RNA sequencing analysis of gene expresssion profiles in Cic-null MZB cells
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PROVIDER: PRJNA1103750 | ENA |
REPOSITORIES: ENA
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Project description:Purpose: The goal of this study is to compare and examine the transcriptional profiles in Cd19-Cre (control) versus Cicf/f;Cd19-Cre (Cic-null) MZB cells,by mRNA sequencing. Methods: MZB cells (CD19+CD93-CD21+CD23-) were sorted by a MoFlo-Astrios (Beckman Coulter). Total RNA was extracted using TRIzol Reagent (GeneAll), according to the manufacturer’s instructions. . A library for mRNA sequencing was prepared using the Truseq Stranded mRNA/Total Library Prep Kit (Illumina) according to the manufacturer’s instructions. Sequencing was performed with Novaseq 6000 (Illumina). Results: Tophat (v2.0.13) was used to map reads for each sample to the mm10 RefSeq reference genome. The aligned results were then added to Cuffdiff (v2.2.0) to identify the differentially expressed genes (DEGs). In total, 775 genes were differentially expressed in Cic-null MZB cells (505 upregulated and 270 downregulated) compared to control cells (Log2 fold-change > 0.5 and P < 0.01). Conclusions: Our study presents the first comparative gene expression analysis of MZB cells from control and B cell-specific Cic-deficient mice. We concluded that CIC deficiency attenuates MZB cell development through downregulation of the NOTCH signaling pathway. The data reported here also provide references for the gene expression profiles of murine MZB cells through TPM.
2024-04-29 | GSE264654 | GEO
Project description:Purpose: The goal of this study is to compare and examine the transcriptional profiles in control versus Cic-deficient B cells, specifically splenic B-1a and Fo B cells, by mRNA sequencing. Methods: Splenic B-1a (IgM+, CD19+, CD5+, CD43+) and Fo B (B220+, CD93-, CD23+, CD21lo-mid) cells were sorted by a MoFlo-XDP (Beckman Coulter). Total RNA was extracted using TRIzol Reagent (GeneAll), according to the manufacturer’s instructions. The DNA library for mRNA sequencing was generated using SMART-seq v4 Ultra Input RNA Kit (Clontech, for B-1a cells) and TruSeq RNA Sample Prep Kit v2 (Illumina, for Fo B cells). DNA libraries were multiplexed and pooled for sequencing on the Illumina Hiseq 4000 platform. Results: Trimmed reads were mapped to mouse reference genome (mm10 RefSeq) with HISAT2, a splice-aware aligner, and transcripts were assembled by StringTie with aligned reads, for known transcripts, novel transcripts, and alternatively spliced transcripts. A total of 712 genes were differentially expressed in Cic-null B-1a cells (325 upregulated and 387 downregulated), while 357 genes were differentially expressed in Cic-deficient Fo B cells (180 upregulated and 178 downregulated) when compared with their respective control cells (fold change >1.2 and P < 0.05). Several known CIC target genes, including Etv1, Etv4, Etv5, Spry4, Spred1, Spred2, Dusp4, Dusp6, and Per2, were included in the list of the upregulated differentially expressed genes (DEGs) in either Cic-null B-1a or Fo B cells or both, validating the reliability of RNA sequencing results. Conclusions: Our study presents the first comparative gene expression analysis of B-1a and Fo B cells from control and B cell-specific Cic-deficient mice. We concluded that CIC deficiency promotes B-1a cell development through enhancing the BCR signaling pathway. The data reported here also provide references for the gene expression profiles of murine B-1a and Fo B cells.
2021-12-16 | GSE163455 | GEO
Project description:Gene expresssion profiles in PPARalpha-Serine280 phosphorylation mutants
| PRJNA445605 | ENA
Project description:Purpose: B-1a cells have a distinct BCR repertoire compared with that of B-2 cells. To examine whether CIC loss affects the BCR repertoire in B-1a cells, we analyzed mRNA sequences of immunoglobulin heavy (Igh) and light (Igk and Igl) chain genes in B-1a cells from 12-week-old control and Cicf/f;Cd19-Cre mice. Methods: Peritoneal cavity B-1a cells (IgM+, CD19+, CD5+, CD43+) were sorted by a MoFlo-XDP (Beckman Coulter). Total RNA was extracted using TRIzol Reagent (GeneAll), according to the manufacturer’s instructions. Long Read iR-Profile Reagent System (iRepertoire) was used to generate NGS libraries covering BCR chains including Igh, Igk, and Igl. Briefly, nested inside and outside primers selectively amplified all V- and C- regions and incorporated communal adaptors. Following clean up, only target amplicons, which contain 5’ and 3’ communal adaptors, were exponentially amplified. Amplified libraries were multiplexed for sequencing on the Illumina Miseq platform. Sequence reads were de-multiplexed according to the barcode sequences. Results: Trimmed reads were mapped to germline V, D and J reference sequences downloaded from the IMGT database. IgH diversity and the usage of variable (V) segments in heavy (Ighv) chain and light (Igkv and Iglv) chain genes were comparable between control and Cic-null B-1a cells. Analysis of non-templated (N)-nucleotide addition at V(D)J junctions revealed that Cic-null B-1a cells have a higher proportion of zero to two N-nucleotides-containing-BCRs than control cells. Conclusions: Our study presents the first comparative BCR repertoire analysis of wild-type and Cic-null B-1a cells. We concluded that CIC deficiency does not dramatically alter the BCR repertoire in B-1a cells.
2021-12-16 | GSE164147 | GEO
Project description:RNA Sequencing Analysis of Gene Expression Profiles in Cic-null B-1a and Follicular B (Fo B) cells
| PRJNA686176 | ENA
Project description:Purpose : The goal of this study is to compare the gene expression profiles between wild-type (WT) and CIC-deficient DP thymocytes to understand the molecular mechanisms of CIC regulation of T cell development, especially in DP thymocytes. Methods : DP thymocytes (lin-CD4+CD8+TCRlo (Lineage : CD11b, CD11c, CD19, NK1.1, Gr-1, γδTCR, and TER119)) from thymus were sorted by a MoFlo-XDP (Beckman Coulter). Total RNA was extracted using RiboEX (GeneAll) according to the manufacturer's instructions. The library for mRNA sequencing was generated using the TruSeq Stranded Total RNA LT Sample Prep Kit (Illumina) and sequencing was performed with NovaSeq 6000 (Illumina). Results : Trimmed reads were mapped to the mouse reference genome (mm10 RefSeq) with HISAT2, and the transcripts were assembled using StringTie. A total of 482 differentially expressed genes (DEGs; fold change > 2 and P-value < 0.05) were generated using edgeR. The 263 upregulated genes included known CIC target genes such as Etv1, Etv4, Etv5, Spry4, Spred1, Dusp4, and Dusp6. Conclusions : Our study represents the first comparative analysis of DP thymocytes from WT and hematopoietic lineage cell-specific Cic deficient mice. We concluded that CIC deficiency leads to impaired positive and negative selection, and TCR signaling in DP cells. The attenuation of TCR signaling is caused by derepression of CIC target genes involved in dephosphorylation of ERK.
2021-05-06 | GSE173909 | GEO
Project description:Purpose: The goals of this study is to compare and examine the transcriptional profile in the secondary mammospheres of control versus CIC-deficient T47D cells by mRNA sequencing and to understand the molecular basis of the CIC regulation of CSC-like properties in luminal type of breast cancer cells. Methods: DNA library for mRNA sequencing of secondary mammospheres derived from control and CIC-deficient T47D breast cancer cells was prepared using a TruSeq Stranded Total RNA LT Sample Prep Kit (Gold) and their libraries sequenced on the NovaSeq sequencer accompanying the NovaSeq 6000 S4 Reagent Kit. The trimmed reads that passed quality filters were mapped to reference genome with HISAT2, followed by assembly of transcript with StringTie. Results: A total of 20377 genes were differentially expressed (10438 upregulated and 9939 downregulated) in the CIC-deficient T47D mammospheres when compared with control mammospheres. Approximately 5% of the transcripts showed differential expression between the control and CIC-deficient secondary mammospheres, with a fold change ≥1.2 and p value <0.05. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Gene Ontology (GO) analyses revealed that CIC-deficient mammospheres differentially expressed genes that are involved in processes associated with cancer progression such as cell cycle, cell proliferation, cell growth, and apoptotic process, as well as autoimmunity. Conclusions: Our results show the first comparative analysis of secondary mammospheres derived from control and CIC-deficient T47D breast cancer cells. The data reported here should also provide reference for expression profiles of CSC-like cells in ER+/PR+/HER2- luminal breast cancer cells. We conclude that CIC deficiency promotes CSC-like properties and thus breast cancer progression through controlling CSC-related pathways including focal adhesion and extracellular matrix (ECM)-receptor interactions, and may also regulate cell cycle, cell proliferation, and apoptosis.
2019-12-18 | GSE142171 | GEO
Project description:CIC-DUX4 sarcoma (CDS) or CIC-rearranged sarcoma is a subcategory of small round cell sarcoma resembling the morphological phenotypes of Ewing sarcoma (ES). Recent clinicopathologic and molecular genetic analyses indicate that CDS is an independent disease entity from ES. Although a few ancillary markers have been used in the differential diagnosis of CDS, additional CDS-specific biomarkers are needed in challenging diagnosis for a more definitive classification. Here we have generated an ex vivo mouse model for CDS by transducing embryonic mesenchymal cells (eMCs) with human CIC-DUX4 cDNA. The recipient mice transplanted with eMCs expressing CIC-DUX4 rapidly developed an aggressive, undifferentiated sarcoma composed of small round to short spindle cells. Gene expression profiles of CDS and eMCs revealed upregulation of CIC-DUX4 downstream genes such as PEA3 family genes, Ccnd2, Crh and Zic1. Immunohistochemical analyses for both mouse and human tumors showed that CCND2 and MUC5AC are reliable biomarkers to distinguish CDS from ES. Gene silencing of CIC-DUX4 as well as Ccnd2, Ret, and Bcl2, that are upregulated in CDS, effectively inhibited tumor growth in vitro. Palbociclib, a CDK4/6 inhibitor, also showed growth inhibition of mouse CDS cells in vitro, while trabectedin induced tumor suppressive effects both in vitro and in vivo. In summary, the CDS mouse model provides important biological information of CDS and is a useful platform to explore novel biomarkers and therapeutic agents for CDS. We used microarrays to detail the global program of gene expression in mouse CDS.
2017-06-21 | GSE90978 | GEO
Project description:Capicua (CIC)’s transcriptional repressor function is implicated in neurodevelopment and in oligodendroglioma (ODG) aetiology. However, CIC’s role in these contexts remains obscure, primarily from our currently limited knowledge regarding its biological functions. Moreover, CIC mutations in ODG invariably co-occur with a neomorphic IDH1/2 mutation, yet the functional relationship between these two genetic events is unknown. Here, we analysed models derived from an E6/E7/hTERT-immortalized (i.e. p53- and RB-deficient) normal human astrocyte cell line. To examine the consequences of CIC loss, we compared transcriptomic and epigenomic profiles between CIC wildtype and knockout cell lines, with and without mutant IDH1 expression. Our analyses revealed dysregulation of neurodevelopmental genes in association with CIC loss. CIC ChIP-seq was also performed to expand upon the currently limited ensemble of known CIC target genes. Among the newly identified direct CIC target genes were EPHA2 and ID1, whose functions are linked to neurodevelopment and the tumourigenicity of in vivo glioma tumour models. NFIA, a known mediator of gliogenesis, was discovered to be uniquely overexpressed in double mutant cells (CIC-knockout + IDH1-mutant). These results identify neurodevelopment and specific genes within this context as candidate targets through which CIC alterations may contribute to the progression of IDH-mutant gliomas.
2021-12-01 | GSE189860 | GEO
Project description:Capicua (CIC)’s transcriptional repressor function is implicated in neurodevelopment and in oligodendroglioma (ODG) aetiology. However, CIC’s role in these contexts remains obscure, primarily from our currently limited knowledge regarding its biological functions. Moreover, CIC mutations in ODG invariably co-occur with a neomorphic IDH1/2 mutation, yet the functional relationship between these two genetic events is unknown. Here, we analysed models derived from an E6/E7/hTERT-immortalized (i.e. p53- and RB-deficient) normal human astrocyte cell line. To examine the consequences of CIC loss, we compared transcriptomic and epigenomic profiles between CIC wildtype and knockout cell lines, with and without mutant IDH1 expression. Our analyses revealed dysregulation of neurodevelopmental genes in association with CIC loss. CIC ChIP-seq was also performed to expand upon the currently limited ensemble of known CIC target genes. Among the newly identified direct CIC target genes were EPHA2 and ID1, whose functions are linked to neurodevelopment and the tumourigenicity of in vivo glioma tumour models. NFIA, a known mediator of gliogenesis, was discovered to be uniquely overexpressed in double mutant cells (CIC-knockout + IDH1-mutant). These results identify neurodevelopment and specific genes within this context as candidate targets through which CIC alterations may contribute to the progression of IDH-mutant gliomas.
2021-12-01 | GSE189857 | GEO