Two novel genes expressed inXenopus germ line: Characteristic features of putative protein structures, their gene expression profiles and their possible roles in gametogenesis and embryogenesis

Audiogenic epilepsy (AE), developing in rodent strains in response to sound, is widely used as the model of generalized convulsive epilepsy, while the molecular mechanisms determining AE are currently poorly understood. The brain region that is crucial for AE development isthe inferior and superior colliculi (IC, SC). We compared IC-SC gene expression profiles in rats with different AE susceptibility using transcriptome analysis.The transcriptomes were obtained from the IC-SC of Wistar rats (with no AE), Krushinsky-Molodkina (KM) strain rats (100% AE susceptible), and ”0” strain rats (with no AE) selected from F2 KM x Wistar hybrids for AE absence. KM gene expression displayed characteristic differences inboth of the strains that were not susceptible to AE. There was increased expression of a number of genes responsible for positive regulation of the MAPK signaling cascade, as well as of genes responsible for the production of interferon and several other cytokines. An increase in the expression levels of theTTR gene was found in KM rats, as well as significantly lower expression of the Msh3 gene (involved in post-replicative DNA repair systems). AE was also describedin the 101/HY mouse strain with a mutation in the locus controlling DNA repair. The DNA repair system defects could be the primary factor leading to the accumulation of mutations, which, in turn, promote AE. Keywords: udiogenic seizure, KM strain, transcriptome, TTR gene, Msh3 gene, DNA repair

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Gene Expression Profiling of Plasma Cell Dyscrasias: The Role of IGH Translocations in the Heterogeneity of Multiple Myeloma.

Blood ◽

10.1182/blood.v104.11.4845.4845 ◽

2004 ◽

Vol 104 (11) ◽

pp. 4845-4845

Author(s):

Antonino Neri ◽

Michela Mattioli ◽

Luca Agnelli ◽

Sonia Fabris ◽

Luca Baldini ◽

...

Keyword(s):

Gene Expression ◽

Multiple Myeloma ◽

Plasma Cell ◽

Plasma Cells ◽

Germ Line ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Plasma Cell Dyscrasia ◽

Transcriptional Level ◽

Plasma Cell Dyscrasias

Abstract Multiple Myeloma (MM) is the most common form of plasma cell dyscrasia, characterized by a marked heterogeneity of genetic lesions and clinical course. It may develop from a premalignant condition (monoclonal gammopathy ofundetermined significance, MGUS) or progress from intra-medullary to extra-medullaryforms (plasma cell leukemia, PCL). To provide insights into the molecular characterization of plasma cell dyscrasias and to investigate the contribution of specific genetic lesions to the biological and clinical heterogeneity of MM, we analyzed the gene expression profiles of plasma cells isolated from 7 MGUS, 39 MM and 6 PCL patients by means of DNA microarrays. MMs resulted highly heterogeneous at transcriptional level, whereas the differential expression of genes mainly involved in DNA metabolism and proliferation distinguished MGUS from PCLs and the majority of MM cases. The clustering of MM patients was mainly driven by the presence of the most recurrent translocations involving the immunoglobulin heavy-chain locus. Distinct signatures have been found to be associated with different lesions: the overexpression of CCND2 and genes involved in cell adhesion pathways was observed in cases with deregulated MAF and MAFB, whereas genes upregulated in cases with the t(4;14) showed apoptosis related functions. In addition, we identified a set of cancer germ-line antigens specifically expressed in a sub-group of MM patients characterized by an aggressive clinical evolution, a finding that could have implications for patient classification and immunotherapy.

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Single-cell analyses of the corneal epithelium: Unique cell types and gene expression profiles

10.1101/2020.08.06.240036 ◽

2020 ◽

Author(s):

Surabhi Sonam ◽

Sushant Bangru ◽

Kimberly J. Perry ◽

Auinash Kalsotra ◽

Jonathan J. Henry

Keyword(s):

Gene Expression ◽

Single Cell ◽

Corneal Epithelium ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Cell Types ◽

Stem Cell Markers ◽

Epithelial Stem Cells ◽

Novel Genes ◽

Corneal Epithelial

ABSTRACTCorneal Epithelial Stem Cells (CESCs) and their proliferative progeny, the Transit Amplifying Cells (TACs), are responsible for homeostasis and maintaining corneal transparency. Owing to our limited knowledge of cell fates and gene activity within the cornea, the search for unique markers to identify and isolate these cells remains crucial for ocular surface reconstruction. We performed single-cell RNA sequencing of corneal epithelial cells from stage 49-51 Xenopus larvae. We identified five main clusters with distinct molecular signatures, which represent apical, basal and keratocyte cell types as well as two discrete proliferative cell types in the bi-layered epithelium. Our data reveal several novel genes expressed in corneal cells and spatiotemporal changes in gene expression during corneal differentiation. Through gene regulatory network analysis, we identified key developmental gene regulons, which guide these different cell states. Our study offers a detailed atlas of single-cell transcriptomes in the frog corneal epithelium. In future, this work will be useful to elucidate the function of novel genes in corneal homeostasis, wound healing and cornea regeneration, which includes lens regeneration in Xenopus.SUMMARY STATEMENTThis study identifies cell types and transcriptional heterogeneity in the corneal epithelium that regulate its differentiation, and facilitates the search for corneal stem cell markers.

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Bioinformatics analysis of gene expression profiles to diagnose crucial and novel genes in glioblastoma multiform

Pathology - Research and Practice ◽

10.1016/j.prp.2018.07.015 ◽

2018 ◽

Vol 214 (9) ◽

pp. 1395-1461 ◽

Cited By ~ 4

Author(s):

Chanabasayya Vastrad ◽

Basavaraj Vastrad

Keyword(s):

Gene Expression ◽

Bioinformatics Analysis ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Novel Genes ◽

Glioblastoma Multiform

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Identification of novel genes that promote persister formation by repressing transcription and cell division in Pseudomonas aeruginosa

Journal of Antimicrobial Chemotherapy ◽

10.1093/jac/dkz214 ◽

2019 ◽

Vol 74 (9) ◽

pp. 2575-2587 ◽

Cited By ~ 3

Author(s):

Yuqing Long ◽

Weixin Fu ◽

Shouyi Li ◽

Huan Ren ◽

Mei Li ◽

...

Keyword(s):

Gene Expression ◽

Pseudomonas Aeruginosa ◽

Cell Division ◽

Light Scattering ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Fresh Medium ◽

Sequencing Analysis ◽

Persister Cells ◽

Novel Genes

AbstractObjectivesBacterial persisters are a small subpopulation of cells that are highly tolerant of antibiotics and contribute to chronic and recalcitrant infections. Global gene expression in Pseudomonas aeruginosa persister cells and genes contributing to persister formation remain largely unknown. The objective of this study was to examine the gene expression profiles of the persister cells and those that regained growth in fresh medium, as well as to identify novel genes related to persister formation.MethodsP. aeruginosa persister cells and those that regrew in fresh medium were collected and subjected to RNA sequencing analysis. Genes up-regulated in the persister cells were overexpressed to evaluate their roles in persister formation. The functions of the persister-contributing genes were assessed with pulse–chase assay, affinity chromatography, fluorescence and electron microscopy, as well as a light-scattering assay.ResultsAn operon containing PA2282–PA2287 was up-regulated in the persister cells and down-regulated in the regrowing cells. PA2285 and PA2287 play key roles in persister formation. PA2285 and PA2287 were found to bind to RpoC and FtsZ, which are involved in transcription and cell division, respectively. Pulse–chase assays demonstrated inhibitory effects of PA2285 and PA2287 on the overall transcription. Meanwhile, light-scattering and microscopy assays demonstrated that PA2285 and PA2287 interfere with cell division by inhibiting FtsZ aggregation. PA2285 and PA2287 are conserved in pseudomonads and their homologous genes in Pseudomonas putida contribute to persister formation.ConclusionsPA2285 and PA2287 are novel bifunctional proteins that contribute to persister formation in P. aeruginosa.

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