Histone crotonylation specifically marks the haploid male germ cell gene expression program

BioEssays ◽  
2011 ◽  
Vol 34 (3) ◽  
pp. 187-193 ◽  
Author(s):  
Emilie Montellier ◽  
Sophie Rousseaux ◽  
Yingming Zhao ◽  
Saadi Khochbin
Keyword(s):  
Gene Expression ◽  
Germ Cell ◽  
Gene Expression Program ◽  
Male Germ Cell ◽  
Haploid Male ◽  
Cell Gene Expression ◽  
Expression Program ◽  
Cell Gene

scholarly journals Single cell genomic characterization reveals the cellular reprogramming of the gastric tumor microenvironment

2019 ◽  
Author(s):  
Anuja Sathe ◽  
Sue Grimes ◽  
Billy T. Lau ◽  
Jiamin Chen ◽  
Carlos Suarez ◽  
...  
Keyword(s):  
Gene Expression ◽  
Tumor Microenvironment ◽  
Single Cell ◽  
Normal Tissue ◽  
Gene Expression Program ◽  
Expression Studies ◽  
Cell Gene Expression ◽  
Gene Expression Studies ◽  
Expression Program ◽  
Cell Gene

ABSTRACTPurposeThe tumor microenvironment (TME) consists of a heterogenous cellular milieu that can influence cancer cell behavior. The characteristics of the cellular TME have a dramatic impact on treatments such as immunotherapy. These features can be revealed with single-cell RNA sequencing (scRNA-seq). We hypothesized that single cell gene expression studies of gastric cancer (GC) together with paired normal tissue and peripheral blood mononuclear cells (PBMCs) would identify critical elements of cellular dysregulation not apparent with other approaches.MethodsSingle cell gene expression studies were conducted on seven patients with GC and one patient with intestinal metaplasia. We sequenced 56,167 cells comprising GC (32,407 cells), paired normal tissue (18,657 cells) and PBMCs (5,103 cells). Protein expression of genes of interest was validated by multiplex immunofluorescence.ResultsTumor epithelium had copy number alterations and a distinct gene expression program compared to normal with intra-tumor heterogeneity. The GC TME was significantly enriched for stromal cells, macrophages, dendritic cells (DCs) and Tregs. TME-exclusive stromal cells expressed extracellular matrix components distinct from normal tissue. Macrophages were transcriptionally heterogenous and did not conform to a binary M1/M2 paradigm. Gene expression program of tumor DCs was unique from PBMC DCs. TME-specific cytotoxic T cells comprised of two exhausted heterogenous subsets. Helper, cytotoxic T, Treg and NK cells expressed multiple immune checkpoint or costimulatory molecules. Receptor-ligand analysis revealed TME-exclusive inter-cellular communication.ConclusionsSingle cell gene expression studies revealed widespread reprogramming across multiple cellular elements in the milieu of the GC TME. Cellular remodeling was delineated by changes in cell numbers, transcriptional states and inter-cellular interactions. This characterization facilitates understanding of tumor biology and enables the identification of novel molecular targets including for cancer immunotherapy.STATEMENT OF TRANSLATIONAL RELEVANCEWe leveraged the power of single-cell genomics to characterize the heterogenous cell types and states in the tumor microenvironment (TME). By profiling thousands of single cells from surgical resections of gastric cancer together with paired normal mucosa and peripheral blood mononuclear cells (PBMCs), we determined the deviations in the TME from physiological conditions. Our analysis revealed a cellular reprogramming of the TME compared to normal mucosa in immune and stromal lineages. We detected transcriptional heterogeneity within macrophages and a TME-specific gene expression program in dendritic cells. Cytotoxic T cells in the TME had heterogenous profiles of exhaustion and expression of multiple immune checkpoint and costimulatory molecules. We constructed a receptor-ligand based inter-cellular communications network that was exclusive to tumor tissue. These discoveries provide information at a highly granular cellular resolution enabling advances in cancer biology, biomarker discovery and identification of treatment targets such as for immunotherapy.

scholarly journals Blimp-1 Orchestrates Plasma Cell Differentiation by Extinguishing the Mature B Cell Gene Expression Program

Immunity ◽  
2002 ◽  
Vol 17 (1) ◽  
pp. 51-62 ◽  
Author(s):  
A.L. Shaffer ◽  
Kuo-I Lin ◽  
Tracy C. Kuo ◽  
Xin Yu ◽  
Elaine M. Hurt ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Differentiation ◽  
B Cell ◽  
Plasma Cell ◽  
Gene Expression Program ◽  
Plasma Cell Differentiation ◽  
Cell Gene Expression ◽  
Expression Program ◽  
Cell Gene

scholarly journals Bcl11b represses a mature T-cell gene expression program in immature CD4+CD8+ thymocytes

2010 ◽  
Vol 40 (8) ◽  
pp. 2143-2154 ◽  
Author(s):  
Philippe Kastner ◽  
Susan Chan ◽  
Walter K. Vogel ◽  
Ling-Juan Zhang ◽  
Acharawan Topark-Ngarm ◽  
...  
Keyword(s):  
Gene Expression ◽  
T Cell ◽  
Gene Expression Program ◽  
Cell Gene Expression ◽  
Expression Program ◽  
Cell Gene

Nucleolin promotes execution of the hematopoietic stem cell gene expression program

Leukemia ◽  
2018 ◽  
Vol 32 (8) ◽  
pp. 1865-1868 ◽  
Author(s):  
Csaba Mahotka ◽  
Sanil Bhatia ◽  
Jutta Kollet ◽  
Edgar Grinstein
Keyword(s):  
Gene Expression ◽  
Stem Cell ◽  
Hematopoietic Stem Cell ◽  
Gene Expression Program ◽  
Hematopoietic Stem ◽  
Cell Gene Expression ◽  
Expression Program ◽  
Cell Gene ◽  
Stem Cell Gene

Evaluation of Novel Mouse-Specific Germ Cell Gene Expression in Embryonic Stem Cell-Derived Germ Cell-Like CellsIn Vitrowith Retinoic Acid Treatment

2018 ◽  
Vol 20 (4) ◽  
pp. 245-255 ◽  
Author(s):  
Maryam Gholamitabar Tabari ◽  
Seyed Gholam Ali Jorsaraei ◽  
Mohammad Ghasemzadeh-Hasankolaei ◽  
Ali Asghar Ahmadi ◽  
Mehdi Amirikia
Keyword(s):  
Gene Expression ◽  
Stem Cell ◽  
Retinoic Acid ◽  
Germ Cell ◽  
Embryonic Stem Cell ◽  
Acid Treatment ◽  
Embryonic Stem ◽  
Retinoic Acid Treatment ◽  
Cell Gene Expression ◽  
Cell Gene

scholarly journals Cross platform analysis of methylation, miRNA and stem cell gene expression data in germ cell tumors highlights characteristic differences by tumor histology

BMC Cancer ◽  
2015 ◽  
Vol 15 (1) ◽  
Author(s):  
Jenny N. Poynter ◽  
Jessica R. B. M. Bestrashniy ◽  
Kevin A. T. Silverstein ◽  
Anthony J. Hooten ◽  
Christopher Lees ◽  
...  
Keyword(s):  
Gene Expression ◽  
Stem Cell ◽  
Germ Cell ◽  
Gene Expression Data ◽  
Germ Cell Tumors ◽  
Expression Data ◽  
Cell Gene Expression ◽  
Cross Platform ◽  
Cell Gene ◽  
Stem Cell Gene

scholarly journals Bcl11b prevents catastrophic autoimmunity by controlling multiple aspects of a regulatory T cell gene expression program

2019 ◽  
Vol 5 (8) ◽  
pp. eaaw0706 ◽  
Author(s):  
Syed Nurul Hasan ◽  
Amit Sharma ◽  
Sayantani Ghosh ◽  
Sung-Wook Hong ◽  
Sinchita Roy-Chowdhuri ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Activation ◽  
Immunological Tolerance ◽  
Gene Expression Program ◽  
Specific Gene ◽  
Molecular Features ◽  
Molecular Events ◽  
Cell Gene Expression ◽  
Genomic Recruitment ◽  
Expression Program

Foxp3 and its protein partners establish a regulatory T (Treg) cell transcription profile and promote immunological tolerance. However, molecular features contributing to a Treg-specific gene expression program are still incompletely understood. We find that the transcription factor Bcl11b is a prominent Foxp3 cofactor with multifaceted functions in Treg biology. Optimal genomic recruitment of Foxp3 and Bcl11b is critically interdependent. Genome-wide occupancy studies coupled with gene expression profiling reveal that Bcl11b, in association with Foxp3, is primarily responsible in establishing a Treg-specific gene activation program. Furthermore, Bcl11b restricts misdirected recruitment of Foxp3 to sites, which would otherwise result in an altered Treg transcriptome profile. Consequently, Treg-specific ablation of Bcl11b results in marked breakdown of immune tolerance, leading to aggressive systemic autoimmunity. Our study provides previously underappreciated mechanistic insights into molecular events contributing to basic aspects of Treg function. Furthermore, it establishes a therapeutic target with potential implications in autoimmunity and cancer.

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