with functional categories associated with physiological difference of the sexes (e.g.,gamete generation and energy production for reproduction in females). In addition, we also detected many differentially spliced genes between the sexes (DSGs, 2,231 and 1,027 in the brain and liver, respectively) which were mainly involved in regulation of RNA splicing and mRNA metabolic process. Interestingly, we found a significant enrichment of DEGs on the X chromosome, but not for DSGs. As for the extent of overlap between the two sets of genes, more than expected overlap of DEGs and DSGs was observed in the brain but not in the liver. This suggests that more complex tissues, such as the brain, may require the intricate and simultaneous interplay of both differential gene expression and splicing of genes to govern sex-specific functions. Overall, our results support that variation in gene expression and alternative splicing are important and complementary mechanisms governing sex differences.
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Affiliation(s)
- Wenli Chen
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Weiwei Zhou
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Qianqian Li
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Xiuguang Mao
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
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Tsirigka A, Theodosiou E, Patsios SI, Tsoureki A, Andreadelli A, Papa E, Aggeli A, Karabelas AJ, Makris AM. Novel evolved Yarrowia lipolytica strains for enhanced growth and lipid content under high concentrations of crude glycerol. Microb Cell Fact 2023; 22:62. [PMID: 37004109 PMCID: PMC10067222 DOI: 10.1186/s12934-023-02072-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 03/24/2023] [Indexed: 04/03/2023] Open
Abstract
BACKGROUND Yarrowia lipolytica is a well-studied oleaginous yeast known for its ability to accumulate and store intracellular lipids, while growing on diverse, non-conventional substrates. Amongst them, crude glycerol, a low-cost by-product of the biodiesel industry, appears to be an interesting option for scaling up a sustainable single-cell oil production process. Adaptive laboratory evolution (ALE) is a powerful tool to force metabolic adaptations endowing tolerance to stressful environmental conditions, generating superior phenotypes with industrial relevance. RESULTS Y. lipolytica MUCL 28849 underwent ALE in a synthetic medium with increasing concentration of pure or crude glycerol as a stressing factor (9-20% v/v) for 520 generations. In one case of pure glycerol, chemical mutagenesis with ethyl methanesulfonate (EMS) was applied prior to ALE. Growth profile, biomass production and lipid content of 660 evolved strains (EVS), revealed 5 superior isolates; exhibiting from 1.9 to 3.6-fold increase of dry biomass and from 1.1 to 1.6-fold increase of lipid concentration compared to the parental strain, when grown in 15% v/v crude glycerol. NGS for differential gene expression analysis, showed induced expression in all EVS affecting nucleosomal structure and regulation of transcription. As strains differentiated, further changes accumulated in membrane transport and protein transport processes. Genes involved in glycerol catabolism and triacylglycerol biosynthesis were overexpressed in two EVS. Mismatches and gaps in the expressed sequences identified altered splicing and mutations in the EVS, with most of them, affecting different components of septin ring formation in the budding process. The selected YLE155 EVS, used for scale-up cultivation in a 3L benchtop bioreactor with 20% v/v crude glycerol, achieved extended exponential phase, twofold increase of dry biomass and lipid yields at 48 h, while citric acid secretion and glycerol consumption rates were 40% and 50% lower, respectively, compared to the parental strain, after 24 h of cultivation. CONCLUSION ALE and EMS-ALE under increasing concentrations of pure or crude glycerol generated novel Y. lipolytica strains with enhanced biomass and lipid content. Differential gene expression analysis and scale-up of YLE155, illustrated the potential of the evolved strains to serve as suitable "chassis" for rational engineering approaches towards both increased lipid accumulation, and production of high-added value compounds, through efficient utilization of crude glycerol.
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Affiliation(s)
- Asimina Tsirigka
- Laboratory of Natural Resources and Renewable Energies, Chemical Process and Energy Resources Institute, Centre for Research and Technology - Hellas, Thermi, Thessaloniki, Greece
- Department of Chemical Engineering, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Eleni Theodosiou
- Institute of Applied Biosciences, Centre for Research and Technology - Hellas, Thermi, Thessaloniki, Greece
| | - Sotiris I Patsios
- Laboratory of Natural Resources and Renewable Energies, Chemical Process and Energy Resources Institute, Centre for Research and Technology - Hellas, Thermi, Thessaloniki, Greece
| | - Antiopi Tsoureki
- Institute of Applied Biosciences, Centre for Research and Technology - Hellas, Thermi, Thessaloniki, Greece
| | - Aggeliki Andreadelli
- Institute of Applied Biosciences, Centre for Research and Technology - Hellas, Thermi, Thessaloniki, Greece
| | - Elisavet Papa
- Institute of Applied Biosciences, Centre for Research and Technology - Hellas, Thermi, Thessaloniki, Greece
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece
| | - Amalia Aggeli
- Department of Chemical Engineering, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Anastasios J Karabelas
- Laboratory of Natural Resources and Renewable Energies, Chemical Process and Energy Resources Institute, Centre for Research and Technology - Hellas, Thermi, Thessaloniki, Greece
| | - Antonios M Makris
- Institute of Applied Biosciences, Centre for Research and Technology - Hellas, Thermi, Thessaloniki, Greece.
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Mierke F, Brink DP, Norbeck J, Siewers V, Andlid T. Functional genome annotation and transcriptome analysis of Pseudozyma hubeiensis BOT-O, an oleaginous yeast that utilizes glucose and xylose at equal rates. Fungal Genet Biol 2023; 166:103783. [PMID: 36870442 DOI: 10.1016/j.fgb.2023.103783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 02/10/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023]
Abstract
Pseudozyma hubeiensis is a basidiomycete yeast that has the highly desirable traits for lignocellulose valorisation of being equally efficient at utilization of glucose and xylose, and capable of their co-utilization. The species has previously mainly been studied for its capacity to produce secreted biosurfactants in the form of mannosylerythritol lipids, but it is also an oleaginous species capable of accumulating high levels of triacylglycerol storage lipids during nutrient starvation. In this study, we aimed to further characterize the oleaginous nature of P. hubeiensis by evaluating metabolism and gene expression responses during storage lipid formation conditions with glucose or xylose as a carbon source. The genome of the recently isolated P. hubeiensis BOT-O strain was sequenced using MinION long-read sequencing and resulted in the most contiguous P. hubeiensis assembly to date with 18.95 Mb in 31 contigs. Using transcriptome data as experimental support, we generated the first mRNA-supported P. hubeiensis genome annotation and identified 6540 genes. 80% of the predicted genes were assigned functional annotations based on protein homology to other yeasts. Based on the annotation, key metabolic pathways in BOT-O were reconstructed, including pathways for storage lipids, mannosylerythritol lipids and xylose assimilation. BOT-O was confirmed to consume glucose and xylose at equal rates, but during mixed glucose-xylose cultivation glucose was found to be taken up faster. Differential expression analysis revealed that only a total of 122 genes were significantly differentially expressed at a cut-off of |log2 fold change| ≥ 2 when comparing cultivation on xylose with glucose, during exponential growth and during nitrogen-starvation. Of these 122 genes, a core-set of 24 genes was identified that were differentially expressed at all time points. Nitrogen-starvation resulted in a larger transcriptional effect, with a total of 1179 genes with significant expression changes at the designated fold change cut-off compared with exponential growth on either glucose or xylose.
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Affiliation(s)
- Friederike Mierke
- Food and Nutrition Science, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden; Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Daniel P Brink
- Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden; Applied Microbiology, Department of Chemistry, Lund University, Lund, Sweden
| | - Joakim Norbeck
- Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Verena Siewers
- Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden.
| | - Thomas Andlid
- Food and Nutrition Science, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
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Sharma N, Shivran M, Singh N, Dubey AK, Singh SK, Sharma N, Gupta R, Vittal H, Singh BP, Sevanthi AM, Singh NK. Differential gene expression associated with flower development of mango (Mangifera indica L.) varieties with different shelf-life. Gene Expr Patterns 2023; 47:119301. [PMID: 36526239 DOI: 10.1016/j.gep.2022.119301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 11/22/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022]
Abstract
Mango (Mangifera indica L.) is one of the most important commercial fruit crop grown in many parts of the world. Major challenges affecting mango trade are short shelf-life, high susceptibility to chilling injury, post-harvest diseases and consumer demand for improved fruit quality. The objective of the present study was to reveal the key regulators present in bud and flower tissues during flower development stage, associated with fruit development and affect the shelf-life of the mango fruit. RNA-sequencing of contrasting genotypes having short and long shelf-life, was carried out. Comparative differential expression pathway studies of long shelf-life (Totapuri) and short shelf-life (Bombay Green) mango genotypes revealed a total of 177 highly differentially expressed genes. Out of 177 total genes, 101 genes from endoplasmic reticulum pathway and very few from gibberellins (3) and jasmonic acid (1) pathway were identified. Genes from endoplasmic reticulum pathway like hsp 90, SRC2, DFRA, CHS, BG3 and ASPG1 mainly up regulated in Bombay Green. Uniprotein B9R8D3 also shows up regulation in Bombay Green. Ethylene insensitive pathway gene EIL1 up regulated in Bombay Green. Gene CAD1 from phenylpropanoid pathway mainly up regulated in Bombay Green. A total of 4 SSRs and 227 SNPs were mined from these pathways specific to the shelf-life. Molecular studies of endoplasmic reticulum, phenylpropanoid, ethylene, polygalacturonase and hormone pathways at the time of bud and flower formation revealed key regulators that determine the shelf-life of mango fruit.
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Affiliation(s)
- Nimisha Sharma
- Division of Fruits and Horticultural Technology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
| | - Mukesh Shivran
- Division of Fruits and Horticultural Technology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Narendra Singh
- Division of Fruits and Horticultural Technology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Anil Kumar Dubey
- Division of Fruits and Horticultural Technology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Sanjay Kumar Singh
- Division of Fruits and Horticultural Technology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Neha Sharma
- IILM Academy of Higher Learning, College of Engineering and Technology Greater, Noida, Uttar Pradesh, 201310, India
| | - Ruchi Gupta
- NGB Diagnostics Private Limited, Noida, UP, 201301, India
| | - Hatkari Vittal
- Division of Fruits and Horticultural Technology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
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Mohindra V, Chowdhury LM, Chauhan N, Paul A, Singh RK, Kushwaha B, Maurya RK, Lal KK, Jena JK. Transcriptome Analysis Revealed Osmoregulation Related Regulatory Networks and Hub Genes in the Gills of Hilsa shad, Tenualosa ilisha, during the Migratory Osmotic Stress. Mar Biotechnol (NY) 2023; 25:161-173. [PMID: 36631626 DOI: 10.1007/s10126-022-10190-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
Tenualosa ilisha (Hilsa shad), an anadromous fish, usually inhabits coastal and estuarine waters, and migrates to freshwater for spawning. In this study, large-scale gill transcriptome analyses from three salinity regions, i.e., fresh, brackish and marine water, revealed 3277 differentially expressed genes (DEGs), out of which 232 were found to be common between marine vs freshwater and brackish vs freshwater. These genes were mapped into 54 KEGG Pathways, and the most significant of these were focal adhesion, adherens junction, tight junction, and PI3K-Akt signaling pathways. A total of 24 osmoregulatory genes were found to be differentially expressed in different habitats. The gene members of slc16 and slc2 families showed a dissimilar pattern of expressions, while two claudin genes (cldn11 & cldn10), transmembrane tm56b, and voltage-gated potassium channel gene kcna10 were downregulated in freshwater samples, as compared to that of brackish and marine environment. Protein-protein interaction (PPI) network analysis of 232 DEGs showed 101 genes to be involved in PPI, while fn1 gene was found to be interacting with the highest number of genes (36). Twenty-five hub genes belonged to 12 functional groups, with muscle structure development with seven genes, forming the major group. These results provided valuable information about the genes, potentially involved in the molecular mechanisms regulating water homeostasis in gills, during migration for spawning and low-salinity adaptation in Hilsa shad. These genes may form the basis for the bio-marker development for adaptation to the stress levied by major environmental changes, due to hatchery/culture conditions.
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Affiliation(s)
- Vindhya Mohindra
- ICAR-National Bureau of Fish Genetic Resources (NBFGR), Canal Ring Road, Dilkusha, Lucknow, 226002, India.
| | - Labrechai Mog Chowdhury
- ICAR-National Bureau of Fish Genetic Resources (NBFGR), Canal Ring Road, Dilkusha, Lucknow, 226002, India
| | - Nishita Chauhan
- ICAR-National Bureau of Fish Genetic Resources (NBFGR), Canal Ring Road, Dilkusha, Lucknow, 226002, India
| | - Alisha Paul
- ICAR-National Bureau of Fish Genetic Resources (NBFGR), Canal Ring Road, Dilkusha, Lucknow, 226002, India
| | - Rajeev Kumar Singh
- ICAR-National Bureau of Fish Genetic Resources (NBFGR), Canal Ring Road, Dilkusha, Lucknow, 226002, India
| | - Basdeo Kushwaha
- ICAR-National Bureau of Fish Genetic Resources (NBFGR), Canal Ring Road, Dilkusha, Lucknow, 226002, India
| | - Rajesh Kumar Maurya
- ICAR-National Bureau of Fish Genetic Resources (NBFGR), Canal Ring Road, Dilkusha, Lucknow, 226002, India
| | - Kuldeep K Lal
- ICAR-National Bureau of Fish Genetic Resources (NBFGR), Canal Ring Road, Dilkusha, Lucknow, 226002, India
| | - J K Jena
- Indian Council of Agricultural Research (ICAR), Krishi Anusandhan Bhawan-II, New Delhi, 110 012, India
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Rai MK. Start codon targeted (SCoT) polymorphism marker in plant genome analysis: current status and prospects. Planta 2023; 257:34. [PMID: 36622439 DOI: 10.1007/s00425-023-04067-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 01/04/2023] [Indexed: 06/17/2023]
Abstract
The present review illustrates a comprehensive overview of the start codon targeted (SCoT) polymorphism marker and their utilization in various applications related to genetic and genomic studies. Start codon targeted (SCoT) polymorphism marker, a targeted fingerprinting marker technique, has gained considerable importance in plant genetics, genomics, and molecular breeding due to its many desirable features. SCoT marker targets the region flanking the start codon, a highly conserved region in plant genes. Therefore, it can distinguish genetic variations in a specific gene that link to a specific trait. It is a simple, novel, cost-effective, highly polymorphic, and reproducible molecular marker for which there is no need for prior sequence information. In the recent past, SCoT markers have been employed in many commercially important and underutilized plant species for a variety of applications, including genetic diversity analysis, interspecific/generic genetic relationships, cultivar/hybrid/species identification, sex determination, construction of linkage map, association mapping/analysis, differential gene expression, and genetic fidelity analysis of tissue culture-raised plants. The main aim of this review is to provide up-to-date information on SCoT markers and their application in many commercially important and underutilized plant species, mainly progress made in the last 8-10 years.
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Affiliation(s)
- Manoj K Rai
- Department of Environmental Science, Indira Gandhi National Tribal University, Amarkantak, MP, 484887, India.
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Pan Y, Surendra A, Liu Z, Ouellet T, Foroud NA. Differential Expression Feature Extraction (DEFE): A Case Study in Wheat FHB RNA-Seq Data Analysis. Methods Mol Biol 2023; 2659:137-159. [PMID: 37249891 DOI: 10.1007/978-1-0716-3159-1_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
In differential gene expression data analysis, one objective is to identify groups of co-expressed genes from a large dataset in order to detect the association between such a group of genes and an experimental condition. This is often done through a clustering approach, such as k-means or bipartition hierarchical clustering, based on particular similarity measures in the grouping process. In such a dataset, the gene differential expression itself is an innate attribute that can be used in the feature extraction process. For example, in a dataset consisting of multiple treatments versus their controls, the expression of a gene in each treatment would have three possible behaviors, upregulated, downregulated, or unchanged. We present in this chapter, a differential expression feature extraction (DEFE) method by using a string consisting of three numerical values at each character to denote such behavior, i.e., 1 = up, 2 = down, and 0 = unchanged, which results in up to 3B differential expression patterns across all B comparisons. This approach has been successfully applied in many research projects, and among these, we demonstrate the strength of DEFE in a case study on RNA-sequencing (RNA-seq) data analysis of wheat challenged with the phytopathogenic fungus, Fusarium graminearum. Combinations of multiple schemes of DEFE patterns revealed groups of genes putatively associated with resistance or susceptibility to FHB.
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Affiliation(s)
- Youlian Pan
- Digital Technologies Research Centre, National Research Council Canada, Ottawa, ON, Canada.
| | - Anuradha Surendra
- Digital Technologies Research Centre, National Research Council Canada, Ottawa, ON, Canada
| | - Ziying Liu
- Digital Technologies Research Centre, National Research Council Canada, Ottawa, ON, Canada
| | - Thérèse Ouellet
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Nora A Foroud
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
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Raj K, Rishi P, Shukla G, Rudramurhty SM, Mongad DS, Kaur A. Possible Contribution of Alternative Transcript Isoforms in Mature Biofilm Growth Phase of Candida glabrata. Indian J Microbiol 2022; 62:583-601. [PMID: 36458226 PMCID: PMC9705674 DOI: 10.1007/s12088-022-01036-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 08/04/2022] [Indexed: 11/05/2022] Open
Abstract
Expression of genome-wide alternative transcript isoforms and differential transcript isoform usage in different biological conditions (isoform switching) are responsible for the varied proteomic functional diversity in higher eukaryotic organisms. However, these mechanisms have not been studied in Candida glabrata, which is a potent eukaryotic opportunistic pathogen. Biofilm formation is an important virulence factor of C. glabrata that withstands antifungal drug stress and overcomes the host-immune response. Here, we present the genome-wide differential transcript isoform expression (DTE) and differential transcript isoform usage (DTU) in a mature biofilm growth phase of C. glabrata (clinical isolate; NCCPF 100,037) using the RNA sequencing approach. The DTE analysis generated 7837 transcript isoforms from the C. glabrata genome (5293 genes in total), and revealed that transcript isoforms generated from 292 genes showed significant DTU in the mature biofilm cells. Gene ontology, pathway analysis and protein-protein interactions of significant transcript isoforms, further substantiated that their specific expression and differential usage is required for transitioning the planktonic cells to biofilm in C. glabrata. The present study reported the possible role of expression of alternative transcript isoforms and differential transcript isoform usage in the mature biofilms of C. glabrata. The observation derived from the study may prove to be beneficial for making future antifungal therapeutic strategies. Supplementary Information The online version contains supplementary material available at 10.1007/s12088-022-01036-7.
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Affiliation(s)
- Khem Raj
- Department of Microbiology, Basic Medical Sciences Block I, South Campus, Panjab University, Sector-25, Chandigarh, 160014 India
| | - Praveen Rishi
- Department of Microbiology, Basic Medical Sciences Block I, South Campus, Panjab University, Sector-25, Chandigarh, 160014 India
| | - Geeta Shukla
- Department of Microbiology, Basic Medical Sciences Block I, South Campus, Panjab University, Sector-25, Chandigarh, 160014 India
| | - Shivaprakash M. Rudramurhty
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - Dattatray S. Mongad
- National Centre for Microbial Resource, National Centre for Cell Sciences (NCCS), Pune, India
| | - Amrita Kaur
- Department of Microbiology, Basic Medical Sciences Block I, South Campus, Panjab University, Sector-25, Chandigarh, 160014 India
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