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1.
bioRxiv ; 2024 May 20.
Article in English | MEDLINE | ID: mdl-38826293

ABSTRACT

Gastrointestinal (GI) B cells and plasma cells (PCs), critical to mucosal homeostasis, play an important role in the host response to HIV-1 infection. Here, high resolution mapping of human B cells and PCs from colon and ileum during both viremic and suppressed HIV-1 infection identified a significant reduction in germinal center (GC) B cells and Follicular Dendritic Cells (FDCs) during HIV-1 viremia. Further, IgA + PCs, the major cellular output of intestinal GCs were significantly reduced during viremic HIV-1 infection. PC-associated transcriptional perturbations, including type I interferon signaling persisted in antiretroviral therapy (ART) treated individuals, suggesting ongoing disruption of the intestinal immune milieu during ART. GI humoral immune perturbations associated with changes in intestinal microbiome composition and systemic inflammation. Herein, we highlight a key immune defect in the GI mucosa due to HIV-1 viremia, with major implications. One Sentence Summary: Major perturbations in intestinal GC dynamics in viremic HIV-1 infection relate to reduced IgA + plasma cells, systemic inflammation and microbiota changes.

2.
Sci Immunol ; 9(94): eadg7549, 2024 Apr 19.
Article in English | MEDLINE | ID: mdl-38640252

ABSTRACT

Vedolizumab (VDZ) is a first-line treatment in ulcerative colitis (UC) that targets the α4ß7- mucosal vascular addressin cell adhesion molecule 1 (MAdCAM-1) axis. To determine the mechanisms of action of VDZ, we examined five distinct cohorts of patients with UC. A decrease in naïve B and T cells in the intestines and gut-homing (ß7+) plasmablasts in circulation of VDZ-treated patients suggested that VDZ targets gut-associated lymphoid tissue (GALT). Anti-α4ß7 blockade in wild-type and photoconvertible (KikGR) mice confirmed a loss of GALT size and cellularity because of impaired cellular entry. In VDZ-treated patients with UC, treatment responders demonstrated reduced intestinal lymphoid aggregate size and follicle organization and a reduction of ß7+IgG+ plasmablasts in circulation, as well as IgG+ plasma cells and FcγR-dependent signaling in the intestine. GALT targeting represents a previously unappreciated mechanism of action of α4ß7-targeted therapies, with major implications for this therapeutic paradigm in UC.


Subject(s)
Colitis, Ulcerative , Humans , Animals , Mice , Colitis, Ulcerative/drug therapy , Integrins , Intestinal Mucosa , Peyer's Patches , Immunoglobulin G/therapeutic use
3.
Cell ; 187(5): 1255-1277.e27, 2024 Feb 29.
Article in English | MEDLINE | ID: mdl-38359819

ABSTRACT

Despite the successes of immunotherapy in cancer treatment over recent decades, less than <10%-20% cancer cases have demonstrated durable responses from immune checkpoint blockade. To enhance the efficacy of immunotherapies, combination therapies suppressing multiple immune evasion mechanisms are increasingly contemplated. To better understand immune cell surveillance and diverse immune evasion responses in tumor tissues, we comprehensively characterized the immune landscape of more than 1,000 tumors across ten different cancers using CPTAC pan-cancer proteogenomic data. We identified seven distinct immune subtypes based on integrative learning of cell type compositions and pathway activities. We then thoroughly categorized unique genomic, epigenetic, transcriptomic, and proteomic changes associated with each subtype. Further leveraging the deep phosphoproteomic data, we studied kinase activities in different immune subtypes, which revealed potential subtype-specific therapeutic targets. Insights from this work will facilitate the development of future immunotherapy strategies and enhance precision targeting with existing agents.


Subject(s)
Neoplasms , Proteogenomics , Humans , Combined Modality Therapy , Genomics , Neoplasms/genetics , Neoplasms/immunology , Neoplasms/therapy , Proteomics , Tumor Escape
5.
Cell ; 186(16): 3476-3498.e35, 2023 08 03.
Article in English | MEDLINE | ID: mdl-37541199

ABSTRACT

To improve the understanding of chemo-refractory high-grade serous ovarian cancers (HGSOCs), we characterized the proteogenomic landscape of 242 (refractory and sensitive) HGSOCs, representing one discovery and two validation cohorts across two biospecimen types (formalin-fixed paraffin-embedded and frozen). We identified a 64-protein signature that predicts with high specificity a subset of HGSOCs refractory to initial platinum-based therapy and is validated in two independent patient cohorts. We detected significant association between lack of Ch17 loss of heterozygosity (LOH) and chemo-refractoriness. Based on pathway protein expression, we identified 5 clusters of HGSOC, which validated across two independent patient cohorts and patient-derived xenograft (PDX) models. These clusters may represent different mechanisms of refractoriness and implicate putative therapeutic vulnerabilities.


Subject(s)
Cystadenocarcinoma, Serous , Ovarian Neoplasms , Proteogenomics , Female , Humans , Cystadenocarcinoma, Serous/drug therapy , Cystadenocarcinoma, Serous/genetics , Ovarian Neoplasms/drug therapy , Ovarian Neoplasms/genetics
6.
bioRxiv ; 2023 Jun 05.
Article in English | MEDLINE | ID: mdl-37333091

ABSTRACT

Ulcerative colitis (UC) is an idiopathic chronic inflammatory disease of the colon with sharply rising global prevalence. Dysfunctional epithelial compartment (EC) dynamics are implicated in UC pathogenesis although EC-specific studies are sparse. Applying orthogonal high-dimensional EC profiling to a Primary Cohort (PC; n=222), we detail major epithelial and immune cell perturbations in active UC. Prominently, reduced frequencies of mature BEST4+OTOP2+ absorptive and BEST2+WFDC2+ secretory epithelial enterocytes were associated with the replacement of homeostatic, resident TRDC+KLRD1+HOPX+ γδ+ T cells with RORA+CCL20+S100A4+ TH17 cells and the influx of inflammatory myeloid cells. The EC transcriptome (exemplified by S100A8, HIF1A, TREM1, CXCR1) correlated with clinical, endoscopic, and histological severity of UC in an independent validation cohort (n=649). Furthermore, therapeutic relevance of the observed cellular and transcriptomic changes was investigated in 3 additional published UC cohorts (n=23, 48 and 204 respectively) to reveal that non-response to anti-Tumor Necrosis Factor (anti-TNF) therapy was associated with EC related myeloid cell perturbations. Altogether, these data provide high resolution mapping of the EC to facilitate therapeutic decision-making and personalization of therapy in patients with UC.

7.
bioRxiv ; 2023 Jan 20.
Article in English | MEDLINE | ID: mdl-36711839

ABSTRACT

Targeting the α4ß7-MAdCAM-1 axis with vedolizumab (VDZ) is a front-line therapeutic paradigm in ulcerative colitis (UC). However, mechanism(s) of action (MOA) of VDZ remain relatively undefined. Here, we examined three distinct cohorts of patients with UC (n=83, n=60, and n=21), to determine the effect of VDZ on the mucosal and peripheral immune system. Transcriptomic studies with protein level validation were used to study drug MOA using conventional and transgenic murine models. We found a significant decrease in colonic and ileal naïve B and T cells and circulating gut-homing plasmablasts (ß7+) in VDZ-treated patients, pointing to gut-associated lymphoid tissue (GALT) targeting by VDZ. Murine Peyer's patches (PP) demonstrated a significant loss cellularity associated with reduction in follicular B cells, including a unique population of epithelium-associated B cells, following anti-α4ß7 antibody (mAb) administration. Photoconvertible (KikGR) mice unequivocally demonstrated impaired cellular entry into PPs in anti-α4ß7 mAb treated mice. In VDZ-treated, but not anti-tumor necrosis factor-treated UC patients, lymphoid aggregate size was significantly reduced in treatment responders compared to non-responders, with an independent validation cohort further confirming these data. GALT targeting represents a novel MOA of α4ß7-targeted therapies, with major implications for this therapeutic paradigm in UC, and for the development of new therapeutic strategies.

8.
Mol Neurodegener ; 17(1): 17, 2022 03 02.
Article in English | MEDLINE | ID: mdl-35236372

ABSTRACT

Alzheimer's disease (AD) is the most common form of dementia, characterized by progressive cognitive impairment and neurodegeneration. Extensive clinical and genomic studies have revealed biomarkers, risk factors, pathways, and targets of AD in the past decade. However, the exact molecular basis of AD development and progression remains elusive. The emerging single-cell sequencing technology can potentially provide cell-level insights into the disease. Here we systematically review the state-of-the-art bioinformatics approaches to analyze single-cell sequencing data and their applications to AD in 14 major directions, including 1) quality control and normalization, 2) dimension reduction and feature extraction, 3) cell clustering analysis, 4) cell type inference and annotation, 5) differential expression, 6) trajectory inference, 7) copy number variation analysis, 8) integration of single-cell multi-omics, 9) epigenomic analysis, 10) gene network inference, 11) prioritization of cell subpopulations, 12) integrative analysis of human and mouse sc-RNA-seq data, 13) spatial transcriptomics, and 14) comparison of single cell AD mouse model studies and single cell human AD studies. We also address challenges in using human postmortem and mouse tissues and outline future developments in single cell sequencing data analysis. Importantly, we have implemented our recommended workflow for each major analytic direction and applied them to a large single nucleus RNA-sequencing (snRNA-seq) dataset in AD. Key analytic results are reported while the scripts and the data are shared with the research community through  GitHub. In summary, this comprehensive review provides insights into various approaches to analyze single cell sequencing data and offers specific guidelines for study design and a variety of analytic directions. The review and the accompanied software tools will serve as a valuable resource for studying cellular and molecular mechanisms of AD, other diseases, or biological systems at the single cell level.


Subject(s)
Alzheimer Disease , Alzheimer Disease/genetics , Alzheimer Disease/metabolism , Animals , Computational Biology , DNA Copy Number Variations , Data Analysis , Mice , Single-Cell Analysis/methods
9.
Cell ; 184(16): 4348-4371.e40, 2021 08 05.
Article in English | MEDLINE | ID: mdl-34358469

ABSTRACT

Lung squamous cell carcinoma (LSCC) remains a leading cause of cancer death with few therapeutic options. We characterized the proteogenomic landscape of LSCC, providing a deeper exposition of LSCC biology with potential therapeutic implications. We identify NSD3 as an alternative driver in FGFR1-amplified tumors and low-p63 tumors overexpressing the therapeutic target survivin. SOX2 is considered undruggable, but our analyses provide rationale for exploring chromatin modifiers such as LSD1 and EZH2 to target SOX2-overexpressing tumors. Our data support complex regulation of metabolic pathways by crosstalk between post-translational modifications including ubiquitylation. Numerous immune-related proteogenomic observations suggest directions for further investigation. Proteogenomic dissection of CDKN2A mutations argue for more nuanced assessment of RB1 protein expression and phosphorylation before declaring CDK4/6 inhibition unsuccessful. Finally, triangulation between LSCC, LUAD, and HNSCC identified both unique and common therapeutic vulnerabilities. These observations and proteogenomics data resources may guide research into the biology and treatment of LSCC.


Subject(s)
Carcinoma, Squamous Cell/genetics , Lung Neoplasms/genetics , Proteogenomics , Acetylation , Adult , Aged , Aged, 80 and over , Cluster Analysis , Cyclin-Dependent Kinase 4/genetics , Cyclin-Dependent Kinase 6/genetics , Epithelial-Mesenchymal Transition/genetics , Female , Gene Expression Regulation, Neoplastic , Humans , Male , Middle Aged , Mutation/genetics , Neoplasm Proteins/metabolism , Phosphorylation , Protein Binding , Receptor Tyrosine Kinase-like Orphan Receptors/metabolism , Receptors, Platelet-Derived Growth Factor/metabolism , Signal Transduction , Ubiquitination
10.
Cancer Cell ; 39(4): 509-528.e20, 2021 04 12.
Article in English | MEDLINE | ID: mdl-33577785

ABSTRACT

Glioblastoma (GBM) is the most aggressive nervous system cancer. Understanding its molecular pathogenesis is crucial to improving diagnosis and treatment. Integrated analysis of genomic, proteomic, post-translational modification and metabolomic data on 99 treatment-naive GBMs provides insights to GBM biology. We identify key phosphorylation events (e.g., phosphorylated PTPN11 and PLCG1) as potential switches mediating oncogenic pathway activation, as well as potential targets for EGFR-, TP53-, and RB1-altered tumors. Immune subtypes with distinct immune cell types are discovered using bulk omics methodologies, validated by snRNA-seq, and correlated with specific expression and histone acetylation patterns. Histone H2B acetylation in classical-like and immune-low GBM is driven largely by BRDs, CREBBP, and EP300. Integrated metabolomic and proteomic data identify specific lipid distributions across subtypes and distinct global metabolic changes in IDH-mutated tumors. This work highlights biological relationships that could contribute to stratification of GBM patients for more effective treatment.


Subject(s)
Brain Neoplasms/metabolism , Glioblastoma/genetics , Glioblastoma/metabolism , Protein Tyrosine Phosphatase, Non-Receptor Type 11/metabolism , Proteogenomics , Brain Neoplasms/pathology , Computational Biology/methods , Glioblastoma/pathology , Humans , Metabolomics/methods , Mutation/genetics , Phospholipase C gamma/genetics , Phospholipase C gamma/metabolism , Phosphorylation/physiology , Protein Tyrosine Phosphatase, Non-Receptor Type 11/genetics , Proteogenomics/methods , Proteomics/methods
11.
Cell ; 183(7): 1962-1985.e31, 2020 12 23.
Article in English | MEDLINE | ID: mdl-33242424

ABSTRACT

We report a comprehensive proteogenomics analysis, including whole-genome sequencing, RNA sequencing, and proteomics and phosphoproteomics profiling, of 218 tumors across 7 histological types of childhood brain cancer: low-grade glioma (n = 93), ependymoma (32), high-grade glioma (25), medulloblastoma (22), ganglioglioma (18), craniopharyngioma (16), and atypical teratoid rhabdoid tumor (12). Proteomics data identify common biological themes that span histological boundaries, suggesting that treatments used for one histological type may be applied effectively to other tumors sharing similar proteomics features. Immune landscape characterization reveals diverse tumor microenvironments across and within diagnoses. Proteomics data further reveal functional effects of somatic mutations and copy number variations (CNVs) not evident in transcriptomics data. Kinase-substrate association and co-expression network analysis identify important biological mechanisms of tumorigenesis. This is the first large-scale proteogenomics analysis across traditional histological boundaries to uncover foundational pediatric brain tumor biology and inform rational treatment selection.


Subject(s)
Brain Neoplasms/genetics , Brain Neoplasms/pathology , Proteogenomics , Brain Neoplasms/immunology , Child , DNA Copy Number Variations/genetics , Gene Expression Regulation, Neoplastic , Gene Regulatory Networks , Genome, Human , Glioma/genetics , Glioma/pathology , Humans , Lymphocytes, Tumor-Infiltrating/immunology , Mutation/genetics , Neoplasm Grading , Neoplasm Recurrence, Local/pathology , Phosphoproteins/metabolism , Phosphorylation , RNA, Messenger/genetics , RNA, Messenger/metabolism , Transcriptome/genetics
12.
Cell ; 182(1): 200-225.e35, 2020 07 09.
Article in English | MEDLINE | ID: mdl-32649874

ABSTRACT

To explore the biology of lung adenocarcinoma (LUAD) and identify new therapeutic opportunities, we performed comprehensive proteogenomic characterization of 110 tumors and 101 matched normal adjacent tissues (NATs) incorporating genomics, epigenomics, deep-scale proteomics, phosphoproteomics, and acetylproteomics. Multi-omics clustering revealed four subgroups defined by key driver mutations, country, and gender. Proteomic and phosphoproteomic data illuminated biology downstream of copy number aberrations, somatic mutations, and fusions and identified therapeutic vulnerabilities associated with driver events involving KRAS, EGFR, and ALK. Immune subtyping revealed a complex landscape, reinforced the association of STK11 with immune-cold behavior, and underscored a potential immunosuppressive role of neutrophil degranulation. Smoking-associated LUADs showed correlation with other environmental exposure signatures and a field effect in NATs. Matched NATs allowed identification of differentially expressed proteins with potential diagnostic and therapeutic utility. This proteogenomics dataset represents a unique public resource for researchers and clinicians seeking to better understand and treat lung adenocarcinomas.


Subject(s)
Adenocarcinoma of Lung/drug therapy , Adenocarcinoma of Lung/genetics , Lung Neoplasms/drug therapy , Lung Neoplasms/genetics , Proteogenomics , Adenocarcinoma of Lung/immunology , Adult , Aged , Aged, 80 and over , Biomarkers, Tumor/metabolism , Carcinogenesis/genetics , Carcinogenesis/pathology , DNA Copy Number Variations/genetics , DNA Methylation/genetics , Female , Humans , Lung Neoplasms/immunology , Male , Middle Aged , Mutation/genetics , Oncogene Proteins, Fusion , Phenotype , Phosphoproteins/metabolism , Proteome/metabolism
14.
Cell ; 179(4): 964-983.e31, 2019 10 31.
Article in English | MEDLINE | ID: mdl-31675502

ABSTRACT

To elucidate the deregulated functional modules that drive clear cell renal cell carcinoma (ccRCC), we performed comprehensive genomic, epigenomic, transcriptomic, proteomic, and phosphoproteomic characterization of treatment-naive ccRCC and paired normal adjacent tissue samples. Genomic analyses identified a distinct molecular subgroup associated with genomic instability. Integration of proteogenomic measurements uniquely identified protein dysregulation of cellular mechanisms impacted by genomic alterations, including oxidative phosphorylation-related metabolism, protein translation processes, and phospho-signaling modules. To assess the degree of immune infiltration in individual tumors, we identified microenvironment cell signatures that delineated four immune-based ccRCC subtypes characterized by distinct cellular pathways. This study reports a large-scale proteogenomic analysis of ccRCC to discern the functional impact of genomic alterations and provides evidence for rational treatment selection stemming from ccRCC pathobiology.


Subject(s)
Carcinoma, Renal Cell/genetics , Neoplasm Proteins/genetics , Proteogenomics , Transcriptome/genetics , Adult , Aged , Aged, 80 and over , Biomarkers, Tumor/genetics , Biomarkers, Tumor/immunology , Carcinoma, Renal Cell/immunology , Carcinoma, Renal Cell/pathology , Disease-Free Survival , Exome/genetics , Female , Gene Expression Regulation, Neoplastic/genetics , Genome, Human/genetics , Humans , Male , Middle Aged , Neoplasm Proteins/immunology , Oxidative Phosphorylation , Phosphorylation/genetics , Signal Transduction/genetics , Transcriptome/immunology , Tumor Microenvironment/genetics , Tumor Microenvironment/immunology , Exome Sequencing
16.
PLoS Genet ; 11(2): e1005020, 2015.
Article in English | MEDLINE | ID: mdl-25714103

ABSTRACT

The development and homeostasis of multicellular organisms relies on gene regulation within individual constituent cells. Gene regulatory circuits that increase the robustness of gene expression frequently incorporate microRNAs as post-transcriptional regulators. Computational approaches, synthetic gene circuits and observations in model organisms predict that the co-regulation of microRNAs and their target mRNAs can reduce cell-to-cell variability in the expression of target genes. However, whether microRNAs directly regulate variability of endogenous gene expression remains to be tested in mammalian cells. Here we use quantitative flow cytometry to show that microRNAs impact on cell-to-cell variability of protein expression in developing mouse thymocytes. We find two distinct mechanisms that control variation in the activation-induced expression of the microRNA target CD69. First, the expression of miR-17 and miR-20a, two members of the miR-17-92 cluster, is co-regulated with the target mRNA Cd69 to form an activation-induced incoherent feed-forward loop. Another microRNA, miR-181a, acts at least in part upstream of the target mRNA Cd69 to modulate cellular responses to activation. The ability of microRNAs to render gene expression more uniform across mammalian cell populations may be important for normal development and for disease.


Subject(s)
Cell Survival/genetics , MicroRNAs/genetics , Protein Biosynthesis/genetics , Thymocytes/metabolism , Animals , Cell Line, Tumor , Flow Cytometry , Gene Expression Regulation, Developmental , Hematopoiesis/genetics , Mice , RNA, Messenger/biosynthesis
17.
Genom Data ; 2: 110-113, 2014 Dec.
Article in English | MEDLINE | ID: mdl-25089258

ABSTRACT

CarD is an essential mycobacterial protein that binds the RNA polymerase (RNAP) and affects the transcriptional profile of Mycobacterium smegmatis and Mycobacterium tuberculosis (6). We predicted that CarD was directly regulating RNAP function but our prior experiments had not determined at what stage of transcription CarD was functioning and at which genes CarD interacted with the RNAP. To begin to address these open questions, we performed Chromatin Immunoprecipitation sequencing (ChIP-seq) to survey the distribution of CarD throughout the M. smegmatis chromosome. The distribution of RNAP subunits ß and σA were also profiled. We expected that RNAP ß would be present throughout transcribed regions and RNAP σA would be predominantly enriched at promoters based on work in Escherichia coli (3), however this had yet to be determined in mycobacteria. The ChIP-seq analyses revealed that CarD was never present on the genome in the absence of RNAP, was primarily associated with promoter regions, and was highly correlated with the distribution of RNAP σA. The colocalization of σA and CarD led us to propose that in vivo, CarD associates with RNAP initiation complexes at most promoters and is therefore a global regulator of transcription initiation. Here we describe in detail the data from the ChIP-seq experiments associated with the study published by Srivastava and colleagues in the Proceedings of the National Academy of Science in 2013 (5) as well as discuss the findings from this dataset in relation to both CarD and mycobacterial transcription as a whole. The ChIP-seq data have been deposited in the Gene Expression Omnibus (GEO) database, www.ncbi.nlm.nih.gov/geo (accession no. GSE48164).

18.
Genome Biol ; 14(9): R95, 2013.
Article in English | MEDLINE | ID: mdl-24020486

ABSTRACT

A large number of computational methods have been developed for analyzing differential gene expression in RNA-seq data. We describe a comprehensive evaluation of common methods using the SEQC benchmark dataset and ENCODE data. We consider a number of key features, including normalization, accuracy of differential expression detection and differential expression analysis when one condition has no detectable expression. We find significant differences among the methods, but note that array-based methods adapted to RNA-seq data perform comparably to methods designed for RNA-seq. Our results demonstrate that increasing the number of replicate samples significantly improves detection power over increased sequencing depth.


Subject(s)
High-Throughput Nucleotide Sequencing/statistics & numerical data , Nerve Tissue Proteins/genetics , RNA/genetics , Sequence Analysis, RNA/statistics & numerical data , Software , Brain Chemistry , Cell Line , Datasets as Topic , Gene Expression , Gene Expression Profiling , Humans , Oligonucleotide Array Sequence Analysis , Sequence Analysis, RNA/methods , Signal-To-Noise Ratio
19.
Mol Cell ; 32(4): 519-28, 2008 Nov 21.
Article in English | MEDLINE | ID: mdl-19026782

ABSTRACT

Small noncoding RNAs function in concert with Argonaute (Ago) proteins to regulate gene expression at the level of transcription, mRNA stability, or translation. Ago proteins bind small RNAs and form the core of silencing complexes. Here, we report the analysis of small RNAs associated with human Ago1 and Ago2 revealed by immunoprecipitation and deep sequencing. Among the reads, we find small RNAs originating from the small nucleolar RNA (snoRNA) ACA45. Moreover, processing of ACA45 requires Dicer activity but is independent of Drosha/DGCR8. Using bioinformatic prediction algorithms and luciferase reporter assays, we uncover the mediator subunit CDC2L6 as one potential mRNA target of ACA45 small RNAs, suggesting a role for ACA45-processing products in posttranscriptional gene silencing. We further identify a number of human snoRNAs with microRNA (miRNA)-like processing signatures. We have, therefore, identified a class of small RNAs in human cells that originate from snoRNAs and can function like miRNAs.


Subject(s)
MicroRNAs/metabolism , RNA, Small Nucleolar/metabolism , Algorithms , Argonaute Proteins , Cell Line , Computational Biology/methods , DEAD-box RNA Helicases/metabolism , Endoribonucleases/metabolism , Eukaryotic Initiation Factor-2/metabolism , Eukaryotic Initiation Factors/metabolism , Genes, Reporter , Humans , Kidney/cytology , Luciferases/metabolism , MicroRNAs/genetics , Models, Biological , RNA Interference , RNA Processing, Post-Transcriptional , RNA, Small Interfering/genetics , RNA, Small Interfering/metabolism , RNA, Small Nucleolar/genetics , RNA-Induced Silencing Complex/genetics , RNA-Induced Silencing Complex/metabolism , Ribonuclease III
20.
Cell ; 132(5): 860-74, 2008 Mar 07.
Article in English | MEDLINE | ID: mdl-18329371

ABSTRACT

To explore the role of Dicer-dependent control mechanisms in B lymphocyte development, we ablated this enzyme in early B cell progenitors. This resulted in a developmental block at the pro- to pre-B cell transition. Gene-expression profiling revealed a miR-17 approximately 92 signature in the 3'UTRs of genes upregulated in Dicer-deficient pro-B cells; a top miR-17 approximately 92 target, the proapoptotic molecule Bim, was highly upregulated. Accordingly, B cell development could be partially rescued by ablation of Bim or transgenic expression of the prosurvival protein Bcl-2. This allowed us to assess the impact of Dicer deficiency on the V(D)J recombination program in developing B cells. We found intact Ig gene rearrangements in immunoglobulin heavy (IgH) and kappa chain loci, but increased sterile transcription and usage of D(H) elements of the DSP family in IgH, and increased N sequence addition in Igkappa due to deregulated transcription of the terminal deoxynucleotidyl transferase gene.


Subject(s)
Antibody Diversity , B-Lymphocytes/cytology , Cell Survival , DEAD-box RNA Helicases/genetics , DEAD-box RNA Helicases/metabolism , Endoribonucleases/genetics , Endoribonucleases/metabolism , 3' Untranslated Regions/chemistry , 3' Untranslated Regions/metabolism , Animals , Blotting, Northern , Gene Expression Profiling , Gene Rearrangement, B-Lymphocyte , Immunoglobulins/genetics , Mice , Mice, Knockout , MicroRNAs/metabolism , Oligonucleotide Array Sequence Analysis , Reverse Transcriptase Polymerase Chain Reaction , Ribonuclease III , Specific Pathogen-Free Organisms
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