632: Analysis of multiple gene co-expression networks identifies CHURC1, GZF1, and RPL15 as negative effectors of CFTR biogenesis and ΔF508-CFTR rescue

Abstract Background We previously reported that expression of a miR-138 mimic or knockdown of SIN3A in primary cultures of cystic fibrosis (CF) airway epithelia increased ΔF508-CFTR mRNA and protein levels, and partially restored CFTR-dependent chloride transport. Global mRNA transcript profiling in ΔF508-CFBE cells treated with miR-138 mimic or SIN3A siRNA identified two genes, SYVN1 and NEDD8, whose inhibition significantly increased ΔF508-CFTR trafficking, maturation, and function. Little is known regarding the dynamic changes in the CFTR gene network during such rescue events. We hypothesized that analysis of condition-specific gene networks from transcriptomic data characterizing ΔF508-CFTR rescue could help identify dynamic gene modules associated with CFTR biogenesis. Methods We applied a computational method, termed M-module, to analyze multiple gene networks, each of which exhibited differential activity compared to a baseline condition. In doing so, we identified both unique and shared gene pathways across multiple differential networks. To construct differential networks, gene expression data from CFBE cells were divided into three groups: (1) siRNA inhibition of NEDD8 and SYVN1; (2) miR-138 mimic and SIN3A siRNA; and (3) temperature (27 °C for 24 h, 40 °C for 24 h, and 27 °C for 24 h followed by 40 °C for 24 h). Results Interrogation of individual networks (e.g., NEDD8/SYVN1 network), combinations of two networks (e.g., NEDD8/SYVN1 + temperature networks), and all three networks yielded sets of 1-modules, 2-modules, and 3-modules, respectively. Gene ontology analysis revealed significant enrichment of dynamic modules in pathways including translation, protein metabolic/catabolic processes, protein complex assembly, and endocytosis. Candidate CFTR effectors identified in the analysis included CHURC1, GZF1, and RPL15, and siRNA-mediated knockdown of these genes partially restored CFTR-dependent transepithelial chloride current to ΔF508-CFBE cells. Conclusions The ability of the M-module to identify dynamic modules involved in ΔF508 rescue provides a novel approach for studying CFTR biogenesis and identifying candidate suppressors of ΔF508.

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New insights into heparan sulphate biosynthesis from the study of mutant mice

Biochemical Society Symposium ◽

10.1042/bss0690047 ◽

2002 ◽

Vol 69 ◽

pp. 47-57 ◽

Cited By ~ 8

Author(s):

Catherine L. R. Merry ◽

John T. Gallagher

Keyword(s):

Growth Factors ◽

Biosynthetic Pathway ◽

Heparan Sulphate ◽

Mutant Mice ◽

Gene Products ◽

Multiple Gene ◽

Adhesion Proteins ◽

Ligand Interactions

Heparan sulphate (HS) is an essential co-receptor for a number of growth factors, morphogens and adhesion proteins. The biosynthetic modifications involved in the generation of a mature HS chain may determine the strength and outcome of HS–ligand interactions. These modifications are catalysed by a complex family of enzymes, some of which occur as multiple gene products. Various mutant mice have now been generated, which lack the function of isolated components of the HS biosynthetic pathway. In this discussion, we outline the key findings of these studies, and use them to put into context our own work concerning the structure of the HS generated by the Hs2st-/- mice.

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Direct Modification of Multiple Gene Homoeologs in Brassica oleracea and Brassica napus Using Doubled Haploid Inducer‐Mediated Genome Editing System

Plant Biotechnology Journal ◽

10.1111/pbi.13632 ◽

2021 ◽

Author(s):

Chao Li ◽

Shifei Sang ◽

MengDan Sun ◽

Jin Yang ◽

YuQin Shi ◽

...

Keyword(s):

Brassica Napus ◽

Brassica Oleracea ◽

Genome Editing ◽

Doubled Haploid ◽

Multiple Gene ◽

Direct Modification ◽

Haploid Inducer

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Antibiotic tolerance is associated with a broad and complex transcriptional response in E. coli

Scientific Reports ◽

10.1038/s41598-021-85509-7 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Heather S. Deter ◽

Tahmina Hossain ◽

Nicholas C. Butzin

Keyword(s):

Transcriptional Regulatory Network ◽

Transcriptional Response ◽

Regulatory Proteins ◽

Health Concern ◽

Transcriptional Networks ◽

Antibiotic Tolerance ◽

Multiple Gene ◽

E Coli ◽

Transcriptional Regulatory ◽

Antibiotic Efficacy

AbstractAntibiotic treatment kills a large portion of a population, while a small, tolerant subpopulation survives. Tolerant bacteria disrupt antibiotic efficacy and increase the likelihood that a population gains antibiotic resistance, a growing health concern. We examined how E. coli transcriptional networks changed in response to lethal ampicillin concentrations. We are the first to apply transcriptional regulatory network (TRN) analysis to antibiotic tolerance by leveraging existing knowledge and our transcriptional data. TRN analysis shows that gene expression changes specific to ampicillin treatment are likely caused by specific sigma and transcription factors typically regulated by proteolysis. These results demonstrate that to survive lethal concentration of ampicillin specific regulatory proteins change activity and cause a coordinated transcriptional response that leverages multiple gene systems.

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Artificial complementary chromatic acclimation gene expression system in Escherichia coli

Microbial Cell Factories ◽

10.1186/s12934-021-01621-3 ◽

2021 ◽

Vol 20 (1) ◽

Author(s):

Dwi Ariyanti ◽

Kazunori Ikebukuro ◽

Koji Sode

Keyword(s):

Gene Expression ◽

Escherichia Coli ◽

Light Exposure ◽

Expression System ◽

Red Light ◽

Green Light ◽

Light Illumination ◽

Multiple Gene ◽

Gene Expression System ◽

Chromatic Acclimation

Abstract Background The development of multiple gene expression systems, especially those based on the physical signals, such as multiple color light irradiations, is challenging. Complementary chromatic acclimation (CCA), a photoreversible process that facilitates the control of cellular expression using light of different wavelengths in cyanobacteria, is one example. In this study, an artificial CCA systems, inspired by type III CCA light-regulated gene expression, was designed by employing a single photosensor system, the CcaS/CcaR green light gene expression system derived from Synechocystis sp. PCC6803, combined with G-box (the regulator recognized by activated CcaR), the cognate cpcG2 promoter, and the constitutively transcribed promoter, the PtrcΔLacO promoter. Results One G-box was inserted upstream of the cpcG2 promoter and a reporter gene, the rfp gene (green light-induced gene expression), and the other G-box was inserted between the PtrcΔLacO promoter and a reporter gene, the bfp gene (red light-induced gene expression). The Escherichia coli transformants with plasmid-encoded genes were evaluated at the transcriptional and translational levels under red or green light illumination. Under green light illumination, the transcription and translation of the rfp gene were observed, whereas the expression of the bfp gene was repressed. Under red light illumination, the transcription and translation of the bfp gene were observed, whereas the expression of the rfp gene was repressed. During the red and green light exposure cycles at every 6 h, BFP expression increased under red light exposure while RFP expression was repressed, and RFP expression increased under green light exposure while BFP expression was repressed. Conclusion An artificial CCA system was developed to realize a multiple gene expression system, which was regulated by two colors, red and green lights, using a single photosensor system, the CcaS/CcaR system derived from Synechocystis sp. PCC6803, in E. coli. The artificial CCA system functioned repeatedly during red and green light exposure cycles. These results demonstrate the potential application of this CCA gene expression system for the production of multiple metabolites in a variety of microorganisms, such as cyanobacteria.

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The CRISPR/Cas9 Minipig—A Transgenic Minipig to Produce Specific Mutations in Designated Tissues

Cancers ◽

10.3390/cancers13123024 ◽

2021 ◽

Vol 13 (12) ◽

pp. 3024

Author(s):

Martin Fogtmann Berthelsen ◽

Maria Riedel ◽

Huiqiang Cai ◽

Søren H. Skaarup ◽

Aage K. O. Alstrup ◽

...

Keyword(s):

Fluorescent Protein ◽

Yellow Fluorescent Protein ◽

Somatic Cells ◽

Genetic Alterations ◽

Lung Epithelial Cells ◽

Target Cells ◽

Multiple Gene ◽

Conditional Expression ◽

Gene Alterations

The generation of large transgenic animals is impeded by complex cloning, long maturation and gastrulation times. An introduction of multiple gene alterations increases the complexity. We have cloned a transgenic Cas9 minipig to introduce multiple mutations by CRISPR in somatic cells. Transgenic Cas9 pigs were generated by somatic cell nuclear transfer and were backcrossed to Göttingen Minipigs for two generations. Cas9 expression was controlled by FlpO-mediated recombination and was visualized by translation from red to yellow fluorescent protein. In vitro analyses in primary fibroblasts, keratinocytes and lung epithelial cells confirmed the genetic alterations executed by the viral delivery of single guide RNAs (sgRNA) to the target cells. Moreover, multiple gene alterations could be introduced simultaneously in a cell by viral delivery of sgRNAs. Cells with loss of TP53, PTEN and gain-of-function mutation in KRASG12D showed increased proliferation, confirming a transformation of the primary cells. An in vivo activation of Cas9 expression could be induced by viral delivery to the skin. Overall, we have generated a minipig with conditional expression of Cas9, where multiple gene alterations can be introduced to somatic cells by viral delivery of sgRNA. The development of a transgenic Cas9 minipig facilitates the creation of complex pre-clinical models for cancer research.

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Positive effects of multiple gene control on the spread of altruism by group selection

Journal of Theoretical Biology ◽

10.1016/j.jtbi.2011.05.017 ◽

2011 ◽

Vol 284 (1) ◽

pp. 1-6 ◽

Cited By ~ 2

Author(s):

Tomáš Kulich ◽

Jaroslav Flegr

Keyword(s):

Group Selection ◽

Gene Control ◽

Multiple Gene ◽

Positive Effects

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Mapping the Germline and Somatic Mutation Interaction Landscape in Indolent and Aggressive Prostate Cancers

Journal of Oncology ◽

10.1155/2019/4168784 ◽

2019 ◽

Vol 2019 ◽

pp. 1-15 ◽

Cited By ~ 2

Author(s):

Tarun Karthik Kumar Mamidi ◽

Jiande Wu ◽

Chindo Hicks

Keyword(s):

Signaling Pathways ◽

Somatic Mutation ◽

Regulatory Networks ◽

Molecular Mechanisms ◽

Somatic Mutations ◽

Multiple Gene ◽

Gene Regulatory ◽

Aggressive Tumors ◽

Prostate Cancers ◽

Mutation Information

Background. A majority of prostate cancers (PCas) are indolent and cause no harm even without treatment. However, a significant proportion of patients with PCa have aggressive tumors that progress rapidly to metastatic disease and are often lethal. PCa develops through somatic mutagenesis, but emerging evidence suggests that germline genetic variation can markedly contribute to tumorigenesis. However, the causal association between genetic susceptibility and tumorigenesis has not been well characterized. The objective of this study was to map the germline and somatic mutation interaction landscape in indolent and aggressive tumors and to discover signatures of mutated genes associated with each type and distinguishing the two types of PCa. Materials and Methods. We integrated germline mutation information from genome-wide association studies (GWAS) with somatic mutation information from The Cancer Genome Atlas (TCGA) using gene expression data from TCGA on indolent and aggressive PCas as the intermediate phenotypes. Germline and somatic mutated genes associated with each type of PCa were functionally characterized using network and pathway analysis. Results. We discovered gene signatures containing germline and somatic mutations associated with each type and distinguishing the two types of PCa. We discovered multiple gene regulatory networks and signaling pathways enriched with germline and somatic mutations including axon guidance, RAR, WINT, MSP-RON, STAT3, PI3K, TR/RxR, and molecular mechanisms of cancer, NF-kB, prostate cancer, GP6, androgen, and VEGF signaling pathways for indolent PCa and MSP-RON, axon guidance, RAR, adipogenesis, and molecular mechanisms of cancer and NF-kB signaling pathways for aggressive PCa. Conclusion. The investigation revealed germline and somatic mutated genes associated with indolent and aggressive PCas and distinguishing the two types of PCa. The study revealed multiple gene regulatory networks and signaling pathways dysregulated by germline and somatic alterations. Integrative analysis combining germline and somatic mutations is a powerful approach to mapping germline and somatic mutation interaction landscape.

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