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Schwartz LC, González VL, Strong EE, Truebano M, Hilbish TJ. Transgressive gene expression and expression plasticity under thermal stress in a stable hybrid zone. Mol Ecol 2024; 33:e17333. [PMID: 38597343 DOI: 10.1111/mec.17333] [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: 06/21/2022] [Revised: 02/21/2024] [Accepted: 03/18/2024] [Indexed: 04/11/2024]
Abstract
Interspecific hybridization can lead to myriad outcomes, including transgressive phenotypes in which the hybrids are more fit than either parent species. Such hybrids may display important traits in the context of climate change, able to respond to novel environmental conditions not previously experienced by the parent populations. While this has been evaluated in an agricultural context, the role of transgressive hybrids under changing conditions in the wild remains largely unexplored; this is especially true regarding transgressive gene expression. Using the blue mussel species complex (genus Mytilus) as a model system, we investigated the effects of hybridization on temperature induced gene expression plasticity by comparing expression profiles in parental species and their hybrids following a 2-week thermal challenge. Hybrid expression plasticity was most often like one parent or the other (50%). However, a large fraction of genes (26%) showed transgressive expression plasticity (i.e. the change in gene expression was either greater or lesser than that of both parent species), while only 2% were intermediately plastic in hybrids. Despite their close phylogenetic relationship, there was limited overlap in the differentially expressed genes responding to temperature, indicating interspecific differences in the responses to high temperature in which responses from hybrids are distinct from both parent species. We also identified differentially expressed long non-coding RNAs (lncRNAs), which we suggest may contribute to species-specific differences in thermal tolerance. Our findings provide important insight into the impact of hybridization on gene expression under warming. We propose transgressive hybrids may play an important role in population persistence under future warming conditions.
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Affiliation(s)
- Lindsey C Schwartz
- Department of Biological Sciences, The University of South Carolina, Columbia, South Carolina, USA
- Department of Invertebrate Zoology, Smithsonian National Museum of Natural History, Washington, District of Columbia, USA
- Department of Biology, University of Louisiana at Lafayette, Lafayette, Louisiana, USA
| | - Vanessa L González
- Informatics and Data Science Center, Smithsonian National Museum of Natural History, Washington, District of Columbia, USA
| | - Ellen E Strong
- Department of Invertebrate Zoology, Smithsonian National Museum of Natural History, Washington, District of Columbia, USA
| | - Manuela Truebano
- Marine Biology and Ecology Research Centre, School of Biological and Marine Sciences, University of Plymouth, Plymouth, UK
| | - Thomas J Hilbish
- Department of Biological Sciences, The University of South Carolina, Columbia, South Carolina, USA
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Babich R, Merutka I, Craig E, Harichandara A, De Silva PMCS, Gunasekara TDKSC, Jayasundara N. Transcriptomic and behavioral analyses reveal unique target tissues and molecular pathways associated with embryonic exposure to low level glyphosate and metal mixtures in zebrafish. Sci Total Environ 2024; 912:169271. [PMID: 38114029 PMCID: PMC10964846 DOI: 10.1016/j.scitotenv.2023.169271] [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: 09/28/2023] [Revised: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 12/21/2023]
Abstract
Investigation of developmental molecular events following exposure to environmentally relevant agrochemical mixtures is critical to predicting their potential long-term ecological and human health risks. Here, we sought to uncover transcriptomic changes during zebrafish (Danio rerio) embryonic development following exposure to glyphosate and co-exposure to metals. Glyphosate is widely used globally with an allowable drinking water limit of 700 ppb. We examined effects of glyphosate (10 ppb) alone and when co-exposed to a metal mixture containing low levels of arsenic (4 ppb), lead (5 ppb), cadmium (2 ppb), and vanadium (15 ppb). This mixture was derived based on behavioral and morphological toxicity findings and environmentally relevant concentrations found in agricultural regions where glyphosate and metals are ubiquitously present. Gene expression patterns coupled to a single-cell transcriptomic dataset revealed that developmental exposure (28-72 h post fertilization) to glyphosate dysregulates expression of developmental genes specific to the central nervous system. Subsequent studies indicated significant suppression of larval zebrafish movement with 10 ppb glyphosate exposure. Studies with glyphosate + metals mixture and metals mixture alone showed unique developmental transcriptomic patterns and behavioral changes compared to glyphosate exposure alone. However, some outcomes (e.g., changes in expression of genes involved in epigenetic regulation and extracellular matrix patterning) were common across all three exposures compared to the control. Notably, glyphosate + metals co-exposure distinctly suppresses lysosomal transcripts and targets renal developmental genes. While further studies are required to uncover the precise nature of the interactions between glyphosate and metals, our study shows that glyphosate at very low levels is a behavioral and neurotoxicant that changes when metals are present. Given this herbicide affects distinctive physiological processes, including renal development and lysosomal dysregulation when co-exposed with metals, we conclude that environmental cation levels should be considered in glyphosate toxicity and risk assessment.
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Affiliation(s)
- Remy Babich
- University of Maine, Orono, ME 14069, United States of America.
| | - Ilaria Merutka
- Nicholas School of the Environment, Duke University, Durham, NC 27708, United States of America
| | - Emily Craig
- University of Maine, Orono, ME 14069, United States of America; Nicholas School of the Environment, Duke University, Durham, NC 27708, United States of America
| | | | | | | | - Nishad Jayasundara
- University of Maine, Orono, ME 14069, United States of America; Nicholas School of the Environment, Duke University, Durham, NC 27708, United States of America
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Ashey J, McKelvie H, Freeman J, Shpilker P, Zane LH, Becker DM, Cowen L, Richmond RH, Paul VJ, Seneca FO, Putnam HM. Characterizing transcriptomic responses to sediment stress across location and morphology in reef-building corals. PeerJ 2024; 12:e16654. [PMID: 38313033 PMCID: PMC10836209 DOI: 10.7717/peerj.16654] [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: 04/20/2023] [Accepted: 11/20/2023] [Indexed: 02/06/2024] Open
Abstract
Anthropogenic activities increase sediment suspended in the water column and deposition on reefs can be largely dependent on colony morphology. Massive and plating corals have a high capacity to trap sediments, and active removal mechanisms can be energetically costly. Branching corals trap less sediment but are more susceptible to light limitation caused by suspended sediment. Despite deleterious effects of sediments on corals, few studies have examined the molecular response of corals with different morphological characteristics to sediment stress. To address this knowledge gap, this study assessed the transcriptomic responses of branching and massive corals in Florida and Hawai'i to varying levels of sediment exposure. Gene expression analysis revealed a molecular responsiveness to sediments across species and sites. Differential Gene Expression followed by Gene Ontology (GO) enrichment analysis identified that branching corals had the largest transcriptomic response to sediments, in developmental processes and metabolism, while significantly enriched GO terms were highly variable between massive corals, despite similar morphologies. Comparison of DEGs within orthogroups revealed that while all corals had DEGs in response to sediment, there was not a concerted gene set response by morphology or location. These findings illuminate the species specificity and genetic basis underlying coral susceptibility to sediments.
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Affiliation(s)
- Jill Ashey
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, United States
| | - Hailey McKelvie
- Department of Computer Science, Tufts University, Medford, Massachusetts, United States
| | - John Freeman
- Department of Computer Science, Tufts University, Medford, Massachusetts, United States
| | - Polina Shpilker
- Department of Computer Science, Tufts University, Medford, Massachusetts, United States
| | - Lauren H. Zane
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, United States
| | - Danielle M. Becker
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, United States
| | - Lenore Cowen
- Department of Computer Science, Tufts University, Medford, Massachusetts, United States
| | - Robert H. Richmond
- Kewalo Marine Lab, University of Hawaii at Manoa, Honolulu, Hawaii, United States
| | - Valerie J. Paul
- Smithsonian Marine Station, Smithsonian, Fort Pierce, Florida, United States
| | | | - Hollie M. Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, United States
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D'Amico-Willman KM, Niederhuth CE, Sovic MG, Anderson ES, Gradziel TM, Fresnedo-Ramírez J. Hypermethylation and small RNA expression are associated with increased age in almond (Prunus dulcis [Mill.] D.A. Webb) accessions. Plant Sci 2024; 338:111918. [PMID: 37956826 DOI: 10.1016/j.plantsci.2023.111918] [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: 07/24/2023] [Revised: 10/20/2023] [Accepted: 11/04/2023] [Indexed: 11/15/2023]
Abstract
The focus of this study is to profile changes in DNA methylation and small RNA expression occurring with increased age in almond breeding germplasm to identify possible biomarkers of age that can be used to assess the potential of individuals to develop aging-related disorders. To profile DNA methylation in almond germplasm, 70 methylomes were generated from almond individuals representing three age cohorts (11, 7, and 2 years old) using an enzymatic methyl-seq approach followed by analysis to call differentially methylated regions (DMRs) within these cohorts. Small RNA (sRNA) expression was profiled in three breeding selections, each from two age cohorts (1 and 6 years old), using sRNA-Seq followed by differential expression analysis. Weighted chromosome-level methylation analysis reveals hypermethylation in 11-year-old almond breeding selections when compared to 2-year-old selections in the CG and CHH contexts. Seventeen consensus DMRs were identified in all age contrasts. sRNA expression differed significantly between the two age cohorts tested, with significantly decreased expression in sRNAs in the 6-year-old selections compared to the 1-year-old. Almond shows a pattern of hypermethylation and decreased sRNA expression with increased age. Identified DMRs and differentially expressed sRNAs could function as putative biomarkers of age following validation in additional age groups.
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Affiliation(s)
| | - Chad E Niederhuth
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Michael G Sovic
- Center for Applied Plant Sciences, The Ohio State University, Columbus, OH 43210, USA
| | - Elizabeth S Anderson
- Department of Horticulture and Crop Science, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH 44691, USA
| | - Thomas M Gradziel
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Jonathan Fresnedo-Ramírez
- Translational Plant Sciences, The Ohio State University, Columbus, OH 43210, USA; Center for Applied Plant Sciences, The Ohio State University, Columbus, OH 43210, USA; Department of Horticulture and Crop Science, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH 44691, USA.
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Lopes KDP, Yu L, Shen X, Qiu Y, Tasaki S, Iatrou A, Beeri MS, Seyfried NT, Menon V, Wang Y, Schneider JA, Cantor H, Bennett DA. Associations of cortical SPP1 and ITGAX with cognition and common neuropathologies in older adults. Alzheimers Dement 2024; 20:525-537. [PMID: 37727065 PMCID: PMC10841499 DOI: 10.1002/alz.13474] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 03/20/2023] [Revised: 06/15/2023] [Accepted: 08/21/2023] [Indexed: 09/21/2023]
Abstract
INTRODUCTION The secreted phosphoprotein 1 (SPP1) gene expressed by CD11c+ cells is known to be associated with microglia activation and neuroinflammatory diseases. As most studies rely on mouse models, we investigated these genes and proteins in the cortical brain tissue of older adults and their role in Alzheimer's disease (AD) and related disorders. METHODS We leveraged protein measurements, single-nuclei, and RNASeq data from the Religious Orders Study and Rush Memory and Aging Project (ROSMAP) of over 1200 samples for association analysis. RESULTS Expression of SPP1 and its encoded protein osteopontin were associated with faster cognitive decline and greater odds of common neuropathologies. At single-cell resolution, integrin subunit alpha X (ITGAX) was highly expressed in microglia, where specific subpopulations were associated with AD and cerebral amyloid angiopathy. DISCUSSION The study provides evidence of SPP1 and ITGAX association with cognitive decline and common neuropathologies identifying a microglial subset associated with disease.
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Affiliation(s)
- Katia de Paiva Lopes
- Rush Alzheimer's Disease CenterRush University Medical CenterChicagoIllinoisUSA
- Department of Neurological SciencesRush University Medical CenterChicagoIllinoisUSA
| | - Lei Yu
- Rush Alzheimer's Disease CenterRush University Medical CenterChicagoIllinoisUSA
- Department of Neurological SciencesRush University Medical CenterChicagoIllinoisUSA
| | - Xianli Shen
- Department of Cancer Immunology and VirologyDana‐Farber Cancer InstituteBostonMassachusettsUSA
- Department of ImmunologyHarvard Medical SchoolBostonMassachusettsUSA
| | - Yiguo Qiu
- Department of Cancer Immunology and VirologyDana‐Farber Cancer InstituteBostonMassachusettsUSA
- Department of ImmunologyHarvard Medical SchoolBostonMassachusettsUSA
- Chongqing International Institute for ImmunologyChongqingChina
| | - Shinya Tasaki
- Rush Alzheimer's Disease CenterRush University Medical CenterChicagoIllinoisUSA
- Department of Neurological SciencesRush University Medical CenterChicagoIllinoisUSA
| | - Artemis Iatrou
- Rush Alzheimer's Disease CenterRush University Medical CenterChicagoIllinoisUSA
- Department of Neurological SciencesRush University Medical CenterChicagoIllinoisUSA
- Department of Psychiatry, McLean HospitalHarvard Medical SchoolBelmontMassachusettsUSA
| | - Michal Schnaider Beeri
- Joseph Sagol Neuroscience Center, Sheba Medical CenterRamat GanIsrael
- Department of PsychiatryIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- The Herbert and Jackeline Krieger Klein Alzheimer's Research CenterRutgers Biomedical and Health Sciences, Rutgers UniversityNew JerseyUSA
| | - Nicholas T. Seyfried
- Goizueta Alzheimer's Disease Research Center, Department of Neurology and Department of BiochemistryEmory University School of MedicineAtlantaGeorgiaUSA
| | - Vilas Menon
- Center for Translational and Computational NeuroimmunologyDepartment of Neurology & Taub Institute for Research on Alzheimer's disease and the Aging BrainColumbia University Irving Medical CenterNew YorkNew YorkUSA
| | - Yanling Wang
- Rush Alzheimer's Disease CenterRush University Medical CenterChicagoIllinoisUSA
- Department of Neurological SciencesRush University Medical CenterChicagoIllinoisUSA
| | - Julie A. Schneider
- Rush Alzheimer's Disease CenterRush University Medical CenterChicagoIllinoisUSA
- Department of Neurological SciencesRush University Medical CenterChicagoIllinoisUSA
- Department of PathologyRush University Medical CenterChicagoIllinoisUSA
| | - Harvey Cantor
- Department of Cancer Immunology and VirologyDana‐Farber Cancer InstituteBostonMassachusettsUSA
- Department of ImmunologyHarvard Medical SchoolBostonMassachusettsUSA
| | - David A. Bennett
- Rush Alzheimer's Disease CenterRush University Medical CenterChicagoIllinoisUSA
- Department of Neurological SciencesRush University Medical CenterChicagoIllinoisUSA
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Karami K, Zerehdaran S, Javadmanesh A. Differential Expression of RNAseq Imprinted Genes from Bovine Females Before and After Puberty. Biochem Genet 2023; 61:2633-2649. [PMID: 37225913 DOI: 10.1007/s10528-023-10395-9] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 05/02/2023] [Indexed: 05/26/2023]
Abstract
The productivity of beef cows depends on early reproduction traits such as puberty and has an economic impact on the efficiency of production system. Imprinted genes modulate many important endocrine processes such as growth, the onset of puberty and maternal reproductive and behavior. The role of imprinted genes in puberty is a challenging subject since they show the reciprocal role of maternal and paternal genomes in progeny. Although, there are evidences of the involvement of imprint genes in puberty in human, the role of this type of genes in the onset of puberty in cattle has not been studied yet. Here we examined the expression of 27 imprinted genes in pre and post puberty in a bovine model to find differentially expressed imprinted genes in maternal-paternal purebreds and reciprocal crosses across eight tissues and discussed the task of these genes in this crucial process of development and in onset of puberty. DLK1 and MKRN3 that previously described as cause of the central precocious puberty (CPP) in human were differentially expressed in this study. Functional annotation analysis of differentially imprinted genes in different tissues showed significant biological processes of cellular response to growth factor stimulus, response to growth factor, response to parathyroid hormone, developmental growth and the importance of alternative splicing. The results of this study have implications in understanding the role of imprinted genes in the onset of puberty in cattle.
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Affiliation(s)
- Keyvan Karami
- Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Saeed Zerehdaran
- Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran.
| | - Ali Javadmanesh
- Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran.
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Asthana A, Chaimov D, Tamburrini R, Gazia C, Gallego A, Lozano T, Heo JH, Byers LN, Tomei A, Fraker CA, Walker SJ, Lee SJ, Opara EC, Orlando G. Decellularized human pancreatic extracellular matrix-based physiomimetic microenvironment for human islet culture. Acta Biomater 2023; 171:261-272. [PMID: 37742726 PMCID: PMC10615794 DOI: 10.1016/j.actbio.2023.09.034] [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: 02/15/2023] [Revised: 09/15/2023] [Accepted: 09/19/2023] [Indexed: 09/26/2023]
Abstract
A strategy that seeks to combine the biophysical properties of inert encapsulation materials like alginate with the biochemical niche provided by pancreatic extracellular matrix (ECM)-derived biomaterials, could provide a physiomimetic pancreatic microenvironment for maintaining long-term islet viability and function in culture. Herein, we have demonstrated that incorporating human pancreatic decellularized ECM within alginate microcapsules results in a significant increase in Glucose Stimulation Index (GSI) and total insulin secreted by encapsulated human islets, compared to free islets and islets encapsulated in only alginate. ECM supplementation also resulted in long-term (58 days) maintenance of GSI levels, similar to that observed in free islets at the first time point (day 5). At early time points in culture, ECM promoted gene expression changes through ECM- and cell adhesion-mediated pathways, while it demonstrated a mitochondria-protective effect in the long-term. STATEMENT OF SIGNIFICANCE: The islet isolation process can damage the islet extracellular matrix, resulting in loss of viability and function. We have recently developed a detergent-free, DI-water based method for decellularization of human pancreas to produce a potent solubilized ECM. This ECM was added to alginate for microencapsulation of human islets, which resulted in significantly higher stimulation index and total insulin production, compared to only alginate capsules and free islets, over long-term culture. Using ECM to preserve islet health and function can improve transplantation outcomes, as well as provide novel materials and platforms for studying islet biology in microfluidic, organ-on-a-chip, bioreactor and 3D bioprinted systems.
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Affiliation(s)
- Amish Asthana
- Department of Surgery, Wake Forest Baptist Medical Center, Medical Center Boulevard, Winston Salem, USA; Wake Forest Institute for Regenerative Medicine, Winston Salem, USA; Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, USA.
| | - Deborah Chaimov
- Department of Surgery, Wake Forest Baptist Medical Center, Medical Center Boulevard, Winston Salem, USA; Wake Forest Institute for Regenerative Medicine, Winston Salem, USA; Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, USA
| | - Riccardo Tamburrini
- Department of Surgery, Wake Forest Baptist Medical Center, Medical Center Boulevard, Winston Salem, USA; Wake Forest Institute for Regenerative Medicine, Winston Salem, USA; Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, USA
| | - Carlo Gazia
- Department of Surgery, Wake Forest Baptist Medical Center, Medical Center Boulevard, Winston Salem, USA; Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, USA; Department of Surgery, Tor Vergata University of Rome, Italy
| | | | | | - Jun-Ho Heo
- Wake Forest Institute for Regenerative Medicine, Winston Salem, USA; Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Lori N Byers
- Department of Surgery, Wake Forest Baptist Medical Center, Medical Center Boulevard, Winston Salem, USA; Wake Forest Institute for Regenerative Medicine, Winston Salem, USA; Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, USA
| | - Alice Tomei
- Diabetes Research Institute, University of Miami, Miami, USA
| | | | - Stephen J Walker
- Wake Forest Institute for Regenerative Medicine, Winston Salem, USA; Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, USA
| | - Sang Jin Lee
- Wake Forest Institute for Regenerative Medicine, Winston Salem, USA; Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, USA
| | - Emmanuel C Opara
- Wake Forest Institute for Regenerative Medicine, Winston Salem, USA; Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, USA
| | - Giuseppe Orlando
- Department of Surgery, Wake Forest Baptist Medical Center, Medical Center Boulevard, Winston Salem, USA; Wake Forest Institute for Regenerative Medicine, Winston Salem, USA; Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, USA.
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Pechanec MY, Mienaltowski MJ. Decoding the transcriptomic expression and genomic methylation patterns in the tendon proper and its peritenon region in the aging horse. BMC Res Notes 2023; 16:267. [PMID: 37821884 PMCID: PMC10566085 DOI: 10.1186/s13104-023-06562-1] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 10/10/2023] [Indexed: 10/13/2023] Open
Abstract
OBJECTIVES Equine tendinopathies are challenging because of the poor healing capacity of tendons commonly resulting in high re-injury rates. Within the tendon, different regions - tendon proper (TP) and peritenon (PERI) - contribute to the tendon matrix in differing capacities during injury and aging. Aged tendons have decreased repair potential; the underlying transcriptional and epigenetic changes that occur in the TP and PERI regions are not well understood. The objective of this study was to assess TP and PERI regional differences in adolescent, midlife, and geriatric horses using RNA sequencing and DNA methylation techniques. RESULTS Differences existed between TP and PERI regions of equine superficial digital flexor tendons by age as evidenced by RNASeq and DNA methylation. Cluster analysis indicated that regional distinctions existed regardless of age. Genes such as DCN, COMP, FN1, and LOX maintained elevated TP expression while genes such as GSN and AHNAK were abundant in PERI. Increased gene activity was present in adolescent and geriatric populations but decreased during midlife. Regional differences in DNA methylation were also noted. Notably, when evaluating all ages of TP against PERI, five genes (HAND2, CHD9, RASL11B, ADGRD1, and COL14A1) had regions of differential methylation as well as differential gene expression.
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Affiliation(s)
- Monica Y Pechanec
- Department of Animal Science, University of California Davis, 2251 Meyer Hall, One Shields Ave, Davis, CA, 95616, USA
| | - Michael J Mienaltowski
- Department of Animal Science, University of California Davis, 2251 Meyer Hall, One Shields Ave, Davis, CA, 95616, USA.
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Wang Y, Popovic Z, Charkoftaki G, Garcia-Milian R, Lam TT, Thompson DC, Chen Y, Vasiliou V. Multi-omics profiling reveals cellular pathways and functions regulated by ALDH1B1 in colon cancer cells. Chem Biol Interact 2023; 384:110714. [PMID: 37716420 PMCID: PMC10807983 DOI: 10.1016/j.cbi.2023.110714] [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: 05/08/2023] [Revised: 07/31/2023] [Accepted: 09/13/2023] [Indexed: 09/18/2023]
Abstract
Colon cancer is the third leading cause of cancer death globally. Although early screenings and advances in treatments have reduced mortality since 1970, identification of novel targets for therapeutic intervention is needed to address tumor heterogeneity and recurrence. Previous work identified aldehyde dehydrogenase 1B1 (ALDH1B1) as a critical factor in colon tumorigenesis. To investigate further, we utilized a human colon adenocarcinoma cell line (SW480) in which the ALDH1B1 protein expression has been knocked down by 80% via shRNA. Through multi-omics (transcriptomics, proteomics, and untargeted metabolomics) analysis, we identified the impact of ALDH1B1 knocking down (KD) on molecular signatures in colon cancer cells. Suppression of ALDH1B1 expression resulted in 357 differentially expressed genes (DEGs), 191 differentially expressed proteins (DEPs) and 891 differentially altered metabolites (DAMs). Functional annotation and enrichment analyses revealed that: (1) DEGs were enriched in integrin-linked kinase (ILK) signaling and growth and development pathways; (2) DEPs were mainly involved in apoptosis signaling and cellular stress response pathways; and (3) DAMs were associated with biosynthesis, intercellular and second messenger signaling. Collectively, the present study provides new molecular information associated with the cellular functions of ALDH1B1, which helps to direct future investigation of colon cancer.
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Affiliation(s)
- Yewei Wang
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT, USA
| | - Zeljka Popovic
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT, USA
| | - Georgia Charkoftaki
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT, USA
| | - Rolando Garcia-Milian
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT, USA; Bioinformatics Support Program, Cushing/Whitney Medical Library, Yale University, New Haven, CT, USA
| | - TuKiet T Lam
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA; Keck MS & Proteomics Resource, Yale School of Medicine, New Haven, CT, USA
| | - David C Thompson
- Department of Clinical Pharmacy, University of Colorado Skaggs School of Pharmacy & Pharmaceutical Sciences, Aurora, CO, USA
| | - Ying Chen
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT, USA.
| | - Vasilis Vasiliou
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT, USA.
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Choi DY, Kim Y. Prostaglandin E 2 mediates chorion formation of the Asian tiger mosquito, Aedes albopictus, at late oogenesis. Insect Mol Biol 2023; 32:484-509. [PMID: 37158315 DOI: 10.1111/imb.12846] [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: 02/06/2023] [Accepted: 04/25/2023] [Indexed: 05/10/2023]
Abstract
Chorion-i.e., the eggshell-is formed during the late stage of oogenesis by follicular epithelium in the ovary. Although the endocrine signal(s) driving choriogenesis remain unclear in mosquitoes, this process in other insects has been suspected to involve the mediation of prostaglandins (PGs). This study tested the role of PG in the choriogenesis of the Asian tiger mosquito, Aedes albopictus, and its influence on controlling the expressions of genes associated with chorion formation by a transcriptome analysis. An immunofluorescence assay showed that PGE2 is localised in follicular epithelium. With the treatment of aspirin, an inhibitor of PG biosynthesis, at mid oogenesis, the PGE2 signal disappeared in the follicular epithelium led to significantly inhibited chorion formation along with a malformed eggshell. Ovary transcriptomes were assessed by RNASeq at the mid and late ovarian developmental stages. Differentially expressed genes (DEGs) exhibiting more than twofold changes in expression levels included 297 genes at mid stage and 500 genes at late stage. These DEGs at these two developmental stages commonly included genes associated with egg and chorion proteins of Ae. albopictus. Most chorion-associated genes were clustered in the 168 Mb region on a chromosome and exhibited significantly induced expressions at both ovarian developmental stages. The inhibition of PG biosynthesis significantly suppressed the expression of the chorion-associated genes while the addition of PGE2 rescued the gene expressions and led to recovery of choriogenesis. These results suggest that PGE2 mediates the choriogenesis of Ae. albopictus.
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Affiliation(s)
- Du-Yeol Choi
- Department of Plant Medicals, College of Life Sciences, Andong National University, Andong, South Korea
| | - Yonggyun Kim
- Department of Plant Medicals, College of Life Sciences, Andong National University, Andong, South Korea
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Chavan S, Schnabel E, Saski C, Frugoli J. Fixation and Laser Capture Microdissection of Plant Tissue for RNA Extraction and RNASeq Library Preparation. Curr Protoc 2023; 3:e844. [PMID: 37486164 DOI: 10.1002/cpz1.844] [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: 07/25/2023]
Abstract
To study the transcriptome of individual plant cells at specific points in time, we developed protocols for fixation, embedding, and sectioning of plant tissue followed by laser capture microdissection (LCM) and processing for RNA recovery. LCM allows the isolation of individual cell types from heterogeneous tissue sections and is particularly suited to plant processing because it does not require the breakdown of cell walls. This approach allows accurate separation of a small volume of cells that can be used to study gene expression profiles in different tissues or cell layers. The technique requires neither separation of cells by enzymatic digestion of any kind nor cell-specific reporter genes, and it allows storage of fixed and embedded tissue for months before capture. The methods for fixation, embedding, sectioning, and capturing of plant cells that we describe yield high-quality RNA suitable for making libraries for RNASeq. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Tissue Preparation for Laser Capture Microdissection Basic Protocol 2: Tissue Sectioning Basic Protocol 3: Laser Capture Microdissection of Embedded Tissue Basic Protocol 4: RNA Extraction from Laser Capture Microdissection Samples.
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Affiliation(s)
- Suchitra Chavan
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina
| | - Elise Schnabel
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina
| | - Christopher Saski
- Department of Plant and Environmental Sciences, Clemson University, Clemson, South Carolina
| | - Julia Frugoli
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina
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12
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Lin G, Huang Z, He B, Jiang K, Su T, Zhao F. Evolutionary Adaptation of Genes Involved in Galactose Derivatives Metabolism in Oil-Tea Specialized Andrena Species. Genes (Basel) 2023; 14:genes14051117. [PMID: 37239477 DOI: 10.3390/genes14051117] [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: 05/05/2023] [Revised: 05/17/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023] Open
Abstract
Oil-tea (Camellia oleifera) is a woody oil crop whose nectar includes galactose derivatives that are toxic to honey bees. Interestingly, some mining bees of the genus Andrena can entirely live on the nectar (and pollen) of oil-tea and are able to metabolize these galactose derivatives. We present the first next-generation genomes for five and one Andrena species that are, respectively, specialized and non-specialized oil-tea pollinators and, combining these with the published genomes of six other Andrena species which did not visit oil-tea, we performed molecular evolution analyses on the genes involved in the metabolizing of galactose derivatives. The six genes (NAGA, NAGA-like, galM, galK, galT, and galE) involved in galactose derivatives metabolism were identified in the five oil-tea specialized species, but only five (with the exception of NAGA-like) were discovered in the other Andrena species. Molecular evolution analyses revealed that NAGA-like, galK, and galT in oil-tea specialized species appeared under positive selection. RNASeq analyses showed that NAGA-like, galK, and galT were significantly up-regulated in the specialized pollinator Andrena camellia compared to the non-specialized pollinator Andrena chekiangensis. Our study demonstrated that the genes NAGA-like, galK, and galT have played an important role in the evolutionary adaptation of the oil-tea specialized Andrena species.
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Affiliation(s)
- Gonghua Lin
- School of Life Sciences, Jinggangshan University, Ji'an 343009, China
| | - Zuhao Huang
- School of Life Sciences, Jinggangshan University, Ji'an 343009, China
| | - Bo He
- School of Life Sciences, Jinggangshan University, Ji'an 343009, China
| | - Kai Jiang
- School of Life Sciences, Jinggangshan University, Ji'an 343009, China
| | - Tianjuan Su
- School of Life Sciences, Jinggangshan University, Ji'an 343009, China
| | - Fang Zhao
- School of Life Sciences, Jinggangshan University, Ji'an 343009, China
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13
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Villano C, Demurtas OC, Esposito S, Granell A, Rambla JL, Piombino P, Frusciante L, Carputo D, Diretto G, Aversano R. Integrative analysis of metabolome and transcriptome profiles to highlight aroma determinants in Aglianico and Falanghina grape berries. BMC Plant Biol 2023; 23:241. [PMID: 37149574 PMCID: PMC10163809 DOI: 10.1186/s12870-023-04251-6] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 04/26/2023] [Indexed: 05/08/2023]
Abstract
BACKGROUND The biochemical makeup of grape berries at harvest is essential for wine quality and depends on a fine transcriptional regulation occurring during berry development. In this study, we conducted a comprehensive survey of transcriptomic and metabolomic changes occurring in different berry tissues and developmental stages of the ancient grapes Aglianico and Falanghina to establish the patterns of the secondary metabolites contributing to their wine aroma and investigate the underlying transcriptional regulation. RESULTS Over two hundred genes related to aroma were found, of which 107 were differentially expressed in Aglianico and 99 in Falanghina. Similarly, 68 volatiles and 34 precursors were profiled in the same samples. Our results showed a large extent of transcriptomic and metabolomic changes at the level of isoprenoids (terpenes, norisoprenoids), green leaf volatiles (GLVs), and amino acid pathways, although the terpenoid metabolism was the most distinctive for Aglianico, and GLVs for Falanghina. Co-expression analysis that integrated metabolome and transcriptome data pinpointed 25 hub genes as points of biological interest in defining the metabolic patterns observed. Among them, three hub genes encoding for terpenes synthases (VvTPS26, VvTPS54, VvTPS68) in Aglianico and one for a GDP-L-galactose phosphorylase (VvGFP) in Falanghina were selected as potential active player underlying the aroma typicity of the two grapes. CONCLUSION Our data improve the understanding of the regulation of aroma-related biosynthetic pathways of Aglianico and Falanghina and provide valuable metabolomic and transcriptomic resources for future studies in these varieties.
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Affiliation(s)
- Clizia Villano
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, Naples, 80055, Italy
| | - Olivia Costantina Demurtas
- Biotechnology Laboratory, Casaccia Research Centre, Italian National Agency for New Technologies, Energy, and Sustainable Development (ENEA), Rome, 00123, Italy
| | - Salvatore Esposito
- CREA Research Centre for Cereal and Industrial Crops (CREA-CI), S.S. 673, km 25, Foggia, 200-71122, Italy
| | - Antonio Granell
- IBMCP Institute for Plant Molecular and Cell Biology (CSIC-UPV), Carrer de l'Enginyer Fausto Elio, s/n, Valencia, 46022, Spain
| | - José Luis Rambla
- IBMCP Institute for Plant Molecular and Cell Biology (CSIC-UPV), Carrer de l'Enginyer Fausto Elio, s/n, Valencia, 46022, Spain
| | - Paola Piombino
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, Naples, 80055, Italy
| | - Luigi Frusciante
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, Naples, 80055, Italy
| | - Domenico Carputo
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, Naples, 80055, Italy
| | - Gianfranco Diretto
- Biotechnology Laboratory, Casaccia Research Centre, Italian National Agency for New Technologies, Energy, and Sustainable Development (ENEA), Rome, 00123, Italy.
| | - Riccardo Aversano
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, Naples, 80055, Italy.
- Department of Biology, Biochemistry and Environmental Sciences, Universitat Jaume I, Castellón de la Plana, 12071, Spain.
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Hesson AM, Langen ES, Plazyo O, Gudjonsson JE, Ganesh SK. Placental transcriptome analysis of hypertensive pregnancies identifies distinct gene expression profiles of preeclampsia superimposed on chronic hypertension. BMC Med Genomics 2023; 16:91. [PMID: 37131171 PMCID: PMC10152005 DOI: 10.1186/s12920-023-01522-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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 04/20/2023] [Indexed: 05/04/2023] Open
Abstract
BACKGROUND The pathogenesis of preeclampsia superimposed on chronic hypertension (SI) is poorly understood relative to preeclampsia (PreE) occurring in pregnant people without chronic hypertension. Placental transcriptomes in pregnancies complicated by PreE and SI have not been previously compared. METHODS We identified pregnant people in the University of Michigan Biorepository for Understanding Maternal and Pediatric Health with hypertensive disorders affecting singleton, euploid gestations (N = 36) along with non-hypertensive control subjects (N = 12). Subjects were grouped as: (1) normotensive (N = 12), (2) chronic hypertensive (N = 13), (3) preterm PreE with severe features (N = 5), (4) term PreE with severe features (N = 11), (5) preterm SI (N = 3), or (6) term SI (N = 4). Bulk RNA sequencing of paraffin-embedded placental tissue was performed. The primary analysis assessed differential gene expression relative to normotensive and chronic hypertensive placentas, where Wald adjusted P values < 0.05 were considered significant. Unsupervised clustering analyses and correlation analyses were performed between conditions of interest, and a gene ontology was constructed. RESULTS Comparing samples from pregnant people with hypertensive diseases to non-hypertensive controls, there were 2290 differentially expressed genes. The log2-fold changes in genes differentially expressed in chronic hypertension correlated better with term (R = 0.59) and preterm (R = 0.63) PreE with severe features than with term (R = 0.21) and preterm (R = 0.22) SI. A relatively poor correlation was observed between preterm SI and preterm PreE with severe features (0.20) as well as term SI and term PreE with severe features (0.31). The majority of significant genes were downregulated in term and preterm SI versus normotensive controls (92.1%, N = 128). Conversely, most term and preterm PreE with severe features genes were upregulated compared to the normotensive group (91.8%, N = 97). Many of the upregulated genes in PreE with the lowest adjusted P values are known markers of abnormal placentation (e.g., PAAPA, KISS1, CLIC3), while the downregulated genes with the greatest adjusted P values in SI have fewer known pregnancy-specific functions. CONCLUSIONS We identified unique placental transcriptional profiles in clinically relevant subgroups of individuals with hypertension in pregnancy. Preeclampsia superimposed on chronic hypertension was molecularly distinct from preeclampsia in individuals without chronic hypertension, and chronic hypertension without preeclampsia, suggesting that preeclampsia superimposed on hypertension may represent a distinct entity.
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Affiliation(s)
- Ashley M Hesson
- Division of Maternal Fetal Medicine, Department of Obstetrics and Gynecology, University of Michigan, 1500 East Medical Center Dr., Ann Arbor, MI, 48109, USA.
| | - Elizabeth S Langen
- Division of Maternal Fetal Medicine, Department of Obstetrics and Gynecology, University of Michigan, 1500 East Medical Center Dr., Ann Arbor, MI, 48109, USA
| | - Olesya Plazyo
- Departments of Dermatology and Immunology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Johann E Gudjonsson
- Departments of Dermatology and Immunology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Santhi K Ganesh
- Division of Cardiovascular Medicine, Department of Internal Medicine, Department of Human Genetics, University of Michigan, MSRB III / Room 7220A, 1150 West Medical Center Dr., Ann Arbor, MI, 48109, USA.
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15
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Hernandez VG, Lechtenberg KJ, Peterson TC, Zhu L, Lucas TA, Bradshaw KP, Owah JO, Dorsey AI, Gentles AJ, Buckwalter MS. Translatome analysis reveals microglia and astrocytes to be distinct regulators of inflammation in the hyperacute and acute phases after stroke. Glia 2023. [PMID: 37067534 DOI: 10.1002/glia.24377] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 03/08/2023] [Accepted: 04/04/2023] [Indexed: 04/18/2023]
Abstract
Neuroinflammation is a hallmark of ischemic stroke, which is a leading cause of death and long-term disability. Understanding the exact cellular signaling pathways that initiate and propagate neuroinflammation after stroke will be critical for developing immunomodulatory stroke therapies. In particular, the precise mechanisms of inflammatory signaling in the clinically relevant hyperacute period, hours after stroke, have not been elucidated. We used the RiboTag technique to obtain microglia and astrocyte-derived mRNA transcripts in a hyperacute (4 h) and acute (3 days) period after stroke, as these two cell types are key modulators of acute neuroinflammation. Microglia initiated a rapid response to stroke at 4 h by adopting an inflammatory profile associated with the recruitment of immune cells. The hyperacute astrocyte profile was marked by stress response genes and transcription factors, such as Fos and Jun, involved in pro-inflammatory pathways such as TNF-α. By 3 days, microglia shift to a proliferative state and astrocytes strengthen their inflammatory response. The astrocyte pro-inflammatory response at 3 days is partially driven by the upregulation of the transcription factors C/EBPβ, Spi1, and Rel, which comprise 25% of upregulated transcription factor-target interactions. Surprisingly, few sex differences across all groups were observed. Expression and log2 fold data for all sequenced genes are available on a user-friendly website for researchers to examine gene changes and generate hypotheses for stroke targets. Taken together, our data comprehensively describe the microglia and astrocyte-specific translatome response in the hyperacute and acute period after stroke and identify pathways critical for initiating neuroinflammation.
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Affiliation(s)
- Victoria G Hernandez
- Department of Neurology and Neurological Sciences, Stanford School of Medicine, Palo Alto, California, USA
| | - Kendra J Lechtenberg
- Department of Neurology and Neurological Sciences, Stanford School of Medicine, Palo Alto, California, USA
| | - Todd C Peterson
- Department of Neurology and Neurological Sciences, Stanford School of Medicine, Palo Alto, California, USA
| | - Li Zhu
- Department of Neurology and Neurological Sciences, Stanford School of Medicine, Palo Alto, California, USA
| | - Tawaun A Lucas
- Department of Neurology and Neurological Sciences, Stanford School of Medicine, Palo Alto, California, USA
| | - Karen P Bradshaw
- Department of Neurology and Neurological Sciences, Stanford School of Medicine, Palo Alto, California, USA
| | - Justice O Owah
- Department of Neurology and Neurological Sciences, Stanford School of Medicine, Palo Alto, California, USA
| | - Alanna I Dorsey
- Department of Neurology and Neurological Sciences, Stanford School of Medicine, Palo Alto, California, USA
| | - Andrew J Gentles
- Department of Pathology, Stanford University, Stanford, California, USA
- Department of Medicine - Biomedical Informatics Research, Stanford University, Stanford, California, USA
| | - Marion S Buckwalter
- Department of Neurology and Neurological Sciences, Stanford School of Medicine, Palo Alto, California, USA
- Department of Neurosurgery, Stanford School of Medicine, Palo Alto, California, USA
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16
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Nichols JH, Williams EP, Parvathareddy J, Cao X, Kong Y, Fitzpatrick E, Webby RJ, Jonsson CB. Upper Respiratory Infection Drives Clinical Signs and Inflammatory Responses Following Heterologous Challenge of SARS-CoV-2 Variants of Concern in K18 Mice. Viruses 2023; 15:v15040946. [PMID: 37112926 PMCID: PMC10144791 DOI: 10.3390/v15040946] [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: 03/09/2023] [Revised: 03/30/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
The evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in the emergence of several variants of concern (VOC) with increased immune evasion and transmissibility. This has motivated studies to assess protection conferred by earlier strains following infection or vaccination to each new VOC. We hypothesized that while NAbs play a major role in protection against infection and disease, a heterologous reinfection or challenge may gain a foothold in the upper respiratory tract (URT) and result in a self-limited viral infection accompanied by an inflammatory response. To test this hypothesis, we infected K18-hACE2 mice with SARS-CoV-2 USA-WA1/2020 (WA1) and, after 24 days, challenged with WA1, Alpha, or Delta. While NAb titers against each virus were similar across all cohorts prior to challenge, the mice challenged with Alpha and Delta showed weight loss and upregulation of proinflammatory cytokines in the URT and lower RT (LRT). Mice challenged with WA1 showed complete protection. We noted increased levels of viral RNA transcripts only in the URT of mice challenged with Alpha and Delta. In conclusion, our results suggested self-limiting breakthrough infections of Alpha or Delta in the URT, which correlated with clinical signs and a significant inflammatory response in mice.
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Affiliation(s)
- Jacob H Nichols
- Department of Microbiology, Immunology and Biochemistry, College of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Evan P Williams
- Department of Microbiology, Immunology and Biochemistry, College of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Jyothi Parvathareddy
- Regional Biocontainment Laboratory, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Xueyuan Cao
- Department of Health Promotion and Disease Prevention, College of Nursing, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Ying Kong
- Department of Microbiology, Immunology and Biochemistry, College of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Elizabeth Fitzpatrick
- Department of Microbiology, Immunology and Biochemistry, College of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Richard J Webby
- St. Jude Children's Research Hospital, Memphis, TN 38163, USA
| | - Colleen B Jonsson
- Department of Microbiology, Immunology and Biochemistry, College of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA
- Regional Biocontainment Laboratory, University of Tennessee Health Science Center, Memphis, TN 38163, USA
- Institute for the Study of Host-Pathogen Systems, University of Tennessee Health Science Center, Memphis, TN 38163, USA
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17
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Jin S, Campbell EJ, Ip CK, Layfield S, Bathgate RAD, Herzog H, Lawrence AJ. Molecular Profiling of VGluT1 AND VGluT2 Ventral Subiculum to Nucleus Accumbens Shell Projections. Neurochem Res 2023:10.1007/s11064-023-03921-z. [PMID: 37017888 DOI: 10.1007/s11064-023-03921-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] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 03/14/2023] [Accepted: 03/24/2023] [Indexed: 04/06/2023]
Abstract
The nucleus accumbens shell is a critical node in reward circuitry, encoding environments associated with reward. Long-range inputs from the ventral hippocampus (ventral subiculum) to the nucleus accumbens shell have been identified, yet their precise molecular phenotype remains to be determined. Here we used retrograde tracing to identify the ventral subiculum as the brain region with the densest glutamatergic (VGluT1-Slc17a7) input to the shell. We then used circuit-directed translating ribosome affinity purification to examine the molecular characteristics of distinct glutamatergic (VGluT1, VGluT2-Slc17a6) ventral subiculum to nucleus accumbens shell projections. We immunoprecipitated translating ribosomes from this population of projection neurons and analysed molecular connectomic information using RNA sequencing. We found differential gene enrichment across both glutamatergic projection neuron subtypes. In VGluT1 projections, we found enrichment of Pfkl, a gene involved in glucose metabolism. In VGluT2 projections, we found a depletion of Sparcl1 and Dlg1, genes known to play a role in depression- and addiction-related behaviours. These findings highlight potential glutamatergic neuronal-projection-specific differences in ventral subiculum to nucleus accumbens shell projections. Together these data advance our understanding of the phenotype of a defined brain circuit.
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Affiliation(s)
- Shubo Jin
- The Florey Institute of Neuroscience and Mental Health, Melbourne Brain Centre, The University of Melbourne, Parkville, Melbourne, VIC, 3052, Australia
- Florey Department of Neuroscience and Mental Health, The University of Melbourne, Parkville, Melbourne, VIC, 3010, Australia
| | - Erin J Campbell
- The Florey Institute of Neuroscience and Mental Health, Melbourne Brain Centre, The University of Melbourne, Parkville, Melbourne, VIC, 3052, Australia.
- Florey Department of Neuroscience and Mental Health, The University of Melbourne, Parkville, Melbourne, VIC, 3010, Australia.
| | - Chi Kin Ip
- Neuroscience Division, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, 2010, Australia
- Faculty of Medicine, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Sharon Layfield
- The Florey Institute of Neuroscience and Mental Health, Melbourne Brain Centre, The University of Melbourne, Parkville, Melbourne, VIC, 3052, Australia
- Florey Department of Neuroscience and Mental Health, The University of Melbourne, Parkville, Melbourne, VIC, 3010, Australia
| | - Ross A D Bathgate
- The Florey Institute of Neuroscience and Mental Health, Melbourne Brain Centre, The University of Melbourne, Parkville, Melbourne, VIC, 3052, Australia
- Florey Department of Neuroscience and Mental Health, The University of Melbourne, Parkville, Melbourne, VIC, 3010, Australia
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, Melbourne, VIC, 3010, Australia
| | - Herbert Herzog
- Neuroscience Division, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, 2010, Australia
- Faculty of Medicine, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Andrew J Lawrence
- The Florey Institute of Neuroscience and Mental Health, Melbourne Brain Centre, The University of Melbourne, Parkville, Melbourne, VIC, 3052, Australia.
- Florey Department of Neuroscience and Mental Health, The University of Melbourne, Parkville, Melbourne, VIC, 3010, Australia.
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18
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Ning Z, Tan X, Yuan Y, Huang K, Pan Y, Tian L, Lu Y, Wang X, Qi R, Lu D, Yang Y, Guan Y, Mamatyusupu D, Xu S. Expression profiles of east-west highly differentiated genes in Uyghur genomes. Natl Sci Rev 2023; 10:nwad077. [PMID: 37138773 PMCID: PMC10150800 DOI: 10.1093/nsr/nwad077] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 02/28/2023] [Indexed: 05/05/2023] Open
Abstract
It remains unknown and debatable how European-Asian-differentiated alleles affect individual phenotypes. Here, we made the first effort to analyze the expression profiles of highly differentiated genes with eastern and western origins in 90 Uyghurs using whole-genome (30× to 60×) and transcriptome data. We screened 921 872 east-west highly differentiated genetic variants, of which ∼4.32% were expression quantitative trait loci (eQTLs), ∼0.12% were alternative splicing quantitative trait loci (sQTLs), and ∼0.12% showed allele-specific expression (ASE). The 8305 highly differentiated eQTLs of strong effects appear to have undergone natural selection, associated with immunity and metabolism. European-origin alleles tend to be more biasedly expressed; highly differentiated ASEs were enriched in diabetes-associated genes, likely affecting the diabetes susceptibility in the Uyghurs. We proposed an admixture-induced expression model to dissect the highly differentiated expression profiles. We provide new insights into the genetic basis of phenotypic differentiation between Western and Eastern populations, advancing our understanding of the impact of genetic admixture.
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Affiliation(s)
| | | | | | - Ke Huang
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China
| | - Yuwen Pan
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Lei Tian
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yan Lu
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xiaoji Wang
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ruicheng Qi
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Dongsheng Lu
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yajun Yang
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yaqun Guan
- Department of Biochemistry and Molecular Biology, Preclinical Medicine College, Xinjiang Medical University, Urumqi 830011, China
| | - Dolikun Mamatyusupu
- College of the Life Sciences and Technology, Xinjiang University, Urumqi 830046, China
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19
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Schwaner C, Farhat S, Barbosa M, Boutet I, Tanguy A, Pales Espinosa E, Allam B. Molecular Features Associated with Resilience to Ocean Acidification in the Northern Quahog, Mercenaria mercenaria. Mar Biotechnol (NY) 2023; 25:83-99. [PMID: 36417051 DOI: 10.1007/s10126-022-10183-3] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 11/08/2022] [Indexed: 06/16/2023]
Abstract
The increasing concentration of CO2 in the atmosphere and resulting flux into the oceans will further exacerbate acidification already threatening coastal marine ecosystems. The subsequent alterations in carbonate chemistry can have deleterious impacts on many economically and ecologically important species including the northern quahog (Mercenaria mercenaria). The accelerated pace of these changes requires an understanding of how or if species and populations will be able to acclimate or adapt to such swift environmental alterations. Thus far, studies have primarily focused on the physiological effects of ocean acidification (OA) on M. mercenaria, including reductions in growth and survival. However, the molecular mechanisms of resilience to OA in this species remains unclear. Clam gametes were fertilized under normal pCO2 and reared under acidified (pH ~ 7.5, pCO2 ~ 1200 ppm) or control (pH ~ 7.9, pCO2 ~ 600 ppm) conditions before sampled at 2 days (larvae), 32 days (postsets), 5 and 10 months (juveniles) and submitted to RNA and DNA sequencing to evaluate alterations in gene expression and genetic variations. Results showed significant shift in gene expression profiles among clams reared in acidified conditions as compared to their respective controls. At 10 months of exposure, significant shifts in allele frequency of single nucleotide polymorphisms (SNPs) were identified. Both approaches highlighted genes coding for proteins related to shell formation, bicarbonate transport, cytoskeleton, immunity/stress, and metabolism, illustrating the role these pathways play in resilience to OA.
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Affiliation(s)
- Caroline Schwaner
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, 11790, USA
| | - Sarah Farhat
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, 11790, USA
| | - Michelle Barbosa
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, 11790, USA
| | - Isabelle Boutet
- Station Biologique de Roscoff, CNRS/Sorbonne Université, Place Georges Teissier, 29680, Roscoff, France
| | - Arnaud Tanguy
- Station Biologique de Roscoff, CNRS/Sorbonne Université, Place Georges Teissier, 29680, Roscoff, France
| | | | - Bassem Allam
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, 11790, USA.
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20
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Konstorum A, Mohanty S, Zhao Y, Melillo A, Vander Wyk B, Nelson A, Tsang S, Blevins TP, Belshe R, Chawla DG, Rondina MT, Gill TM, Montgomery RR, Allore HG, Kleinstein SH, Shaw AC. Platelet response to influenza vaccination reflects effects of aging. Aging Cell 2023; 22:e13749. [PMID: 36656789 PMCID: PMC9924941 DOI: 10.1111/acel.13749] [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: 05/16/2022] [Revised: 10/21/2022] [Accepted: 11/15/2022] [Indexed: 01/20/2023] Open
Abstract
Platelets are uniquely positioned as mediators of not only hemostasis but also innate immunity. However, how age and geriatric conditions such as frailty influence platelet function during an immune response remains unclear. We assessed the platelet transcriptome at baseline and following influenza vaccination in Younger (age 21-35) and Older (age ≥65) adults (including community-dwelling individuals who were largely non-frail and skilled nursing facility (SNF)-resident adults who nearly all met criteria for frailty). Prior to vaccination, we observed an age-associated increase in the expression of platelet activation and mitochondrial RNAs and decrease in RNAs encoding proteins mediating translation. Age-associated differences were also identified in post-vaccination response trajectories over 28 days. Using tensor decomposition analysis, we found increasing RNA expression of genes in platelet activation pathways in young participants, but decreasing levels in (SNF)-resident adults. Translation RNA trajectories were inversely correlated with these activation pathways. Enhanced platelet activation was found in community-dwelling older adults at the protein level, compared to young individuals both prior to and post-vaccination; whereas SNF residents showed decreased platelet activation compared to community-dwelling older adults that could reflect the influence of decreased translation RNA expression. Our results reveal alterations in the platelet transcriptome and activation responses that may contribute to age-associated chronic inflammation and the increased incidence of thrombotic and pro-inflammatory diseases in older adults.
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Affiliation(s)
- Anna Konstorum
- Department of PathologyYale School of MedicineNew HavenConnecticutUSA
| | - Subhasis Mohanty
- Department of Internal Medicine, Section of Infectious DiseasesYale School of MedicineNew HavenConnecticutUSA
| | - Yujiao Zhao
- Section of Rheumatology, Department of Internal MedicineYale School of MedicineNew HavenConnecticutUSA
| | - Anthony Melillo
- Department of PathologyYale School of MedicineNew HavenConnecticutUSA
| | - Brent Vander Wyk
- Department of Internal Medicine, Section of Geriatrics and Program on AgingYale School of MedicineNew HavenConnecticutUSA
| | - Allison Nelson
- Department of Internal Medicine, Section of Infectious DiseasesYale School of MedicineNew HavenConnecticutUSA
| | - Sui Tsang
- Department of Internal Medicine, Section of Geriatrics and Program on AgingYale School of MedicineNew HavenConnecticutUSA
| | - Tamara P. Blevins
- Division of Infectious Diseases, Department of MedicineSaint Louis University School of MedicineSt. LouisMissouriUSA
| | - Robert B. Belshe
- Division of Infectious Diseases, Department of MedicineSaint Louis University School of MedicineSt. LouisMissouriUSA
| | - Daniel G. Chawla
- Program in Computational Biology and BioinformaticsYale UniversityNew HavenConnecticutUSA
| | - Matthew T. Rondina
- Departments of Internal Medicine and Pathology, and the Molecular Medicine ProgramUniversity of Utah HealthSalt Lake CityUtahUSA
- Department of Medicine and the GRECCGeorge E. Wahlen VAMCSalt Lake CityUtahUSA
| | - Thomas M. Gill
- Department of Internal Medicine, Section of Geriatrics and Program on AgingYale School of MedicineNew HavenConnecticutUSA
| | - Ruth R. Montgomery
- Section of Rheumatology, Department of Internal MedicineYale School of MedicineNew HavenConnecticutUSA
| | - Heather G. Allore
- Department of Internal Medicine, Section of Geriatrics and Program on AgingYale School of MedicineNew HavenConnecticutUSA
| | - Steven H. Kleinstein
- Department of PathologyYale School of MedicineNew HavenConnecticutUSA
- Program in Computational Biology and BioinformaticsYale UniversityNew HavenConnecticutUSA
| | - Albert C. Shaw
- Department of Internal Medicine, Section of Infectious DiseasesYale School of MedicineNew HavenConnecticutUSA
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21
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Hafez AI, Soriano B, Elsayed AA, Futami R, Ceprian R, Ramos-Ruiz R, Martinez G, Roig FJ, Torres-Font MA, Naya-Catala F, Calduch-Giner JA, Trilla-Fuertes L, Gamez-Pozo A, Arnau V, Sempere-Luna JM, Perez-Sanchez J, Gabaldon T, Llorens C. Client Applications and Server-Side Docker for Management of RNASeq and/or VariantSeq Workflows and Pipelines of the GPRO Suite. Genes (Basel) 2023; 14. [PMID: 36833195 DOI: 10.3390/genes14020267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 01/08/2023] [Accepted: 01/14/2023] [Indexed: 01/22/2023] Open
Abstract
The GPRO suite is an in-progress bioinformatic project for -omics data analysis. As part of the continued growth of this project, we introduce a client- and server-side solution for comparative transcriptomics and analysis of variants. The client-side consists of two Java applications called "RNASeq" and "VariantSeq" to manage pipelines and workflows based on the most common command line interface tools for RNA-seq and Variant-seq analysis, respectively. As such, "RNASeq" and "VariantSeq" are coupled with a Linux server infrastructure (named GPRO Server-Side) that hosts all dependencies of each application (scripts, databases, and command line interface software). Implementation of the Server-Side requires a Linux operating system, PHP, SQL, Python, bash scripting, and third-party software. The GPRO Server-Side can be installed, via a Docker container, in the user's PC under any operating system or on remote servers, as a cloud solution. "RNASeq" and "VariantSeq" are both available as desktop (RCP compilation) and web (RAP compilation) applications. Each application has two execution modes: a step-by-step mode enables each step of the workflow to be executed independently, and a pipeline mode allows all steps to be run sequentially. "RNASeq" and "VariantSeq" also feature an experimental, online support system called GENIE that consists of a virtual (chatbot) assistant and a pipeline jobs panel coupled with an expert system. The chatbot can troubleshoot issues with the usage of each tool, the pipeline jobs panel provides information about the status of each computational job executed in the GPRO Server-Side, while the expert system provides the user with a potential recommendation to identify or fix failed analyses. Our solution is a ready-to-use topic specific platform that combines the user-friendliness, robustness, and security of desktop software, with the efficiency of cloud/web applications to manage pipelines and workflows based on command line interface software.
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22
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Najafi M, Guo Y, Andersson G, Humblot P, Bongcam-Rudloff E. Gene Networks and Pathways Involved in LPS-Induced Proliferative Response of Bovine Endometrial Epithelial Cells. Genes (Basel) 2022; 13. [PMID: 36553609 DOI: 10.3390/genes13122342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/02/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
Lipopolysaccharide (LPS) is a component of the outer membrane of Gram-negative bacteria involved in the pathogenic processes leading to mastitis and metritis in animals such as dairy cattle. LPS causes cell proliferation associated with endometrium inflammation. Former in vitro studies have demonstrated that LPS induces an intense stimulation of the proliferation of a pure population of bovine endometrial epithelial cells. In a follow-up transcriptomic study based on RNA-sequencing data obtained after 24 h exposure of primary bovine endometrial epithelial cells to 0, 2, and 8 μg/mL LPS, 752 and 727 differentially expressed genes (DEGs) were detected between the controls and LPS-treated samples that encode proteins known to be associated with either proliferation or apoptosis, respectively. The present bioinformatic analysis was performed to decipher the gene networks involved to obtain a deeper understanding of the mechanisms underlying the proliferative and apoptosis processes. Our findings have revealed 116 putative transcription factors (TFs) and the most significant number of interactions between these TFs and DEGs belong to NFKβ1, TP53, STAT1, and HIF1A. Moreover, our results provide novel insights into the early signaling and metabolic pathways in bovine endometrial epithelial cells associated with the innate immune response and cell proliferation to Escherichia coli-LPS infection. The results further indicated that LPS challenge elicited a strong transcriptomic response, leading to potent activation of pro-inflammatory pathways that are associated with a marked endometrial cancer, Toll-like receptor, NFKβ, AKT, apoptosis, and MAPK signaling pathways. This effect may provide a mechanistic explanation for the relationship between LPS and cell proliferation.
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23
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Basu P, Martins-Green M. Signaling Pathways Associated with Chronic Wound Progression: A Systems Biology Approach. Antioxidants (Basel) 2022; 11. [PMID: 36009225 DOI: 10.3390/antiox11081506] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 07/25/2022] [Accepted: 07/25/2022] [Indexed: 11/23/2022] Open
Abstract
Previously we have shown that several oxidative stress-driven pathways in cutaneous chronic wounds are dysregulated in the first 48 h post-wounding. Here, we performed an RNASeq analysis of tissues collected up to day 20 after wounding, when we have determined full chronicity is established. Weighted Gene Correlation Network Analysis was performed in R segregating the genes into 14 modules. Genes in the modules significantly correlated (p < 0.05) to early and full chronicity were used for pathway analysis using pathfindR. In early chronicity, we observed enrichment of several pathways. Dysregulation of Ephrin/Eph signaling leads to growth cone collapse and impairs neuronal regeneration. Adra2b and Adra2a overexpression in early and full chronicity, respectively, decreased cAMP production and impaired re-epithelialization and granulation tissue formation. Several pathways involving a Smooth-muscle-actin (Acta1) were also enriched with Acta1 overexpression contributing to impaired angiogenesis. During full chronicity, the ‘JAK-STAT’ pathway was suppressed undermining host defenses against infection. Wnt signaling was also suppressed, impairing re-epithelialization and granulation tissue formation. Biomarkers of cancer such as overexpression of SDC1 and constitutive activation of ErbB2/HER2 were also identified. In conclusion, we show that during progression to full chronicity, numerous signaling pathways are dysregulated, including some related to carcinogenesis, suggesting that chronic wounds behave much like cancer. Experimental verification in vivo could identify candidates for treatment of chronic wounds.
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24
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Yellapu NK, Ly T, Sardiu ME, Pei D, Welch DR, Thompson JA, Koestler DC. Synergistic anti-proliferative activity of JQ1 and GSK2801 in triple-negative breast cancer. BMC Cancer 2022; 22:627. [PMID: 35672711 PMCID: PMC9173973 DOI: 10.1186/s12885-022-09690-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 05/23/2022] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Triple-negative breast cancer (TNBC) constitutes 10-20% of breast cancers and is challenging to treat due to a lack of effective targeted therapies. Previous studies in TNBC cell lines showed in vitro growth inhibition when JQ1 or GSK2801 were administered alone, and enhanced activity when co-administered. Given their respective mechanisms of actions, we hypothesized the combinatorial effect could be due to the target genes affected. Hence the target genes were characterized for their expression in the TNBC cell lines to prove the combinatorial effect of JQ1 and GSK2801. METHODS RNASeq data sets of TNBC cell lines (MDA-MB-231, HCC-1806 and SUM-159) were analyzed to identify the differentially expressed genes in single and combined treatments. The topmost downregulated genes were characterized for their downregulated expression in the TNBC cell lines treated with JQ1 and GSK2801 under different dose concentrations and combinations. The optimal lethal doses were determined by cytotoxicity assays. The inhibitory activity of the drugs was further characterized by molecular modelling studies. RESULTS Global expression profiling of TNBC cell lines using RNASeq revealed different expression patterns when JQ1 and GSK2801 were co-administered. Functional enrichment analyses identified several metabolic pathways (i.e., systemic lupus erythematosus, PI3K-Akt, TNF, JAK-STAT, IL-17, MAPK, Rap1 and signaling pathways) enriched with upregulated and downregulated genes when combined JQ1 and GSK2801 treatment was administered. RNASeq identified downregulation of PTPRC, MUC19, RNA5-8S5, KCNB1, RMRP, KISS1 and TAGLN (validated by RT-qPCR) and upregulation of GPR146, SCARA5, HIST2H4A, CDRT4, AQP3, MSH5-SAPCD1, SENP3-EIF4A1, CTAGE4 and RNASEK-C17orf49 when cells received both drugs. In addition to differential gene regulation, molecular modelling predicted binding of JQ1 and GSK2801 with PTPRC, MUC19, KCNB1, TAGLN and KISS1 proteins, adding another mechanism by which JQ1 and GSK2801 could elicit changes in metabolism and proliferation. CONCLUSION JQ1-GSK2801 synergistically inhibits proliferation and results in selective gene regulation. Besides suggesting that combinatorial use could be useful therapeutics for the treatment of TNBC, the findings provide a glimpse into potential mechanisms of action for this combination therapy approach.
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Affiliation(s)
- Nanda Kumar Yellapu
- Department of Biostatistics & Data Science, University of Kansas, Medical Center, KS, Kansas City, USA
- The University of Kansas Cancer Center, Kansas City, KS, USA
| | - Thuc Ly
- The University of Kansas Cancer Center, Kansas City, KS, USA
- Department of Cancer Biology, University of Kansas, Medical Center, KS, Kansas City, USA
| | - Mihaela E Sardiu
- Department of Biostatistics & Data Science, University of Kansas, Medical Center, KS, Kansas City, USA
- The University of Kansas Cancer Center, Kansas City, KS, USA
| | - Dong Pei
- Department of Biostatistics & Data Science, University of Kansas, Medical Center, KS, Kansas City, USA
- The University of Kansas Cancer Center, Kansas City, KS, USA
| | - Danny R Welch
- The University of Kansas Cancer Center, Kansas City, KS, USA
- Department of Cancer Biology, University of Kansas, Medical Center, KS, Kansas City, USA
- Departments of Molecular & Integrative Physiology and Internal Medicine, University of Kansas, Medical Center, KS, Kansas City, USA
| | - Jeffery A Thompson
- Department of Biostatistics & Data Science, University of Kansas, Medical Center, KS, Kansas City, USA.
- The University of Kansas Cancer Center, Kansas City, KS, USA.
| | - Devin C Koestler
- Department of Biostatistics & Data Science, University of Kansas, Medical Center, KS, Kansas City, USA.
- The University of Kansas Cancer Center, Kansas City, KS, USA.
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25
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Wang D, Rolfe PA, Foernzler D, O'Rourke D, Zhao S, Scheuenpflug J, Feng Z. Comparison of Two Illumina Whole Transcriptome RNA Sequencing Library Preparation Methods Using Human Cancer FFPE Specimens. Technol Cancer Res Treat 2022; 21:15330338221076304. [PMID: 35138205 PMCID: PMC8832632 DOI: 10.1177/15330338221076304] [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] [Indexed: 12/05/2022] Open
Abstract
Objective: RNA extraction and library preparation from formalin-fixed, paraffin-embedded (FFPE) samples are crucial pre-analytical steps towards achieving optimal downstream RNA sequencing (RNASeq) results. In this study, we assessed 2 Illumina library preparation methods for RNA-Seq analysis using archived FFPE samples from human cancer indications at 2 independent vendors. Methods: Twenty-five FFPE samples from 5 indications (non-small cell lung cancer, colorectal cancer, renal carcinoma, breast cancer, and hepatocellular carcinoma) were included, covering a wide range of sample storage durations (3-25 years-old), sample qualities, and specimen types (resection vs core needle biopsy). Each sample was processed independently by both vendors. Total RNA was isolated using the Qiagen miRNeasy FFPE kit followed by library construction using either TruSeq Stranded Total RNA library preparation kit with Ribo-Zero Gold, or TruSeq RNA Access library preparation kit. Libraries were normalized to 20 pM and sequenced on an Illumina HiSeq 2500 using V3 chemistry in paired-end mode with a read length of 2 × 50 bp. The data were processed through a standard RNASeq pipeline to produce counts and transcripts per millions for each gene in each sample to compare 2 library kits at 2 different vendors. Results: Our data showed that TruSeq RNA Access libraries yield over 80% exonic reads across different quality samples, indicating higher selectivity of the exome pull down by the capture approach compared to the random priming of the TruSeq Stranded Total kit. The overall QC data for FFPE RNA extraction, library preparation, and sequencing generated by the 2 vendors are comparable, and downstream gene expression quantification results show high concordance as well. With the TruSeq Stranded Total kit, the mean Spearman correlation between vendors was 0.87 and the mean Pearson correlation was 0.76. With the TruSeq RNA Access kit, the mean Spearman correlation between vendors was 0.89 and the mean Pearson correlation was 0.73. Interestingly, examination of the cross-vendor correlations compared to various common QC statistics suggested that library concentration is better correlated with consistency between vendors than is the RNA quantity. Conclusions: Our analyses provide evidence to guide selection of sequencing methods for FFPE samples in which the sample quality may be severely compromised.
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Affiliation(s)
- Danyi Wang
- 189697Global Clinical Biomarkers and Companion Diagnostics, Translational Medicine, Global Development, EMD Serono Research and Development Institute, Billerica, MA, USA
| | - P Alexander Rolfe
- 2792Immunology and Immuno-Oncology Bioinformatics, Translational Medicine, Global Development, EMD Serono Research and Development Institute, Billerica, MA, USA
| | - Dorothee Foernzler
- 189697Global Clinical Biomarkers and Companion Diagnostics, Translational Medicine, Global Development, EMD Serono Research and Development Institute, Billerica, MA, USA
| | - Dennis O'Rourke
- 189697Global Clinical Biomarkers and Companion Diagnostics, Translational Medicine, Global Development, EMD Serono Research and Development Institute, Billerica, MA, USA
| | - Sheng Zhao
- Oncology Bioinformatics, Translational Medicine, Global Development, Merck KGaA, Darmstadt, Germany
| | - Juergen Scheuenpflug
- Global Clinical Biomarkers and Companion Diagnostics, Translational Medicine, Global Development, Merck KGaA, Darmstadt, Germany
| | - Zheng Feng
- 189697Global Clinical Biomarkers and Companion Diagnostics, Translational Medicine, Global Development, EMD Serono Research and Development Institute, Billerica, MA, USA
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26
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Pinel GD, Horder JL, King JR, McIntyre A, Mongan NP, López GG, Benest AV. Endothelial Cell RNA-Seq Data: Differential Expression and Functional Enrichment Analyses to Study Phenotypic Switching. Methods Mol Biol 2022; 2441:369-426. [PMID: 35099752 DOI: 10.1007/978-1-0716-2059-5_29] [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: 11/25/2022]
Abstract
RNA-seq is a common approach used to explore gene expression data between experimental conditions or cell types and ultimately leads to information that can shed light on the biological processes involved and inform further hypotheses. While the protocols required to generate samples for sequencing can be performed in most research facilities, the resulting computational analysis is often an area in which researchers have little experience. Here we present a user-friendly bioinformatics workflow which describes the methods required to take raw data produced by RNA sequencing to interpretable results. Widely used and well documented tools are applied. Data quality assessment and read trimming were performed by FastQC and Cutadapt, respectively. Following this, STAR was utilized to map the trimmed reads to a reference genome and the alignment was analyzed by Qualimap. The subsequent mapped reads were quantified by featureCounts. DESeq2 was used to normalize and perform differential expression analysis on the quantified reads, identifying differentially expressed genes and preparing the data for functional enrichment analysis. Gene set enrichment analysis identified enriched gene sets from the normalized count data and clusterProfiler was used to perform functional enrichment against the GO, KEGG, and Reactome databases. Example figures of the functional enrichment analysis results were also generated. The example data used in the workflow are derived from HUVECs, an in vitro model used in the study of endothelial cells, published and publicly available for download from the European Nucleotide Archive.
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Affiliation(s)
- Guillermo Díez Pinel
- Neuronal and Vascular Biology Group, UCL Institute of Ophthalmology, University College London, London, UK
| | - Joseph L Horder
- Endothelial Quiescence Group, Centre for Cancer Sciences, Biodiscovery Institute, School of Medicine, University of Nottingham, Nottingham, UK
| | - John R King
- School of Mathematics, Faculty of Science, University of Nottingham, Nottingham, UK
| | - Alan McIntyre
- Hypoxia and Acidosis Group, Center for Cancer Sciences, Biodiscovery Institute, University of Nottingham, Nottingham, UK
| | - Nigel P Mongan
- School of Veterinary Medicine and Science, Biodiscovery Institute, University of Nottingham, Nottingham, UK
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA
| | - Gonzalo Gómez López
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Andrew V Benest
- Endothelial Quiescence Group, Centre for Cancer Sciences, Biodiscovery Institute, School of Medicine, University of Nottingham, Nottingham, UK.
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27
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Hunnicutt KE, Good JM, Larson EL. Unraveling patterns of disrupted gene expression across a complex tissue. Evolution 2022; 76:275-291. [PMID: 34882778 PMCID: PMC9355168 DOI: 10.1111/evo.14420] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 07/10/2021] [Revised: 11/11/2021] [Accepted: 11/26/2021] [Indexed: 02/03/2023]
Abstract
Whole tissue RNASeq is the standard approach for studying gene expression divergence in evolutionary biology and provides a snapshot of the comprehensive transcriptome for a given tissue. However, whole tissues consist of diverse cell types differing in expression profiles, and the cellular composition of these tissues can evolve across species. Here, we investigate the effects of different cellular composition on whole tissue expression profiles. We compared gene expression from whole testes and enriched spermatogenesis populations in two species of house mice, Mus musculus musculus and M. m. domesticus, and their sterile and fertile F1 hybrids, which differ in both cellular composition and regulatory dynamics. We found that cellular composition differences skewed expression profiles and differential gene expression in whole testes samples. Importantly, both approaches were able to detect large-scale patterns such as disrupted X chromosome expression, although whole testes sampling resulted in decreased power to detect differentially expressed genes. We encourage researchers to account for histology in RNASeq and consider methods that reduce sample complexity whenever feasible. Ultimately, we show that differences in cellular composition between tissues can modify expression profiles, potentially altering inferred gene ontological processes, insights into gene network evolution, and processes governing gene expression evolution.
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Affiliation(s)
| | - Jeffrey M. Good
- University of Montana, Division of Biological Sciences, Missoula, MO, 59812
| | - Erica L. Larson
- University of Denver, Department of Biological Sciences, Denver, CO, 80208
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28
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Larizza L, Calzari L, Alari V, Russo S. Genes for RNA-binding proteins involved in neural-specific functions and diseases are downregulated in Rubinstein-Taybi iNeurons. Neural Regen Res 2022; 17:5-14. [PMID: 34100419 PMCID: PMC8451555 DOI: 10.4103/1673-5374.314286] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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] [Indexed: 11/24/2022] Open
Abstract
Taking advantage of the fast-growing knowledge of RNA-binding proteins (RBPs) we review the signature of downregulated genes for RBPs in the transcriptome of induced pluripotent stem cell neurons (iNeurons) modelling the neurodevelopmental Rubinstein Taybi Syndrome (RSTS) caused by mutations in the genes encoding CBP/p300 acetyltransferases. We discuss top and functionally connected downregulated genes sorted to “RNA processing” and “Ribonucleoprotein complex biogenesis” Gene Ontology clusters. The first set of downregulated RBPs includes members of hnRNHP (A1, A2B1, D, G, H2-H1, MAGOHB, PAPBC), core subunits of U small nuclear ribonucleoproteins and Serine-Arginine splicing regulators families, acting in precursor messenger RNA alternative splicing and processing. Consistent with literature findings on reduced transcript levels of serine/arginine repetitive matrix 4 (SRRM4) protein, the main regulator of the neural-specific microexons splicing program upon depletion of Ep300 and Crebbp in mouse neurons, RSTS iNeurons show downregulated genes for proteins impacting this network. We link downregulated genes to neurological disorders including the new HNRNPH1-related intellectual disability syndrome with clinical overlap to RSTS. The set of downregulated genes for Ribosome biogenesis includes several components of ribosomal subunits and nucleolar proteins, such NOP58 and fibrillarin that form complexes with snoRNAs with a central role in guiding post-transcriptional modifications needed for rRNA maturation. These nucleolar proteins are “dual” players as fibrillarin is also required for epigenetic regulation of ribosomal genes and conversely NOP58-associated snoRNA levels are under the control of NOP58 interactor BMAL1, a transcriptional regulator of the circadian rhythm. Additional downregulated genes for “dual specificity” RBPs such as RUVBL1 and METTL1 highlight the links between chromatin and the RBP-ome and the contribution of perturbations in their cross-talk to RSTS. We underline the hub position of CBP/p300 in chromatin regulation, the impact of its defect on neurons’ post-transcriptional regulation of gene expression and the potential use of epidrugs in therapeutics of RBP-caused neurodevelopmental disorders.
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Affiliation(s)
- Lidia Larizza
- Cytogenetics and Molecular Genetics Laboratory, IRCCS Istituto Auxologico Italiano, Milano, Italy
| | - Luciano Calzari
- Cytogenetics and Molecular Genetics Laboratory, IRCCS Istituto Auxologico Italiano, Milano, Italy
| | - Valentina Alari
- Cytogenetics and Molecular Genetics Laboratory, IRCCS Istituto Auxologico Italiano, Milano, Italy
| | - Silvia Russo
- Cytogenetics and Molecular Genetics Laboratory, IRCCS Istituto Auxologico Italiano, Milano, Italy
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29
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Valencia K, Sainz C, Bértolo C, de Biurrun G, Agorreta J, Azpilikueta A, Larrayoz MJ, Bosco G, Zandueta C, Redrado M, Redín E, Exposito F, Serrano D, Echepare M, Ajona D, Melero I, Pio R, Thomas R, Calvo A, Montuenga LM. Two alternative cell line models for the study of multiorganic metastasis and immunotherapy in Lung Squamous Cell Carcinoma. Dis Model Mech 2021; 15:273637. [PMID: 34870316 PMCID: PMC8822220 DOI: 10.1242/dmm.049137] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 05/27/2021] [Accepted: 11/29/2021] [Indexed: 11/20/2022] Open
Abstract
There is a paucity of adequate mouse models and cell lines available to study lung squamous cell carcinoma (LUSC). We have generated and characterized two models of phenotypically different transplantable LUSC cell lines (UN-SCC679 and UN-SCC680) derived from an N-nitroso-tris-chloroethylurea (NTCU) chemically-induced mouse model in A/J mice. Furthermore, we genetically characterized and compared both LUSC cell lines by performing whole exome and RNA sequencing. These experiments revealed similar genetic and transcriptomic patterns that may correspond to the classical LUSC human subtype. In addition, we compared the immune landscape generated by both tumor cells lines in vivo and assessed their response to immune checkpoint inhibition. The differences between the two cell lines are a good model for the remarkable heterogeneity of human squamous cell carcinoma. Study of the metastatic potential of these models revealed that both cell lines represent the human LUSC organotropism to the brain, bones, liver and adrenal glands. In summary, we have generated a very valuable cell line tools for LUSC research that recapitulates the complexity of the human disease.
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Affiliation(s)
- Karmele Valencia
- Program in Solid Tumors, CIMA-University of Navarra, Pamplona, Spain.,Consorcio de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Navarra Health Research Institute (IDISNA), Pamplona, Spain.,Department of Biochemistry and Genetics, School of Sciences, University of Navarra, Pamplona, Spain
| | - Cristina Sainz
- Program in Solid Tumors, CIMA-University of Navarra, Pamplona, Spain.,Navarra Health Research Institute (IDISNA), Pamplona, Spain
| | - Cristina Bértolo
- Program in Solid Tumors, CIMA-University of Navarra, Pamplona, Spain.,Navarra Health Research Institute (IDISNA), Pamplona, Spain
| | - Gabriel de Biurrun
- Department of Environmental Biology School of Sciences, University of Navarra, Pamplona, Spain
| | - Jackeline Agorreta
- Program in Solid Tumors, CIMA-University of Navarra, Pamplona, Spain.,Department of Health Sciences, Biochemistry Area, Public University of Navarra, Pamplona, Spain
| | - Arantza Azpilikueta
- Program of Immunology and Immunotherapy, CIMA-University of Navarra, Pamplona, Spain
| | - Marta J Larrayoz
- Program in Solid Tumors, CIMA-University of Navarra, Pamplona, Spain.,Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, Pamplona, Spain.,Consorcio de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Navarra Health Research Institute (IDISNA), Pamplona, Spain
| | - Graziella Bosco
- Department of Translational Genomics, Medical Faculty, University of Cologne, 50931 Cologne, Germany
| | - Carolina Zandueta
- Program in Solid Tumors, CIMA-University of Navarra, Pamplona, Spain.,Consorcio de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Miriam Redrado
- Program in Solid Tumors, CIMA-University of Navarra, Pamplona, Spain.,Navarra Health Research Institute (IDISNA), Pamplona, Spain
| | - Esther Redín
- Program in Solid Tumors, CIMA-University of Navarra, Pamplona, Spain.,Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, Pamplona, Spain.,Consorcio de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Navarra Health Research Institute (IDISNA), Pamplona, Spain
| | - Francisco Exposito
- Program in Solid Tumors, CIMA-University of Navarra, Pamplona, Spain.,Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, Pamplona, Spain.,Consorcio de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Navarra Health Research Institute (IDISNA), Pamplona, Spain
| | - Diego Serrano
- Program in Solid Tumors, CIMA-University of Navarra, Pamplona, Spain.,Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, Pamplona, Spain.,Navarra Health Research Institute (IDISNA), Pamplona, Spain
| | - Mirari Echepare
- Program in Solid Tumors, CIMA-University of Navarra, Pamplona, Spain.,Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, Pamplona, Spain.,Navarra Health Research Institute (IDISNA), Pamplona, Spain
| | - Daniel Ajona
- Program in Solid Tumors, CIMA-University of Navarra, Pamplona, Spain.,Consorcio de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Navarra Health Research Institute (IDISNA), Pamplona, Spain.,Department of Biochemistry and Genetics, School of Sciences, University of Navarra, Pamplona, Spain
| | - Ignacio Melero
- Consorcio de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Navarra Health Research Institute (IDISNA), Pamplona, Spain.,Program of Immunology and Immunotherapy, CIMA-University of Navarra, Pamplona, Spain.,Department of Oncology, Clínica Universidad de Navarra, Pamplona, Spain
| | - Ruben Pio
- Program in Solid Tumors, CIMA-University of Navarra, Pamplona, Spain.,Consorcio de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Navarra Health Research Institute (IDISNA), Pamplona, Spain.,Department of Biochemistry and Genetics, School of Sciences, University of Navarra, Pamplona, Spain
| | - Roman Thomas
- Department of Translational Genomics, Medical Faculty, University of Cologne, 50931 Cologne, Germany.,Department of Pathology, University Hospital Cologne, 50937 Cologne, Germany.,German Cancer Research Center, German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Alfonso Calvo
- Program in Solid Tumors, CIMA-University of Navarra, Pamplona, Spain.,Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, Pamplona, Spain.,Consorcio de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Navarra Health Research Institute (IDISNA), Pamplona, Spain
| | - Luis M Montuenga
- Program in Solid Tumors, CIMA-University of Navarra, Pamplona, Spain.,Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, Pamplona, Spain.,Consorcio de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Navarra Health Research Institute (IDISNA), Pamplona, Spain
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Basu P, Kim JH, Saeed S, Martins-Green M. Using systems biology approaches to identify signalling pathways activated during chronic wound initiation. Wound Repair Regen 2021; 29:881-898. [PMID: 34536049 DOI: 10.1111/wrr.12963] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 04/29/2021] [Revised: 07/18/2021] [Accepted: 08/04/2021] [Indexed: 12/30/2022]
Abstract
Chronic wounds are a significant health problem worldwide. However, nothing is known about how chronic wounds initiate and develop. Here we use a chronic wound model in diabetic mice and a Systems Biology Approach using nanoString nCounter technology and weighted gene correlation network analysis (WGCNA), with tissues collected at 6, 12, 24 and 48 h post-wounding, to identify metabolic signalling pathways involved in initiation of chronicity. Normalized counts obtained from the nanoString nCounter Mouse Metabolic Panel were used for the WGCNA, which groups genes into co-expression modules to visualize the correlation network. Genes with significant module membership and gene trait significance (p < 0.05) were used to identify signalling pathways that are important for the development of chronicity. The pathway analysis using the Reactome database showed stabilization of PTEN, which down-regulates PI3K/AKT1, which in turn down-regulates Nrf2, as shown by ELISA, thus disabling antioxidant production, resulting in high oxidative stress levels. We find that pathways involved in inflammation, including those that generate pro-inflammatory lipids derived from arachidonic acid metabolism, IFNγ and catecholamines, occur. Moreover, HIF3α is over-expressed, potentially blocking Hif1α and preventing activation of growth factors and cytokines that promote granulation tissue formation. We also find that FGF1 is under-expressed, while thrombospondin-1 is over-expressed, resulting in decreased angiogenesis, a process that is critical for healing. Finally, enzymes involved in glycolysis are down-regulated, resulting in decreased production of pyruvate, a molecule critical for ATP production, leading to extensive cell death and wound paralysis. These findings offer new avenues of study that may lead to the development of novel treatments of CW to be administered right after debridement.
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Affiliation(s)
- Proma Basu
- Department of Molecular, Cell and Systems Biology, UC, Riverside, California, USA
| | - Jane Hannah Kim
- Department of Molecular, Cell and Systems Biology, UC, Riverside, California, USA
| | - Shayan Saeed
- Department of Molecular, Cell and Systems Biology, UC, Riverside, California, USA
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31
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Barnett LMA, Kramer NE, Buerger AN, Love DH, Bisesi JH, Cummings BS. Transcriptomic Analysis of the Differential Nephrotoxicity of Diverse Brominated Flame Retardants in Rat and Human Renal Cells. Int J Mol Sci 2021; 22:ijms221810044. [PMID: 34576211 PMCID: PMC8465879 DOI: 10.3390/ijms221810044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 09/09/2021] [Accepted: 09/11/2021] [Indexed: 12/13/2022] Open
Abstract
Brominated flame retardants (BFRs) are environmentally persistent, are detected in humans, and some have been banned due to their potential toxicity. BFRs are developmental neurotoxicants and endocrine disruptors; however, few studies have explored their potential nephrotoxicity. We addressed this gap in the literature by determining the toxicity of three different BFRs (tetrabromobisphenol A (TBBPA), hexabromocyclododecane (HBCD), and tetrabromodiphenyl ether (BDE-47)) in rat (NRK 52E) and human (HK-2 and RPTEC) tubular epithelial cells. All compounds induced time- and concentration-dependent toxicity based on decreases in MTT staining and changes in cell and nuclear morphology. The toxicity of BFRs was chemical- and cell-dependent, and human cells were more susceptible to all three BFRs based on IC50s after 48 h exposure. BFRs also had chemical- and cell-dependent effects on apoptosis as measured by increases in annexin V and PI staining. The molecular mechanisms mediating this toxicity were investigated using RNA sequencing. Principal components analysis supported the hypothesis that BFRs induce different transcriptional changes in rat and human cells. Furthermore, BFRs only shared nine differentially expressed genes in rat cells and five in human cells. Gene set enrichment analysis demonstrated chemical- and cell-dependent effects; however, some commonalities were also observed. Namely, gene sets associated with extracellular matrix turnover, the coagulation cascade, and the SNS-related adrenal cortex response were enriched across all cell lines and BFR treatments. Taken together, these data support the hypothesis that BFRs induce differential toxicity in rat and human renal cell lines that is mediated by differential changes in gene expression.
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Affiliation(s)
| | - Naomi E Kramer
- Interdisciplinary Toxicology Program, University of Georgia, Athens, GA 30602, USA
| | - Amanda N Buerger
- Department of Environmental and Global Health and Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL 32611, USA
| | - Deirdre H Love
- Department of Environmental and Global Health and Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL 32611, USA
| | - Joseph H Bisesi
- Department of Environmental and Global Health and Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL 32611, USA
| | - Brian S Cummings
- Interdisciplinary Toxicology Program, University of Georgia, Athens, GA 30602, USA
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA 30602, USA
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32
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Pant A, Chen Y, Kuppa A, Du X, Halligan BD, Speliotes EK. Perturbation of TM6SF2 Expression Alters Lipid Metabolism in a Human Liver Cell Line. Int J Mol Sci 2021; 22:9758. [PMID: 34575933 PMCID: PMC8471112 DOI: 10.3390/ijms22189758] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/02/2021] [Accepted: 09/03/2021] [Indexed: 11/30/2022] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) is caused by excess lipid accumulation in hepatocytes. Genome-wide association studies have identified a strong association of NAFLD with non-synonymous E167K amino acid mutation in the transmembrane 6 superfamily member 2 (TM6SF2) protein. The E167K mutation reduces TM6SF2 stability, and its carriers display increased hepatic lipids and lower serum triglycerides. However, the effects of TM6SF2 on hepatic lipid metabolism are not completely understood. We overexpressed wild-type or E167K variant of TM6SF2 or knocked down TM6SF2 expression in lipid-treated Huh-7 cells and used untargeted lipidomic analysis, RNAseq transcriptome analysis, and fluorescent imaging to determine changes in hepatic lipid metabolism. Both TM6SF2 knockdown and E167K overexpression increased hepatic lipid accumulation, while wild-type overexpression decreased acylglyceride levels. We also observed lipid chain remodeling for acylglycerides by TM6SF2 knockdown, leading to a relative increase in species with shorter, more saturated side chains. RNA-sequencing revealed differential expression of several lipid metabolizing genes, including genes belonging to AKR1 family and lipases, primarily in cells with TM6SF2 knockdown. Taken together, our data show that overexpression of TM6SF2 gene or its loss-of-function changes hepatic lipid species composition and expression of lipid metabolizing genes. Additionally, our data further confirms a loss-of-function effect for the E167K variant.
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Affiliation(s)
- Asmita Pant
- Division of Gastroenterology and Hepatology, University of Michigan Health System, Ann Arbor, MI 48109, USA; (A.P.); (Y.C.); (A.K.); (X.D.); (B.D.H.)
| | - Yue Chen
- Division of Gastroenterology and Hepatology, University of Michigan Health System, Ann Arbor, MI 48109, USA; (A.P.); (Y.C.); (A.K.); (X.D.); (B.D.H.)
| | - Annapurna Kuppa
- Division of Gastroenterology and Hepatology, University of Michigan Health System, Ann Arbor, MI 48109, USA; (A.P.); (Y.C.); (A.K.); (X.D.); (B.D.H.)
| | - Xiaomeng Du
- Division of Gastroenterology and Hepatology, University of Michigan Health System, Ann Arbor, MI 48109, USA; (A.P.); (Y.C.); (A.K.); (X.D.); (B.D.H.)
| | - Brian D. Halligan
- Division of Gastroenterology and Hepatology, University of Michigan Health System, Ann Arbor, MI 48109, USA; (A.P.); (Y.C.); (A.K.); (X.D.); (B.D.H.)
| | - Elizabeth K. Speliotes
- Division of Gastroenterology and Hepatology, University of Michigan Health System, Ann Arbor, MI 48109, USA; (A.P.); (Y.C.); (A.K.); (X.D.); (B.D.H.)
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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Natarajan P, Ahn E, Reddy UK, Perumal R, Prom LK, Magill C. RNA-Sequencing in Resistant (QL3) and Susceptible (Theis) Sorghum Cultivars Inoculated With Johnsongrass Isolates of Colletotrichum sublineola. Front Genet 2021; 12:722519. [PMID: 34456979 PMCID: PMC8385561 DOI: 10.3389/fgene.2021.722519] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 06/08/2021] [Accepted: 07/22/2021] [Indexed: 12/02/2022] Open
Abstract
Gene expression was analyzed at 0- and 24-h post-inoculation of two inbred sorghum cultivars known to differ in response to inoculation with Colletotrichum sublineola, the fungal pathogen that causes anthracnose. QL3 is reported to have quantitative resistance, while Theis is susceptible to most pathotypes of the pathogen; RNASeq identified over 3,000 specific genes in both cultivars as showing significant changes in expression following inoculation; in all but one gene, the changes in QL3 and Thies were in the same direction. Many other genes showed significant changes in only one of the two cultivars. Overall, more genes were downregulated than upregulated. Differences in changes in expression levels of a few genes suggested potential roles for the difference in disease response between QL3 and Theis, but did not identify known resistance genes. Gene ontology (GO) and pathway enrichment analysis identified upregulation of 23 transcription factor encoding genes as well as genes involved in the production of secondary metabolites, which are part of a typical host defense reaction.
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Affiliation(s)
- Purushothaman Natarajan
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, West Virginia, WV, United States
| | - Ezekiel Ahn
- Department of Plant Pathology and Microbiology, Texas A & M University, College Station, TX, United States
| | - Umesh K Reddy
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, West Virginia, WV, United States
| | - Ramasamy Perumal
- Agricultural Research Center, Kansas State University, Hays, KS, United States
| | - Louis K Prom
- Crop Germplasm Research Unit, USDA-ARS Southern Plains Agricultural Research Center, College Station, TX, United States
| | - Clint Magill
- Department of Plant Pathology and Microbiology, Texas A & M University, College Station, TX, United States
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34
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Balaji H, Demers I, Wuerdemann N, Schrijnder J, Kremer B, Klussmann JP, Huebbers CU, Speel EM. Causes and Consequences of HPV Integration in Head and Neck Squamous Cell Carcinomas: State of the Art. Cancers (Basel) 2021; 13:4089. [PMID: 34439243 DOI: 10.3390/cancers13164089] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/10/2021] [Accepted: 08/11/2021] [Indexed: 12/29/2022] Open
Abstract
A constantly increasing incidence in high-risk Human Papillomaviruses (HPV)s driven head and neck squamous cell carcinomas (HNSCC)s, especially of oropharyngeal origin, is being observed. During persistent infections, viral DNA integration into the host genome may occur. Studies are examining if the physical status of the virus (episomal vs. integration) affects carcinogenesis and eventually has further-reaching consequences on disease progression and outcome. Here, we review the literature of the most recent five years focusing on the impact of HPV integration in HNSCCs, covering aspects of detection techniques used (from PCR up to NGS approaches), integration loci identified, and associations with genomic and clinical data. The consequences of HPV integration in the human genome, including the methylation status and deregulation of genes involved in cell signaling pathways, immune evasion, and response to therapy, are also summarized.
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35
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Trujillo-Montenegro JH, Rodríguez Cubillos MJ, Loaiza CD, Quintero M, Espitia-Navarro HF, Salazar Villareal FA, Viveros Valens CA, González Barrios AF, De Vega J, Duitama J, Riascos JJ. Unraveling the Genome of a High Yielding Colombian Sugarcane Hybrid. Front Plant Sci 2021; 12:694859. [PMID: 34484261 PMCID: PMC8414525 DOI: 10.3389/fpls.2021.694859] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 06/07/2021] [Indexed: 05/04/2023]
Abstract
Recent developments in High Throughput Sequencing (HTS) technologies and bioinformatics, including improved read lengths and genome assemblers allow the reconstruction of complex genomes with unprecedented quality and contiguity. Sugarcane has one of the most complicated genomes among grassess with a haploid length of 1Gbp and a ploidies between 8 and 12. In this work, we present a genome assembly of the Colombian sugarcane hybrid CC 01-1940. Three types of sequencing technologies were combined for this assembly: PacBio long reads, Illumina paired short reads, and Hi-C reads. We achieved a median contig length of 34.94 Mbp and a total genome assembly of 903.2 Mbp. We annotated a total of 63,724 protein coding genes and performed a reconstruction and comparative analysis of the sucrose metabolism pathway. Nucleotide evolution measurements between orthologs with close species suggest that divergence between Saccharum officinarum and Saccharum spontaneum occurred <2 million years ago. Synteny analysis between CC 01-1940 and the S. spontaneum genome confirms the presence of translocation events between the species and a random contribution throughout the entire genome in current sugarcane hybrids. Analysis of RNA-Seq data from leaf and root tissue of contrasting sugarcane genotypes subjected to water stress treatments revealed 17,490 differentially expressed genes, from which 3,633 correspond to genes expressed exclusively in tolerant genotypes. We expect the resources presented here to serve as a source of information to improve the selection processes of new varieties of the breeding programs of sugarcane.
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Affiliation(s)
- Jhon Henry Trujillo-Montenegro
- Centro de Investigación de la Caña de Azúcar de Colombia (CENICAÑA), Cali, Colombia
- Research Group in Bioinformatics, Department of Computer Science, Faculty of Engineering, Universidad Del Valle,Cali, Colombia
| | - María Juliana Rodríguez Cubillos
- Grupo de Diseño de Productos y Procesos, Department of Chemical and Food Engineering, Faculty of Engineering, Universidad de los Andes, Bogotá, Colombia
| | | | - Manuel Quintero
- Centro de Investigación de la Caña de Azúcar de Colombia (CENICAÑA), Cali, Colombia
| | | | | | | | - Andrés Fernando González Barrios
- Grupo de Diseño de Productos y Procesos, Department of Chemical and Food Engineering, Faculty of Engineering, Universidad de los Andes, Bogotá, Colombia
| | - José De Vega
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | - Jorge Duitama
- Systems and Computing Engineering Department, Universidad de los Andes, Bogotá, Colombia
| | - John J. Riascos
- Centro de Investigación de la Caña de Azúcar de Colombia (CENICAÑA), Cali, Colombia
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36
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He L, Liu H, Cheng C, Xu M, He L, Li L, Yao J, Zhang W, Zhai Z, Luo Q, Sun J, Yang T, Xu S. RNA sequencing reveals transcriptomic changes in tobacco (Nicotiana tabacum) following NtCPS2 knockdown. BMC Genomics 2021; 22:467. [PMID: 34162328 PMCID: PMC8220664 DOI: 10.1186/s12864-021-07796-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 06/10/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Amber-like compounds form in tobacco (Nicotiana tabacum) during leaf curing and impact aromatic quality. In particular, cis-abienol, a polycyclic labdane-related diterpenoid, is of research interest as a precursor of these compounds. Glandular trichome cells specifically express copalyl diphosphate synthase (NtCPS2) at high levels in tobacco, which, together with NtABS, are major regulators of cis-abienol biosynthesis in tobacco. RESULTS To identify the genes involved in the biosynthesis of cis-abienol in tobacco, we constructed transgenic tobacco lines based on an NtCPS2 gene-knockdown model using CRISPR/Cas9 genome-editing technology to inhibit NtCPS2 function in vitro. In mutant plants, cis-abienol and labdene diol contents decreased, whereas the gibberellin and abscisic acid (ABA) contents increased compared with those in wild-type tobacco plants. RNA sequencing analysis revealed the presence of 9514 differentially expressed genes (DEGs; 4279 upregulated, 5235 downregulated) when the leaves of wild-type and NtCPS2-knockdown tobacco plants were screened. Among these DEGs, the genes encoding cis-abienol synthase, ent-kaurene oxidase, auxin/ABA-related proteins, and transcription factors were found to be involved in various biological and physiochemical processes, including diterpenoid biosynthesis, plant hormone signal transduction, and plant-pathogen interactions. CONCLUSIONS The present study provides insight into the unique transcriptome profile of NtCPS2 knockdown tobacco, allowing for a better understanding of the biosynthesis of cis-abienol in tobacco.
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Affiliation(s)
- Lingxiao He
- College of Tobacco Science, Henan Agricultural University, National Tobacco Cultivation & Physiology & Biochemistry Research Centre, Scientific Observation and Experiment Station of Henan, Ministry of Agriculture, Zhengzhou, 450002 China
| | - Huabing Liu
- Technology Center, China Tobacco Zhejiang Industry Co, Ltd., Hangzhou, 310008 China
| | - Changhe Cheng
- Technology Center, China Tobacco Zhejiang Industry Co, Ltd., Hangzhou, 310008 China
| | - Min Xu
- China National Tobacco Corporation Henan company, Zhengzhou, 450002 Henan China
| | - Lei He
- China National Tobacco Corporation Henan company, Zhengzhou, 450002 Henan China
| | - Lihua Li
- China National Tobacco Corporation Henan company, Zhengzhou, 450002 Henan China
| | - Jian Yao
- China National Tobacco Corporation Henan company, Zhengzhou, 450002 Henan China
| | - Wenjun Zhang
- Hunan Tobacco Corporation Changsha Company, Changsha, 410007 Hunan China
| | - Zhengguang Zhai
- Hunan Tobacco Corporation Changsha Company, Changsha, 410007 Hunan China
| | - Qinzhan Luo
- Guangxi Zhuang Autonomous Region Tobacco Corporation Baise Company, Baise, 533000 Guangxi China
| | - Jutao Sun
- College of Tobacco Science, Henan Agricultural University, National Tobacco Cultivation & Physiology & Biochemistry Research Centre, Scientific Observation and Experiment Station of Henan, Ministry of Agriculture, Zhengzhou, 450002 China
| | - Tiezhao Yang
- College of Tobacco Science, Henan Agricultural University, National Tobacco Cultivation & Physiology & Biochemistry Research Centre, Scientific Observation and Experiment Station of Henan, Ministry of Agriculture, Zhengzhou, 450002 China
| | - Shixiao Xu
- College of Tobacco Science, Henan Agricultural University, National Tobacco Cultivation & Physiology & Biochemistry Research Centre, Scientific Observation and Experiment Station of Henan, Ministry of Agriculture, Zhengzhou, 450002 China
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37
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Young JA, Buchman M, Duran-Ortiz S, Kruse C, Bell S, Kopchick JJ, Berryman DE, List EO. Transcriptome profiling of insulin sensitive tissues from GH deficient mice following GH treatment. Pituitary 2021; 24:384-399. [PMID: 33433889 PMCID: PMC8122029 DOI: 10.1007/s11102-020-01118-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/19/2020] [Indexed: 11/30/2022]
Abstract
PURPOSE Most studies that have examined the transcriptional response to GH have been performed with a single tissue. Thus, the current study performed RNASeq across three insulin-sensitive tissues of GH-treated GH deficient (GHKO) mice. METHODS GHKO mice were injected with recombinant human GH (hGH) or vehicle daily for 5 days and adipose, liver, and muscle tissues were collected 4 h after the final injection. RNA was isolated from the tissues and sequenced. Genes that were differentially expressed between GH and vehicle treatments were further analyzed. Enrichment analysis and topology-aware pathway analysis were performed. RESULTS GHKO mice treated with hGH had expected phenotypic alterations, with increased body, fat, fluid, liver, and muscle mass, and increased serum IGF-1 and insulin. 55 Genes were differentially expressed in all three tissues, including the canonical GH targets Igf1, Igfals, and Cish. Enrichment analysis confirmed the canonical GH response in select tissues, such as cell proliferation, metabolism, and fibrosis. The JAK/STAT pathway was the only pathway significantly altered in all three tissues. CONCLUSIONS As expected, GH caused expression changes of many known target genes, although new candidate GH targets were identified. Liver and muscle appear to be more GH sensitive than adipose tissue due to the larger number of DEG and pathways significantly altered, but adipose still has a characteristic GH response. The diversity of changes uncovered in all three tissues after 5 days of GH treatment highlights the multiplicity of GH's effects in its target tissues.
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Affiliation(s)
- Jonathan A. Young
- Edison Biotechnology Institute, Ohio University, Athens, OH 45701, USA
- Department of Biomedical Sciences, Heritage College of Osteopathic Medicine, Ohio University, Athens, OH 45701, USA
| | - Mat Buchman
- Edison Biotechnology Institute, Ohio University, Athens, OH 45701, USA
| | | | - Colin Kruse
- Edison Biotechnology Institute, Ohio University, Athens, OH 45701, USA
| | - Stephen Bell
- Edison Biotechnology Institute, Ohio University, Athens, OH 45701, USA
| | - John J. Kopchick
- Edison Biotechnology Institute, Ohio University, Athens, OH 45701, USA
- Department of Biomedical Sciences, Heritage College of Osteopathic Medicine, Ohio University, Athens, OH 45701, USA
| | - Darlene E. Berryman
- Edison Biotechnology Institute, Ohio University, Athens, OH 45701, USA
- Department of Biomedical Sciences, Heritage College of Osteopathic Medicine, Ohio University, Athens, OH 45701, USA
- The Diabetes Institute at Ohio University, Ohio University, Athens, OH 45701, USA
- Indicates co-senior authors. Please send correspondence to Edward O. List, Edison Biotechnology Institute, Ohio University, Athens, OH 45701, USA.
| | - Edward O. List
- Edison Biotechnology Institute, Ohio University, Athens, OH 45701, USA
- Indicates co-senior authors. Please send correspondence to Edward O. List, Edison Biotechnology Institute, Ohio University, Athens, OH 45701, USA.
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38
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Scalise M, Torella M, Marino F, Ravo M, Giurato G, Vicinanza C, Cianflone E, Mancuso T, Aquila I, Salerno L, Nassa G, Agosti V, De Angelis A, Urbanek K, Berrino L, Veltri P, Paolino D, Mastroroberto P, De Feo M, Viglietto G, Weisz A, Nadal-Ginard B, Ellison-Hughes GM, Torella D. Atrial myxomas arise from multipotent cardiac stem cells. Eur Heart J 2021; 41:4332-4345. [PMID: 32330934 PMCID: PMC7735815 DOI: 10.1093/eurheartj/ehaa156] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 12/22/2019] [Accepted: 03/03/2020] [Indexed: 12/11/2022] Open
Abstract
Aims Cardiac myxomas usually develop in the atria and consist of an acid-mucopolysaccharide-rich myxoid matrix with polygonal stromal cells scattered throughout. These human benign tumours are a valuable research model because of the rarity of cardiac tumours, their clinical presentation and uncertain origin. Here, we assessed whether multipotent cardiac stem/progenitor cells (CSCs) give rise to atrial myxoma tissue. Methods and results Twenty-three myxomas were collected and analysed for the presence of multipotent CSCs. We detected myxoma cells positive for c-kit (c-kitpos) but very rare Isl-1 positive cells. Most of the c-kitpos cells were blood lineage-committed CD45pos/CD31pos cells. However, c-kitpos/CD45neg/CD31neg cardiac myxoma cells expressed stemness and cardiac progenitor cell transcription factors. Approximately ≤10% of the c-kitpos/CD45neg/CD31neg myxoma cells also expressed calretinin, a characteristic of myxoma stromal cells. In vitro, the c-kitpos/CD45neg/CD31neg myxoma cells secrete chondroitin-6-sulfate and hyaluronic acid, which are the main components of gelatinous myxoma matrix in vivo. In vitro, c-kitpos/CD45neg/CD31neg myxoma cells have stem cell properties being clonogenic, self-renewing, and sphere forming while exhibiting an abortive cardiac differentiation potential. Myxoma-derived CSCs possess a mRNA and microRNA transcriptome overall similar to normal myocardium-derived c-kitpos/CD45neg/CD31negCSCs , yet showing a relatively small and relevant fraction of dysregulated mRNA/miRNAs (miR-126-3p and miR-335-5p, in particular). Importantly, myxoma-derived CSCs but not normal myocardium-derived CSCs, seed human myxoma tumours in xenograft’s in immunodeficient NOD/SCID mice. Conclusion Myxoma-derived c-kitpos/CD45neg/CD31neg CSCs fulfill the criteria expected of atrial myxoma-initiating stem cells. The transcriptome of these cells indicates that they belong to or are derived from the same lineage as the atrial multipotent c-kitpos/CD45neg/CD31neg CSCs. Taken together the data presented here suggest that human myxomas could be the first-described CSC-related human heart disease. ![]()
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Affiliation(s)
- Mariangela Scalise
- Department of Experimental and Clinical Medicine, Molecular and Cellular Cardiology, Magna Graecia University, Viale Europa, 88100 Catanzaro, Italy
| | - Michele Torella
- Department of Translational Medical Sciences, AORN dei Colli/Monaldi Hospital, University of Campania "L. Vanvitelli", Via Leonardo Bianchi, 80131 Naples, Italy
| | - Fabiola Marino
- Department of Experimental and Clinical Medicine, Molecular and Cellular Cardiology, Magna Graecia University, Viale Europa, 88100 Catanzaro, Italy
| | - Maria Ravo
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", Laboratory of Molecular Medicine and Genomics, University of Salerno, Via Salvador Allende, 84081 Baronissi (Salerno), Italy.,Genomix4Life, Spin-Off of the Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry, University of Salerno, Via Salvador Allende, 84081 Baronissi (Salerno), Italy
| | - Giorgio Giurato
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", Laboratory of Molecular Medicine and Genomics, University of Salerno, Via Salvador Allende, 84081 Baronissi (Salerno), Italy.,Genomix4Life, Spin-Off of the Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry, University of Salerno, Via Salvador Allende, 84081 Baronissi (Salerno), Italy
| | - Carla Vicinanza
- Department of Experimental and Clinical Medicine, Molecular and Cellular Cardiology, Magna Graecia University, Viale Europa, 88100 Catanzaro, Italy
| | - Eleonora Cianflone
- Department of Experimental and Clinical Medicine, Molecular and Cellular Cardiology, Magna Graecia University, Viale Europa, 88100 Catanzaro, Italy.,Department of Medical and Surgical Sciences, Magna Graecia University, Viale Europa, 88100 Catanzaro, Italy
| | - Teresa Mancuso
- Department of Experimental and Clinical Medicine, Molecular and Cellular Cardiology, Magna Graecia University, Viale Europa, 88100 Catanzaro, Italy
| | - Iolanda Aquila
- Department of Experimental and Clinical Medicine, Molecular and Cellular Cardiology, Magna Graecia University, Viale Europa, 88100 Catanzaro, Italy
| | - Luca Salerno
- Department of Experimental and Clinical Medicine, Molecular and Cellular Cardiology, Magna Graecia University, Viale Europa, 88100 Catanzaro, Italy
| | - Giovanni Nassa
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", Laboratory of Molecular Medicine and Genomics, University of Salerno, Via Salvador Allende, 84081 Baronissi (Salerno), Italy
| | - Valter Agosti
- Department of Experimental and Clinical Medicine, Magna Graecia University, Viale Europa, 88100 Catanzaro, Italy
| | - Antonella De Angelis
- Department of Experimental and Clinical Medicine, Magna Graecia University, Viale Europa, 88100 Catanzaro, Italy
| | - Konrad Urbanek
- Department of Experimental and Clinical Medicine, Molecular and Cellular Cardiology, Magna Graecia University, Viale Europa, 88100 Catanzaro, Italy.,Department of Experimental Medicine, University of Campania "L. Vanvitelli", Via Santa Maria di Costantinopoli, 80138 Naples, Italy
| | - Liberato Berrino
- Department of Experimental Medicine, University of Campania "L. Vanvitelli", Via Santa Maria di Costantinopoli, 80138 Naples, Italy
| | - Pierangelo Veltri
- Department of Medical and Surgical Sciences, Magna Graecia University, Viale Europa, 88100 Catanzaro, Italy
| | - Donatella Paolino
- Department of Experimental and Clinical Medicine, Magna Graecia University, Viale Europa, 88100 Catanzaro, Italy
| | - Pasquale Mastroroberto
- Department of Experimental and Clinical Medicine, Magna Graecia University, Viale Europa, 88100 Catanzaro, Italy
| | - Marisa De Feo
- Department of Translational Medical Sciences, AORN dei Colli/Monaldi Hospital, University of Campania "L. Vanvitelli", Via Leonardo Bianchi, 80131 Naples, Italy
| | - Giuseppe Viglietto
- Department of Experimental and Clinical Medicine, Magna Graecia University, Viale Europa, 88100 Catanzaro, Italy
| | - Alessandro Weisz
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", Laboratory of Molecular Medicine and Genomics, University of Salerno, Via Salvador Allende, 84081 Baronissi (Salerno), Italy.,Genomix4Life, Spin-Off of the Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry, University of Salerno, Via Salvador Allende, 84081 Baronissi (Salerno), Italy
| | - Bernardo Nadal-Ginard
- Department of Experimental and Clinical Medicine, Molecular and Cellular Cardiology, Magna Graecia University, Viale Europa, 88100 Catanzaro, Italy
| | - Georgina M Ellison-Hughes
- Centre for Human and Applied Physiological Sciences and Centre for Stem Cells and Regenerative Medicine, School of Basic and Medical Biosciences, Faculty of Life Sciences & Medicine, King's College London, Guys Campus - Great Maze Pond rd, SE1 1UL London, UK
| | - Daniele Torella
- Department of Experimental and Clinical Medicine, Molecular and Cellular Cardiology, Magna Graecia University, Viale Europa, 88100 Catanzaro, Italy
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Abstract
Background Most insects are relatively short-lived, with a maximum lifespan of a few weeks, like the aging model organism, the fruit-fly Drosophila melanogaster. By contrast, the queens of many social insects (termites, ants and some bees) can live from a few years to decades. This makes social insects promising models in aging research providing insights into how a long reproductive life can be achieved. Yet, aging studies on social insect reproductives are hampered by a lack of quantitative data on age-dependent survival and time series analyses that cover the whole lifespan of such long-lived individuals. We studied aging in queens of the drywood termite Cryptotermes secundus by determining survival probabilities over a period of 15 years and performed transcriptome analyses for queens of known age that covered their whole lifespan. Results The maximum lifespan of C. secundus queens was 13 years, with a median maximum longevity of 11.0 years. Time course and co-expression network analyses of gene expression patterns over time indicated a non-gradual aging pattern. It was characterized by networks of genes that became differentially expressed only late in life, namely after ten years, which associates well with the median maximum lifespan for queens. These old-age gene networks reflect processes of physiological upheaval. We detected strong signs of stress, decline, defense and repair at the transcriptional level of epigenetic control as well as at the post-transcriptional level with changes in transposable element activity and the proteostasis network. The latter depicts an upregulation of protein degradation, together with protein synthesis and protein folding, processes which are often down-regulated in old animals. The simultaneous upregulation of protein synthesis and autophagy is indicative of a stress-response mediated by the transcription factor cnc, a homolog of human nrf genes. Conclusions Our results show non-linear senescence with a rather sudden physiological upheaval at old-age. Most importantly, they point to a re-wiring in the proteostasis network and stress as part of the aging process of social insect queens, shortly before queens die. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07649-4.
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Affiliation(s)
- José Manuel Monroy Kuhn
- Department of Evolutionary Biology & Ecology, Institute of Biology I, Albert Ludwig University of Freiburg, Hauptstr. 1, D-79104, Freiburg (i. Brsg.), Germany. .,Computational Discovery Research, Institute for Diabetes and Obesity, Helmholtz Zentrum München, Ingolstaedter Landstr. 1, D-85764, Neuherberg, Germany.
| | - Karen Meusemann
- Department of Evolutionary Biology & Ecology, Institute of Biology I, Albert Ludwig University of Freiburg, Hauptstr. 1, D-79104, Freiburg (i. Brsg.), Germany.,Australian National Insect Collection, CSIRO National Research Collections Australia, Clunies Ross Street, Acton, ACT 2601, Canberra, Australia
| | - Judith Korb
- Department of Evolutionary Biology & Ecology, Institute of Biology I, Albert Ludwig University of Freiburg, Hauptstr. 1, D-79104, Freiburg (i. Brsg.), Germany.
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40
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Heath-Heckman E, Yoo S, Winchell C, Pellegrino M, Angstadt J, Lammardo VB, Bautista D, De-Miguel FF, Weisblat D. Transcriptional profiling of identified neurons in leech. BMC Genomics 2021; 22:215. [PMID: 33765928 PMCID: PMC7992859 DOI: 10.1186/s12864-021-07526-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 09/03/2020] [Accepted: 03/11/2021] [Indexed: 12/13/2022] Open
Abstract
Background While leeches in the genus Hirudo have long been models for neurobiology, the molecular underpinnings of nervous system structure and function in this group remain largely unknown. To begin to bridge this gap, we performed RNASeq on pools of identified neurons of the central nervous system (CNS): sensory T (touch), P (pressure) and N (nociception) neurons; neurosecretory Retzius cells; and ganglia from which these four cell types had been removed. Results Bioinformatic analyses identified 3565 putative genes whose expression differed significantly among the samples. These genes clustered into 9 groups which could be associated with one or more of the identified cell types. We verified predicted expression patterns through in situ hybridization on whole CNS ganglia, and found that orthologous genes were for the most part similarly expressed in a divergent leech genus, suggesting evolutionarily conserved roles for these genes. Transcriptional profiling allowed us to identify candidate phenotype-defining genes from expanded gene families. Thus, we identified one of eight hyperpolarization-activated cyclic-nucleotide gated (HCN) channels as a candidate for mediating the prominent sag current in P neurons, and found that one of five inositol triphosphate receptors (IP3Rs), representing a sub-family of IP3Rs absent from vertebrate genomes, is expressed with high specificity in T cells. We also identified one of two piezo genes, two of ~ 65 deg/enac genes, and one of at least 16 transient receptor potential (trp) genes as prime candidates for involvement in sensory transduction in the three distinct classes of leech mechanosensory neurons. Conclusions Our study defines distinct transcriptional profiles for four different neuronal types within the leech CNS, in addition to providing a second ganglionic transcriptome for the species. From these data we identified five gene families that may facilitate the sensory capabilities of these neurons, thus laying the basis for future work leveraging the strengths of the leech system to investigate the molecular processes underlying and linking mechanosensation, cell type specification, and behavior. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07526-0.
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Affiliation(s)
- Elizabeth Heath-Heckman
- Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA, USA. .,Current address: Department of Integrative Biology, Michigan State University, East Lansing, MI, USA.
| | - Shinja Yoo
- Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Christopher Winchell
- Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Maurizio Pellegrino
- Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA, USA.,Current address: Invitae Corporation, San Francisco, CA, USA
| | - James Angstadt
- Department of Biology, Siena College, Loudonville, New York, NY, USA
| | | | - Diana Bautista
- Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Francisco F De-Miguel
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - David Weisblat
- Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
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41
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Li W, Song P, Xin Y, Kuang Z, Liu Q, Ge F, Zhu L, Zhang X, Tao Y, Zhang W. The Effects of Luminescent CdSe Quantum Dot-Functionalized Antimicrobial Peptides Nanoparticles on Antibacterial Activity and Molecular Mechanism. Int J Nanomedicine 2021; 16:1849-1867. [PMID: 33707943 PMCID: PMC7943780 DOI: 10.2147/ijn.s295928] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 02/15/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND With the development of bacterial resistance, the range of effective antibiotics is increasingly becoming more limited. The effective use of nanoscale antimicrobial peptides (AP) in therapeutic and diagnostic methods is a strategy for new antibiotics. METHODS Combining both AP and cadmium selenide (CdSe) into a composite material may result in a reagent with novel properties, such as enhanced antibacterial activity, fluorescence and favorable stability in aqueous solution. RESULTS AP-loaded CdSe NPs (AP-CdSe NPs) showed strong antibacterial activity against multidrug-resistant (MDR) Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus) in vitro and in vivo. Colony-forming unit (CFU) and minimum inhibitory concentration (MIC) assays showed that AP-CdSe NPs have highly effective antibacterial activity. The quantitative analysis of apoptosis by flow cytometry analysis further confirmed that MDR E. coli and S. aureus treated with AP-CdSe NPs had death rates of 98.76% and 99.13%, respectively. Also, AP-CdSe NPs was found to inhibit bacterial activity in an in vivo bacteremia model in mice infected with S. aureus. In addition, the antibacterial mechanism of AP-CdSe NPs was determined by RNA sequencing analysis. Gene ontology (GO) analysis and Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis revealed the molecular mechanism of the antibacterial effect of AP-CdSe NPs. Importantly, histopathology analysis, and hematological toxicity analysis indicated that AP-CdSe NPs had few side effects. CONCLUSION These results demonstrate that AP loaded on CdSe NPs had a higher water solubility, bioavailability and antibacterial effect compared with raw AP. This study reports findings that are helpful for the design and development of antibacterial treatment strategies based on AP.
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Affiliation(s)
- Wanzhen Li
- School of Biological and Food Engineering, Anhui Polytechnic University, Wuhu, Anhui, 241000, People's Republic of China
| | - Ping Song
- School of Biological and Food Engineering, Anhui Polytechnic University, Wuhu, Anhui, 241000, People's Republic of China
| | - Ying Xin
- School of Biological and Food Engineering, Anhui Polytechnic University, Wuhu, Anhui, 241000, People's Republic of China
| | - Zhao Kuang
- School of Biological and Food Engineering, Anhui Polytechnic University, Wuhu, Anhui, 241000, People's Republic of China
| | - Qin Liu
- School of Biological and Food Engineering, Anhui Polytechnic University, Wuhu, Anhui, 241000, People's Republic of China
| | - Fei Ge
- School of Biological and Food Engineering, Anhui Polytechnic University, Wuhu, Anhui, 241000, People's Republic of China
| | - Longbao Zhu
- School of Biological and Food Engineering, Anhui Polytechnic University, Wuhu, Anhui, 241000, People's Republic of China
| | - Xuguang Zhang
- Bankpeptide Biological Technology Company, Hefei, Anhui, 230031, People's Republic of China
| | - Yugui Tao
- School of Biological and Food Engineering, Anhui Polytechnic University, Wuhu, Anhui, 241000, People's Republic of China
| | - Weiwei Zhang
- School of Biological and Food Engineering, Anhui Polytechnic University, Wuhu, Anhui, 241000, People's Republic of China
- Bankpeptide Biological Technology Company, Hefei, Anhui, 230031, People's Republic of China
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42
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Maulding ND, Kavanagh D, Zimmerman K, Coppola G, Carpenter TO, Jue NK, Braddock DT. Genetic pathways disrupted by ENPP1 deficiency provide insight into mechanisms of osteoporosis, osteomalacia, and paradoxical mineralization. Bone 2021; 142:115656. [PMID: 32980560 PMCID: PMC7744330 DOI: 10.1016/j.bone.2020.115656] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 09/17/2020] [Accepted: 09/18/2020] [Indexed: 12/16/2022]
Abstract
Ectonucleotide phosphatase/phosphodiesterase 1 (ENPP1) deficiency results in either lethal arterial calcifications ('Generalized Arterial Calcification of Infancy' - GACI), phosphate wasting rickets ('Autosomal Recessive Hypophosphatemic Rickets type 2' - ARHR2), early onset osteoporosis, or progressive spinal rigidity ('Ossification of the Posterior Longitudinal Ligament' - OPLL). As ENPP1 generates a strong endogenous mineralization inhibitor - extracellular pyrophosphate (PPi) - ENPP1 deficiency should not result in reduced bone volume, and therefore the mechanism ENPP1 associated osteoporosis is not apparent given current understanding of the enzyme's function. To investigate genetic pathways driving the skeletal phenotype of ENPP1 deficiency we compared gene expression in Enpp1asj/asj mice and WT sibling pairs by RNAseq and qPCR in whole bones, and in the liver and kidney by qPCR, directly correlating gene expression with measures of bone microarchitectural and biomechanical phenotypes. Unbiased analysis of the differentially expressed genes compared to relevant human disease phenotypes revealed that Enpp1asj/asj mice exhibit strong signatures of osteoporosis, ARHR2 and OPLL. We found that ENPP1 deficient mice exhibited reduced gene transcription of Wnt ligands in whole bone and increased transcription of soluble Wnt inhibitors in the liver and kidney, suggestive of multiorgan inhibition of Wnt activity. Consistent with Wnt suppression in bone, Collagen gene pathways in bone were significantly decreased and Fgf23 was significantly increased, all of which directly correlated with bone microarchitectural defects and fracture risk in Enpp1asj/asj mice. Moreover, the bone findings in 10-week old mice correlated with Enpp1 transcript counts but not plasma [PPi], suggesting that the skeletal phenotype at 10 weeks is driven by catalytically independent ENPP1 function. In contrast, the bone findings in 23-week Enpp1asj/asj mice strongly correlated with plasma PPi, suggesting that chronically low PPi drives the skeletal phenotype in older mice. Finally, correlation between Enpp1 and Fgf23 transcription suggested ENPP1 regulation of Fgf23, which we confirmed by dosing Enpp1asj/asj mice with soluble ENPP1-Fc and observing suppression of intact plasma FGF23 and ALP. In summary, our findings suggest that osteoporosis associated with ENPP1 deficiency involves the suppression of Wnt via catalytically independent Enpp1 pathways, and validates Enpp1asj/asj mice as tools to better understand OPLL and Paradoxical Mineralization Disorders.
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Affiliation(s)
- Nathan D Maulding
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Dillon Kavanagh
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Kristin Zimmerman
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Gianfilippo Coppola
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Thomas O Carpenter
- Department of Pediatrics at Yale University School of Medicine, New Haven, CT 06510, USA
| | - Nathaniel K Jue
- Department of Biology and Chemistry, California State University, Monterey Bay, CA, USA.
| | - Demetrios T Braddock
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06510, USA.
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43
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Gorgun C, Ceresa D, Lesage R, Villa F, Reverberi D, Balbi C, Santamaria S, Cortese K, Malatesta P, Geris L, Quarto R, Tasso R. Dissecting the effects of preconditioning with inflammatory cytokines and hypoxia on the angiogenic potential of mesenchymal stromal cell (MSC)-derived soluble proteins and extracellular vesicles (EVs). Biomaterials 2020; 269:120633. [PMID: 33453634 DOI: 10.1016/j.biomaterials.2020.120633] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [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: 08/18/2020] [Revised: 11/30/2020] [Accepted: 12/22/2020] [Indexed: 02/07/2023]
Abstract
Mesenchymal stromal cells (MSCs) are characterized by a regulatory phenotype and respond promptly to the environmental signals modulating their secretory activity. An appropriate preconditioning may induce MSCs to release secretomes with an enhanced regenerative potential. However, it fails to take into account that secretomes are composed by both soluble factors and extracellular vesicles (EVs), whose functions could be altered differently by the preconditioning approach. Here we demonstrate that the MSC secretome is strongly modulated by the simultaneous stimulation with hypoxia and pro-inflammatory cytokines, used to mimic the harsh environment present at the site of injury. We observed that the environmental variations strongly influenced the angiogenic potential of the different secretome fractions. Upon inflammation, the pro-angiogenic capacity of the soluble component of the MSC secretome was strongly inhibited, regardless of the oxygen level, while the EV-encapsulated component was not significantly affected by the inflammatory stimuli. These effects were accompanied by the modulation of the secreted proteins. On one hand, inflammation-activated MSCs release proteins mainly involved in the interaction with innate immune cells and in tissue remodeling/repair; on the other hand, when MSCs are not exposed to an inflamed environment, they respond to the different oxygen levels modulating the expression of proteins involved in the angiogenic process. The cargo content (in terms of miRNAs) of the corresponding EV fractions was less sensitive to the influence of the external stimuli. Our findings suggest that the therapeutic efficacy of MSC-based therapies could be enhanced by selecting the appropriate preconditioning approach and carefully discriminating its effects on the different secretome components.
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Affiliation(s)
- Cansu Gorgun
- Department of Experimental Medicine (DIMES), University of Genova, Genova, Italy; U.O. Cellular Oncology, IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Davide Ceresa
- U.O. Cellular Oncology, IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Raphaelle Lesage
- Prometheus, Division of Skeletal Tissue Engineering, KU Leuven, Leuven, Belgium; Biomechanics Section, Department of Mechanical Engineering, KU Leuven, Leuven, Belgium
| | - Federico Villa
- U.O. Cellular Oncology, IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Daniele Reverberi
- U.O. Molecular Pathology, IRCCS Ospedale Policlinico, San Martino, Genova, Italy
| | - Carolina Balbi
- Laboratory of Cellular and Molecular Cardiology, Cardiocentro Ticino Foundation, 6900, Lugano, Switzerland
| | - Sara Santamaria
- Department of Experimental Medicine (DIMES), University of Genova, Genova, Italy
| | - Katia Cortese
- Department of Experimental Medicine (DIMES), University of Genova, Genova, Italy
| | - Paolo Malatesta
- Department of Experimental Medicine (DIMES), University of Genova, Genova, Italy; U.O. Cellular Oncology, IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Liesbet Geris
- Prometheus, Division of Skeletal Tissue Engineering, KU Leuven, Leuven, Belgium; Biomechanics Section, Department of Mechanical Engineering, KU Leuven, Leuven, Belgium; Biomechanics Research Unit, GIGA in Silico Medicine, University of Liège, Liège, Belgium
| | - Rodolfo Quarto
- Department of Experimental Medicine (DIMES), University of Genova, Genova, Italy; U.O. Cellular Oncology, IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Roberta Tasso
- Department of Experimental Medicine (DIMES), University of Genova, Genova, Italy; U.O. Cellular Oncology, IRCCS Ospedale Policlinico San Martino, Genova, Italy.
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44
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Hathy E, Szabó E, Varga N, Erdei Z, Tordai C, Czehlár B, Baradits M, Jezsó B, Koller J, Nagy L, Molnár MJ, Homolya L, Nemoda Z, Apáti Á, Réthelyi JM. Investigation of de novo mutations in a schizophrenia case-parent trio by induced pluripotent stem cell-based in vitro disease modeling: convergence of schizophrenia- and autism-related cellular phenotypes. Stem Cell Res Ther 2020; 11:504. [PMID: 33246498 PMCID: PMC7694414 DOI: 10.1186/s13287-020-01980-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 09/23/2020] [Accepted: 10/18/2020] [Indexed: 12/30/2022] Open
Abstract
Background De novo mutations (DNMs) have been implicated in the etiology of schizophrenia (SZ), a chronic debilitating psychiatric disorder characterized by hallucinations, delusions, cognitive dysfunction, and decreased community functioning. Several DNMs have been identified by examining SZ cases and their unaffected parents; however, in most cases, the biological significance of these mutations remains elusive. To overcome this limitation, we have developed an approach of using induced pluripotent stem cell (iPSC) lines from each member of a SZ case-parent trio, in order to investigate the effects of DNMs in cellular progenies of interest, particularly in dentate gyrus neuronal progenitors. Methods We identified a male SZ patient characterized by early disease onset and negative symptoms, who is a carrier of 3 non-synonymous DNMs in genes LRRC7, KHSRP, and KIR2DL1. iPSC lines were generated from his and his parents’ peripheral blood mononuclear cells using Sendai virus-based reprogramming and differentiated into neuronal progenitor cells (NPCs) and hippocampal dentate gyrus granule cells. We used RNASeq to explore transcriptomic differences and calcium (Ca2+) imaging, cell proliferation, migration, oxidative stress, and mitochondrial assays to characterize the investigated NPC lines. Results NPCs derived from the SZ patient exhibited transcriptomic differences related to Wnt signaling, neuronal differentiation, axonal guidance and synaptic function, and decreased Ca2+ reactivity to glutamate. Moreover, we could observe increased cellular proliferation and alterations in mitochondrial quantity and morphology. Conclusions The approach of reprograming case-parent trios represents an opportunity for investigating the molecular effects of disease-causing mutations and comparing these in cell lines with reduced variation in genetic background. Our results are indicative of a partial overlap between schizophrenia and autism-related phenotypes in the investigated family. Limitations Our study investigated only one family; therefore, the generalizability of findings is limited. We could not derive iPSCs from two other siblings to test for possible genetic effects in the family that are not driven by DNMs. The transcriptomic and functional assays were limited to the NPC stage, although these variables should also be investigated at the mature neuronal stage.
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Affiliation(s)
- Edit Hathy
- National Brain Research Project (NAP) Molecular Psychiatry Research Group, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary
| | - Eszter Szabó
- Molecular Cell Biology Research Group, Institute of Enzymology, Research Center for Natural Sciences, 1117 Magyar tudósok körútja 2, Budapest, Hungary
| | - Nóra Varga
- Molecular Cell Biology Research Group, Institute of Enzymology, Research Center for Natural Sciences, 1117 Magyar tudósok körútja 2, Budapest, Hungary
| | - Zsuzsa Erdei
- Molecular Cell Biology Research Group, Institute of Enzymology, Research Center for Natural Sciences, 1117 Magyar tudósok körútja 2, Budapest, Hungary
| | - Csongor Tordai
- National Brain Research Project (NAP) Molecular Psychiatry Research Group, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary
| | - Boróka Czehlár
- National Brain Research Project (NAP) Molecular Psychiatry Research Group, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary
| | - Máté Baradits
- National Brain Research Project (NAP) Molecular Psychiatry Research Group, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary
| | - Bálint Jezsó
- Molecular Cell Biology Research Group, Institute of Enzymology, Research Center for Natural Sciences, 1117 Magyar tudósok körútja 2, Budapest, Hungary
| | - Júlia Koller
- Institute of Rare Disorders and Genomic Medicine, Semmelweis University, Budapest, Hungary
| | - László Nagy
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Mária Judit Molnár
- Institute of Rare Disorders and Genomic Medicine, Semmelweis University, Budapest, Hungary
| | - László Homolya
- Molecular Cell Biology Research Group, Institute of Enzymology, Research Center for Natural Sciences, 1117 Magyar tudósok körútja 2, Budapest, Hungary
| | - Zsófia Nemoda
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary
| | - Ágota Apáti
- Molecular Cell Biology Research Group, Institute of Enzymology, Research Center for Natural Sciences, 1117 Magyar tudósok körútja 2, Budapest, Hungary.
| | - János M Réthelyi
- National Brain Research Project (NAP) Molecular Psychiatry Research Group, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary. .,Department of Psychiatry and Psychotherapy, Semmelweis University, Balassa utca 6, Budapest, 1083, Hungary.
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45
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Domenichiello AF, Sapio MR, Loydpierson AJ, Maric D, Goto T, Horowitz MS, Keyes GS, Yuan ZX, Majchrzak-Hong SF, Mannes AJ, Iadarola MJ, Ramsden CE. Molecular Pathways Linking Oxylipins to Nociception in Rats. J Pain 2021; 22:275-99. [PMID: 33031942 DOI: 10.1016/j.jpain.2020.09.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/31/2020] [Accepted: 09/24/2020] [Indexed: 12/19/2022]
Abstract
Oxylipins are lipid peroxidation products that participate in nociceptive, inflammatory, and vascular responses to injury. Effects of oxylipins depend on tissue-specific differences in accumulation of precursor polyunsaturated fatty acids and the expression of specific enzymes to transform the precursors. The study of oxylipins in nociception has presented technical challenges leading to critical knowledge gaps in the way these molecules operate in nociception. We applied a systems-based approach to characterize oxylipin precursor fatty acids, and expression of genes coding for proteins involved in biosynthesis, transport, signaling and inactivation of pro- and antinociceptive oxylipins in pain circuit tissues. We further linked these pathways to nociception by demonstrating intraplantar carrageenan injection induced gene expression changes in oxylipin biosynthetic pathways. We determined functional-biochemical relevance of the proposed pathways in rat hind paw and dorsal spinal cord by measuring basal and stimulated levels of oxylipins throughout the time-course of carrageenan-induced inflammation. Finally, when oxylipins were administered by intradermal injection we observed modulation of nociceptive thermal hypersensitivity, providing a functional-behavioral link between oxylipins, their molecular biosynthetic pathways, and involvement in pain and nociception. Together, these findings advance our understanding of molecular lipidomic systems linking oxylipins and their precursors to nociceptive and inflammatory signaling pathways in rats. PERSPECTIVE: We applied a systems approach to characterize molecular pathways linking precursor lipids and oxylipins to nociceptive signaling. This systematic, quantitative evaluation of the molecular pathways linking oxylipins to nociception provides a framework for future basic and clinical research investigating the role of oxylipins in pain.
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Mevy JP, Loriod B, Liu X, Corre E, Torres M, Büttner M, Haguenauer A, Reiter IM, Fernandez C, Gauquelin T. Response of Downy Oak (Quercus pubescens Willd.) to Climate Change: Transcriptome Assembly, Differential Gene Analysis and Targeted Metabolomics. Plants (Basel) 2020; 9:E1149. [PMID: 32899727 DOI: 10.3390/plants9091149] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 08/20/2020] [Accepted: 09/01/2020] [Indexed: 01/15/2023]
Abstract
Global change scenarios in the Mediterranean basin predict a precipitation reduction within the coming hundred years. Therefore, increased drought will affect forests both in terms of adaptive ecology and ecosystemic services. However, how vegetation might adapt to drought is poorly understood. In this report, four years of climate change was simulated by excluding 35% of precipitation above a downy oak forest. RNASeq data allowed us to assemble a genome-guided transcriptome. This led to the identification of differentially expressed features, which was supported by the characterization of target metabolites using a metabolomics approach. We provided 2.5 Tb of RNASeq data and the assembly of the first genome guided transcriptome of Quercus pubescens. Up to 5724 differentially expressed transcripts were obtained; 42 involved in plant response to drought. Transcript set enrichment analysis showed that drought induces an increase in oxidative pressure that is mitigated by the upregulation of ubiquitin-like protein protease, ferrochelatase, oxaloacetate decarboxylase and oxo-acid-lyase activities. Furthermore, the downregulation of auxin biosynthesis and transport, carbohydrate storage metabolism were observed as well as the concomitant accumulation of metabolites, such as oxalic acid, malate and isocitrate. Our data suggest that early metabolic changes in the resistance of Q. pubescens to drought involve a tricarboxylic acid (TCA) cycle shunt through the glyoxylate pathway, galactose metabolism by reducing carbohydrate storage and increased proteolytic activity.
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Paredes J, Zabaleta J, Garai J, Ji P, Imtiaz S, Spagnardi M, Alvarado J, Li L, Akadri M, Barrera K, Munoz-Sagastibelza M, Gupta R, Alshal M, Agaronov M, Talus H, Wang X, Carethers JM, Williams JL, Martello LA. Immune-Related Gene Expression and Cytokine Secretion Is Reduced Among African American Colon Cancer Patients. Front Oncol 2020; 10:1498. [PMID: 32983990 PMCID: PMC7492388 DOI: 10.3389/fonc.2020.01498] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [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: 11/18/2019] [Accepted: 07/13/2020] [Indexed: 12/11/2022] Open
Abstract
Background: Colorectal cancer is the third most deadly cancer among African Americans (AA). When compared to Caucasian Americans (CA), AA present with more advanced disease and lower survival rates. Here, we investigated if differences in tumor immunology could be contributive to disparities observed between these populations. Methods: We examined gene expression of tumor and non-tumor adjacent tissues from AA and CA by whole transcriptome sequencing, and generated scores for immune cell populations by NanoString. In addition, we utilized “The Cancer Genome Atlas” (TCGA) database from AA and CA as a validation cohort. Finally, we measured the secretion of cytokines characteristic of effector T helper cell (Th) subsets by ELISA using plasma from each AA and CA participant. Results: Colon tumors from AA patients showed significant fold-change increase in gene expression when compared to CA for FOXP3 (6.22 vs. 3.22), IL1B (103 vs. 11.4) and IL8 (220 vs. 28.9) (p < 0.05). In contrast, among CA we observed statistically higher gene expression of markers associated with antitumor activity such as GZMB (Granzyme B), IFNG and the immunotherapy targets PDL1 (CD274) and CTLA4 (p < 0.05). TCGA data validated our observed higher gene expression of GZMB and PDL1 in CA patients when compared to AA. Notably, our observations on immune cell populations show that AA tumors have significantly higher number of exhausted CD8+ cells (p < 0.01), mast cells (p < 0.02) and increased T regulatory cells when compared to CA. AA colon cancer patients differed from CA in cytokine production patterns in plasma (i.e., reduced IL-12). Conclusions: Our study demonstrates significant differences of the immunological profiles of colon tumors from AA compared to CA that suggest a deficiency of appropriate immune defense mechanisms in terms of gene expression, recruitment of immune cells and systemic secretion of cytokines. As such, these immune differences could be mitigated through population-specific therapeutic approaches.
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Affiliation(s)
- Jenny Paredes
- Division of Gastroenterology and Hepatology, Department of Medicine, SUNY Downstate Medical Center, Brooklyn, NY, United States
| | - Jovanny Zabaleta
- Department of Pediatrics, Louisiana State University Health Sciences Center, New Orleans, LA, United States.,Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Jone Garai
- Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Ping Ji
- Department of Family, Population and Preventive Medicine, Stony Brook University, Stony Brook, NY, United States
| | - Sayed Imtiaz
- Department of Surgery, SUNY Downstate Medical Center, Brooklyn, NY, United States
| | - Marzia Spagnardi
- Division of Gastroenterology and Hepatology, Department of Medicine, SUNY Downstate Medical Center, Brooklyn, NY, United States
| | - Joussette Alvarado
- Department of Genetics, Louisiana State University Health Sciences Center, Loyola University New Orleans, New Orleans, LA, United States
| | - Li Li
- Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Mubarak Akadri
- Division of Gastroenterology and Hepatology, Department of Medicine, SUNY Downstate Medical Center, Brooklyn, NY, United States
| | - Kaylene Barrera
- Department of Surgery, SUNY Downstate Medical Center, Brooklyn, NY, United States
| | - Maria Munoz-Sagastibelza
- Division of Gastroenterology and Hepatology, Department of Medicine, SUNY Downstate Medical Center, Brooklyn, NY, United States
| | - Raavi Gupta
- Department of Pathology, SUNY Downstate Medical Center, Brooklyn, NY, United States
| | - Mohamed Alshal
- Department of Pathology, SUNY Downstate Medical Center, Brooklyn, NY, United States
| | - Maksim Agaronov
- Department of Pathology, Kings County Hospital, Brooklyn, NY, United States
| | - Henry Talus
- Department of Surgery, Kings County Hospital, Brooklyn, NY, United States
| | - Xuefeng Wang
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, United States
| | - John M Carethers
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Jennie L Williams
- Department of Family, Population and Preventive Medicine, Stony Brook University, Stony Brook, NY, United States
| | - Laura A Martello
- Division of Gastroenterology and Hepatology, Department of Medicine, SUNY Downstate Medical Center, Brooklyn, NY, United States
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48
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Sasidharan Nair V, Saleh R, Toor SM, Alajez NM, Elkord E. Transcriptomic Analyses of Myeloid-Derived Suppressor Cell Subsets in the Circulation of Colorectal Cancer Patients. Front Oncol 2020; 10:1530. [PMID: 32984004 PMCID: PMC7492613 DOI: 10.3389/fonc.2020.01530] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 06/10/2020] [Accepted: 07/16/2020] [Indexed: 12/24/2022] Open
Abstract
Myeloid-derived suppressor cells (MDSCs) promote tumor immune evasion and favor tumorigenesis by activating various tumor-promoting downstream signals. MDSC expansion is evident in the circulation and tumor microenvironment of many solid tumors including colorectal cancer (CRC). We have recently reported the transcriptomic profiles of tumor-infiltrating MDSCs in CRC patients and uncovered pathways, which could potentially assist tumor progression. In this study, we sorted different subsets of circulating MDSCs in CRC patients and investigated their transcriptomic profiles in order to disclose pathways, which could potentially contribute to disease progression. The sorted subsets included polymorphonuclear/granulocytic MDSCs (PMN-MDSCs), immature MDSCs (I-MDSCs), and monocytic MDSCs (M-MDSCs). Our functional annotation analyses revealed that multiple pathways including DNA damage-, chemotaxis-, apoptosis-, mitogen-activated protein kinase-, transforming growth factor β-, and myeloid differentiation–related transcripts were higher in PMN-MDSCs, compared with monocytic antigen-presenting cells (APCs) or I-MDSCs. Furthermore, genes related to Janus kinase (JAK)–signal transducer and activator of transcription (STAT) were also elevated in PMN-MDSCs. These data suggest that upregulation of JAK-STAT pathway could trigger multiple downstream targets in PMN-MDSCs, which favor tumor progression. Additionally, we found that pathways including phosphatidyl inositol 3-kinase (PI3K), interleukin 6, and TGF-β in M-MDSCs and cell cycle–related pathways in I-MDSCs were upregulated, compared with monocytic APCs. Moreover, acetylation-related genes were upregulated in both PMN-MDSCs and M-MDSCs. This latter finding implicates that epigenetic modifications could also play a role in the regulation of multiple tumor-promoting genes in PMN-MDSCs and M-MDSCs. Taken together, this study reveals various signaling pathways, which regulate the function of MDSC subsets in the circulation of CRC patients. However, functional studies are warranted to support these findings.
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Affiliation(s)
- Varun Sasidharan Nair
- Cancer Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar
| | - Reem Saleh
- Cancer Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar
| | - Salman M Toor
- Cancer Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar
| | - Nehad M Alajez
- Cancer Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar
| | - Eyad Elkord
- Cancer Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar
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49
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Mironov KS, Shumskaya M, Los DA. Construction of prokaryotic strand-specific primary-transcripts saturated RNASeq library by controlled heat magnesium-dependent mRNA degradation. Biochimie 2020; 177:63-67. [PMID: 32805305 DOI: 10.1016/j.biochi.2020.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 06/05/2020] [Revised: 07/26/2020] [Accepted: 08/02/2020] [Indexed: 02/01/2023]
Abstract
The main limiting factors for RNA-Seq analysis are quality and quantity of the isolated mRNA. In prokaryotes, the proportion of messenger RNA to total RNA is rather low. Therefore, the main strategy of library preparation for sequencing is mRNA enrichment. Ribosomal and transfer RNAs, both monophosphorylated at the 5'-ends, are the major fractions of total RNA, while the bulk of primary transcripts is triphosphorylated at the 5'-teminus. Due to its low molecular weight, transfer RNA could be easily removed by a quick precipitation in LiCl solution. Ribosomal RNA may be degraded enzymatically by 5'-end terminal exonuclease XRN-1. These steps allow enriching samples in mRNA during the first stages of RNA-Seq library preparation. The desired level of fragmentation of enriched mRNA necessary for the 2nd generation sequencing can be controlled by the duration of incubation at elevated temperatures in the presence of Mg2+-ions. Here, we describe a simple protocol for construction of the primary prokaryotic mRNA-saturated library without long depletion procedures.
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Affiliation(s)
- Kirill S Mironov
- Department of Molecular Biosystems, K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya Street 35, 127276, Moscow, Russia.
| | - Maria Shumskaya
- Department of Biology, School of Natural Sciences, Kean University, 1000 Morris Ave, Union, NJ, 07083, USA
| | - Dmitry A Los
- Department of Molecular Biosystems, K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya Street 35, 127276, Moscow, Russia
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50
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Agarwal D, Gireesh-Babu P, Pavan-Kumar A, Koringa P, Joshi CG, Chaudhari A. Transcriptome analysis of Clarias magur brain and gonads suggests neuro-endocrine inhibition of milt release from captive GnRH-induced males. Genomics 2020; 112:4041-4052. [PMID: 32650102 DOI: 10.1016/j.ygeno.2020.07.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 05/04/2020] [Revised: 06/18/2020] [Accepted: 07/03/2020] [Indexed: 10/24/2022]
Abstract
Transcriptome analysis of Clarias magur brain and gonads at preparatory, mature, 6 and 16 h post-GnRH injection (hpi) stages yielded 9.5 GB data with 39,738 contigs. Sequences of 45 reproductive genes were identified for the first time in C. magur along with unique and differentially expressed genes. The expression of 20 genes was validated by qRT-PCR. Upregulation of Cyp11A1, Cyp17A1 and FTZF1 genes in the 16hpi testis accompanied by the 17β-HSD3 expression indicates testosterone (T) synthesis in response to LH surge, while reduced expression of CYP11B1 suggests a high T: 11-KT ratio. It is evident by the gene expression analysis that the inhibitory neurotransmitter GABA, altered T: 11-KT, increased testicular bile acids, and oxytocin-like neuropeptide in the male brain, appear to be involved in arresting the pulsatile motion of testicular smooth muscles. The work generates important leads for an effective induced breeding strategy for silurid catfish.
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Affiliation(s)
- Deepak Agarwal
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Fisheries Education, Mumbai, India
| | - P Gireesh-Babu
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Fisheries Education, Mumbai, India
| | - A Pavan-Kumar
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Fisheries Education, Mumbai, India
| | - Prakash Koringa
- Animal Biotechnology Department, Anand Agricultural University, Anand, India
| | - C G Joshi
- Animal Biotechnology Department, Anand Agricultural University, Anand, India
| | - Aparna Chaudhari
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Fisheries Education, Mumbai, India.
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