Transcriptome profiling associated with CARD11 overexpression in Colorectal Cancer implicates a potential role for Tumour Immune Microenvironment and Cancer pathways modulation via NF-κB
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1106895 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR28867700.fastq.gz | Fastqsanger.gz | |||
| SRR28867701.fastq.gz | Fastqsanger.gz | |||
| SRR28867702.fastq.gz | Fastqsanger.gz | |||
| SRR28867703.fastq.gz | Fastqsanger.gz | |||
| SRR28867704.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 35 |
Similar Datasets
Project description:The immune system plays a critical role in inflammation by initiating responses to infection or tissue damage. NF-κB pathway plays a key role in inflammation and innate immunity, as well as other cellular activities. Furthermore, dysregulation of this well-choreographed pathway has been observed in many diseases, including cancer. CARD11 is a key molecule in the BCL-10, MALT1 (CBM) complex which is involved in transducing the signal downstream of the NF-κB pathway. This study aims to understand how overexpression of CARD11 adversely affects the prognosis in colorectal cancer (CRC) as it progresses towards aggressive form of the disease and the role that CARD11 plays in modulating the immune response across the different stages of CRC. To identify some of the cellular pathways activated as a result of CARD11, whole tran-scriptomics analysis was carried comparing the transcriptomic profile of CARD11-overexpressed HCT-116 and HT-29 CRC cell lines with empty vector-transfected cell lines as well as comparing adenoma and carcinoma CRC patients with CARD11- and CARD11+ expression. The whole tran-scriptomics and bioinformatics analysis results strongly suggested that CARD11 appears to play a key role in CRC progression. Absolute Gene Set Enrichment Analysis (absGSEA) on HCT-116 transcriptomics data showed that CARD11 overexpression promotes cell growth, and tissue re-modeling as well as enhancing the cell’s immune response. Some of the underlying genes in-volved in such processes through co-expression with CARD11 include EP300, KDM5A, HIF1A, NFKBIZ, and DUSP1. Results for HT-29 showed that CARD11 overexpression induces chemotaxis and ECM organization pathways through co-expression of IL1RN, MDK, and SPP1 as well as var-ious chemokines including CXCL1, CXCL3 and CCL22 which were shown to contribute to the more invasive stage of CRC. For patients, the adenoma patients include genes related to tumour immune microenvironment such as IL6ST, genes related to collagen family as well as other genes related to transition to CRC such as GLI3 and PIEZO2. While carcinoma patients show dramatic increase in the expression of MAPK8IP2 in CARD11+ carcinoma patients in addition to other genes related to cancer processes including EMB, EPHB6, and CPEB4. Taken together, the results show that CARD11 overexpression contributes to the progression of CRC through modu-lation of various tumour immune microenvironment pathways and activation of cancer path-ways possibly via the dysregulation of NF-κB. To our knowledge, this is probably the first study that investigates the role of CARD11 in CRC and the genes and pathways associated with CARD11 overexpression may provide insights into the early diagnostic and possible therapeutic targets for CRC.
2024-07-31 | GSE266390 | GEO
Project description:Several “primary atopic disorders” are linked to monogenic defects that attenuate TCR signaling, favoring T helper 2 (TH2) cell differentiation. Patients with CARD11-associated atopy with dominant interference of NF-κB signaling (CADINS) disease suffer from severe atopy, caused by germline loss-of-function/dominant interfering (LOF/DI) CARD11 variants. The CARD11 scaffold enables TCR-induced activation of NF-κB, mTORC1, and JNK signaling, yet the function of CARD11-dependent JNK signaling in T cells remains nebulous. Here we show that CARD11 is critical for TCR-induced activation of JNK1 and JNK2, as well as canonical JUN/FOS AP-1 family members. Patient-derived CARD11 DI variants attenuated wild-type CARD11 JNK signaling, mirroring effects on NF-κB. Transcriptome profiling revealed JNK inhibition upregulated TCR-induced expression of GATA3 and NFATC1, key transcription factors for TH2 cell development. Further, impaired CARD11-JNK signaling was linked to enhanced GATA3 expression in CADINS patient T cells. Our findings reveal a novel intrinsic mechanism connecting impaired CARD11-dependent JNK signaling to enhanced GATA3/NFAT2 induction and TH2 cell differentiation in CADINS patients.
2025-02-28 | GSE288360 | GEO
Project description:This SuperSeries is composed of the following subset Series: GSE40171: RNA sequencing of circulating tumour cells implicates WNT signaling in pancreatic cancer metastasis (mouse data) GSE40174: RNA sequencing of circulating tumour cells implicates WNT signaling in pancreatic cancer metastasis (human data) Refer to individual Series
2012-08-17 | E-GEOD-40176 | biostudies-arrayexpress
Project description:NF-κB has an essential role in innate immune response and inflammation and is involved in cancer development and progression. We apply the SEC-PCP-SILAC method incorporating metabolic labeling, size exclusion chromatography and protein correlation profiling to construct a complex network of interactome rearrangement in response to NF-κB modulation in breast cancer cells. Our interaction network represents a complex insight into the dynamics of MCF-7 protein interactome associated with NF-κB pathway. Our dataset could serve as a basis for future studies characterizing role of NF-κB in breast cancer cellular pathways. This PRIDE project includes results from SILAC labeled and label-free replicates from the SEC-PCP-SILAC analysis of protein complexes in MCF-7 cells with inhibited and uninhibited NF-κB pathway, results from the immunoprecipitation experiment aimed at interaction partners of NF-κB factor RELA, analysis of total proteome after NF-κB inhibition, and results from SEC fractionation of untreated and unlabeled MCF-7 cells.
2024-02-28 | PXD040125 | Pride
Project description:Background: The most aggressive subtype of breast cancer, triple-negative breast cancer (TNBC), has a worse prognosis and a higher probability of relapse since there is a narrow range of treatment options. Identifying and testing potential therapeutic targets for the treatment of TNBC is of high priority. Methods: Using a transcriptional signature of triple-negative breast cancer collected from Gene Expression Omnibus (GEO), CMap was utilized to reposition compounds for the treatment of TNBC. CCK8 and colony formation experiments were performed to detect the effect of the candidate drug on the proliferation of TNBC cells, while flow cytometry was used to detect cell apoptosis. Meanwhile, transwell assay was implemented to detect cell metastasis change caused by the candidate drug. Moreover, the proteomic approach was presently ongoing to evaluate the underlying mechanism of the candidate drug in TNBC. Furthermore, drug affinity responsive target stability (DARTS) coupled with LC-MS/MS was carried out to explore the potential drug target candidate in TNBC cells. Results: We found that the most widely used medication, eugenol, reduced the growth and metastasis of TNBC cells. According to the underlying mechanism revealed by proteomics, eugenol could inhibit TNBC cell proliferation via the NOD1-NF-κB signaling pathway. DARTS experiment further revealed that eugenol may bind to NF-κB in TNBC cells. Concludes: Our findings pointed out that eugenol was a potential candidate drug for the treatment of TNBC.
2023-05-10 | PXD039305 | Pride
Project description:Caspase recruitment domain-containing protein 11 (CARD11) is a multi-domain scaffolding protein critical for the adaptive immune response that is required for antigen receptor signaling to canonical NF-kB, mTOR, JNK, and AKT. Oncogenic gain-of-function (GOF) CARD11 mutants, implicated in a variety of lymphomas, bypass normal regulation and signal constitutively. In a mouse model expressing the lymphoma-associated GOF mutation CARD11 C49Y, we observed splenomegaly concomitant with B cell expansion that was most pronounced for Marginal Zone (MZ) B cells. CARD11C49Y/C49Y MZ B cells exhibited enhanced cell-autonomous survivability and elevated basal levels of the precursor NF-kB subunit p100, which was inducibly processed, leading to elevated nuclear p52 levels in response to BAFF. We show in a heterologous assay that active CARD11 variants can inhibit basal NIK-induced p100 processing to p52 independently of their ability to activate canonical NF-kB. Our results reveal an unexpected ability of CARD11 GOF mutants to potentiate the noncanonical NF-kB pathway through p100 accumulation, which likely contributes to the dysregulated B cell expansion observed in lymphomas that harbor CARD11 GOF variants.
2025-10-09 | GSE287097 | GEO
Project description:Activation of NFkB pathway by CARD11 Cy3-labelled untreated sample and Cy5-labelled treated sample were hybridized to a Lymphochip microarray.
2010-07-01 | E-GEOD-3896 | biostudies-arrayexpress
Project description:Aims: Polystyrene microplastics (PS-MPs) are emerging environmental pollutants, but their impact on lung cancer treatment remains unclear. This study investigates how PS-MPs affect radiotherapy efficacy in lung cancer, focusing on their role in ferroptosis regulation and NF-κB pathway activation. Results: PS-MPs were rapidly internalized by lung cancer cells and remained detectable across multiple passages. Exposure to PS-MPs promoted lung cancer cell proliferation, increased mitochondrial length, and elevated Ki67 and c-Myc expression. Following ionizing radiation, PS-MPs significantly attenuated radiation-induced ferroptosis, as evidenced by reduced mitochondrial damage, lipid peroxidation, and GSH depletion. Transcriptomic analysis revealed that PS-MPs activated the NF-κB pathway, leading to increased phosphorylation of IKKβ, IκBα degradation, and enhanced nuclear translocation of NF-κB. In vivo, PS-MPs accumulated in lung tumor-bearing mice, reducing radiotherapy efficacy by increasing tumor volume and weight while decreasing survival rates. Knockdown of NF-κB restored ferroptosis sensitivity and mitigated PS-MPs-induced radioresistance, confirming the NF-κB-dependent inhibition of ferroptosis. Innovation and Conclusion: This study provides the first evidence that PS-MPs impair radiotherapy efficacy in lung cancer by suppressing ferroptosis via NF-κB activation. Unlike previous research focusing on microplastic toxicity in normal tissues, our findings highlight their oncological impact and potential role as an environmental factor influencing cancer therapy resistance. These results emphasize the need for further investigation into microplastics as emerging disruptors of redox homeostasis in oncology and their broader implications for environmental and cancer research.
2025-09-08 | GSE307179 | GEO
Project description:Activation of NFkB pathway by CARD11 Keywords: time series design
2006-03-30 | GSE3896 | GEO
Project description:Post-translational modification of NF-κB subunits provides a mechanism to differentially regulate their activity in response to the many stimuli that can induce this pathway. However, the physiological significance of these modifications is largely unknown and it remains unclear if these have a critical role in the normal and pathological functions of NF-κB in vivo. Among these, phosphorylation of the RelA(p65) Thr505 residue has been described as an important regulator of NF-κB activity in cell lines but its physiological significance was not known. Therefore, to learn more about the role of this pathway in vivo, we generated a knockin mouse with a RelA T505A mutation. Unlike RelA knockout mice, the RelA T505A mice develop normally but exhibit aberrant hepatocyte proliferation following liver partial hepatectomy or damage resulting from carbon tetrachloride treatment. Consistent with these effects, RelA T505A mice exhibit earlier onset of cancer in the N-nitrosodiethylamine (DEN) model of hepatocellular carcinoma. This data reveals a critical pathway controlling NF-κB function in the liver that acts to suppress tumour-promoting activities of RelA.
2015-11-30 | E-MTAB-3596 | biostudies-arrayexpress