Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Targeting KDM4A epigenetically activates tumor cell-intrinsic immunity and overcomes resistance to PD1 blockade in squamous cell carcinoma by inducing DNA replication stress

ABSTRACT: To investigate the mechanisms by which KDM4A knockout ameliorates the invasive growth and metastasis of primary mouse squamous cell carcinoma (SCC), we isolated fresh SCCs from tumor cell-specific KDM4A knockout and control mice, and then did the whole transcriptome analysis using RNA-Seq. Results showed that KDM4A knockout stimulated anti-tumor immunity.

ORGANISM(S): Mus musculus

PROVIDER: GSE137953 | GEO | 2021/03/23

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

KDM4A regulated genes in human squamous carcinoma cells

Project description:To establish a robust cellular model system for screening genes associated with cell invasion, we over-expressed the oncogenic translocated promoter region (Tpr)-MET proteins in SCC23 cells (SCC23/MET). Using a functional siRNA screen, we identified that the histone demethylase KDM4A played a critical role in the invasive growth and metastasis of SCC mediated by the Oncogenic MET. To investigate the molecular mechanism through which KDM4A inhibit the tumor cell invasion, we knock-down KDM4A in SCC23/MET cell and performed a gene microarray to examine which genes may be regulaged by kDM4A. We generated two stable cell lines. one was infected with virus containing scramble and another infected with virus infected with virus containing KDM4A shRNA. Total RNA were extracted from these two cell lines and subject to microarray.

2013-05-03 | E-GEOD-44238 | biostudies-arrayexpress

KDM4A regulated genes in human squamous carcinoma cells

2013-05-03 | GSE44238 | GEO

2.5 dpc Uterus Chip-Seq of Kdm4a mice

Project description:Purpose: ChipSeq allows us to identify binding sites of target proteins of interest in the genome, helping create a global profile for the same. Kdm4a is a H3K9me3 histone demethylase that acts to prevent spurious accumulation of this repressive mark at H3K4me3 positive transcription start sites. To complement transcriptome data from Kdm4a mice, we performed Chip-Seq on 2.5dpc mouse uterus of 8-10 week old littermate control and Kdm4a knockout mice for Kdm4a, H3K9me3 and H3K4me3. This would help us check which of the target genes with changed gene expression was due to the direct change in histone lanscape in absence of Kdm4a.

2017-08-17 | GSE96591 | GEO

Identification of Kdm4a, b and c target genes in MLL-AF9 transformed mouse GMPs (L-GMP) [gene expression]

Project description:In this study we identify genes, that are deregulated in Kdm4a, b and c triple knockout L-GMP cells compared WT L-GMP cells. Four MLL-AF9 transformed L-GMP cell lines conditional knockout for Kdm4a, b and c, were derived from leukemic mice. The cells were treated with 4-hydroxytamoxifen and total RNA was prepared from 0h, 48h and 96h time points.

2016-06-02 | E-GEOD-81298 | biostudies-arrayexpress

2.5 dpc female HPG axis RNASeq of Kdm4a wildtype and knockout mice

Project description:Purpose: We performed RNA-Seq on 2.5dpc mouse hypothalamus, pituitary, ovary and uterus of 8-10 week old littermate female control and Kdm4a knockout mice. Upon observing for the extent of altered genes of physiological relevance to observed female infertility phenotype, this would help us narrow down the most relevant tissue to perform genome wide ChipSeq binding profiles for Kdm4a, H3K4me3 and H3K9me3. This dataset would present likely target genes under direct control of Kdm4a.

2017-08-17 | GSE96685 | GEO

Identification of Kdm4a and c target genes in MLL-AF9 transformed mouse GMPs (L-GMP) [ChIP-seq]

Project description:In this study we identify genes, that are bound by Kdm4a and Kdm4c in L-GMP cells. MLL-AF9 transformed L-GMP cell lines conditional knockout for Kdm4a, b and c, were derived from leukemic mice. The cells were treated with 4-hydroxytamoxifen and chromatin was prepared from untreated cells (Ctrl) and cells treated for 96hr.

2016-06-02 | E-GEOD-81299 | biostudies-arrayexpress

KDM4A regulated gene expression in human prostate cancer LNCaP cell

Project description:Histone lysine demethylase KDM4A is overexpressed in prostate cancer and plays a crucial role in tumor growth and survival. To understand the mechanisms underlying KDM4A-depedent cell growth and survival, microarray analysis was performed in LNCaP cells transduced with control or KDM4A specific-knockdown construct. The role of KDM4A in prostate carcinogenesis involves activation of E2F1 and androgen receptor transcriptional profiles. LNCaP cells were transduced by lentivirus carrying control pLKO.1 (empty vector) or shKDM4A construct (KDM4A-specific shRNA) for three days, followed by RNA extraction. Affymetrix GeneChip Human Genome U133 Plus 2.0 Arrays were used for microarray analysis.

2016-07-26 | E-GEOD-77928 | biostudies-arrayexpress

Targeting KDM4A epigenetically activates tumor cell-intrinsic immunity and overcomes resistance to PD1 blockade in squamous cell carcinoma by inducing DNA replication stress

Project description:Targeting KDM4A epigenetically activates tumor cell-intrinsic immunity and overcomes resistance to PD1 blockade in squamous cell carcinoma by inducing DNA replication stress

| PRJNA573945 | ENA

SMARTSeq_v4 paired end mRNA Seq of Kdm4a control mutant oocytes and preimplantation embryos

Project description:Purpose: The goal of this study was to generate paired-end mRNA Seq transcriptomes of control and Kdm4a mutant oocytes, 2-cell, 4-cell and 8-cell preimplantation embryos to study the dynamics of differentially expressed genes during early development Methods: MII oocytes were isolated from wildtype and Kdm4a knockout mice. 16 MII oocytes from each genotype were washed in M2 medim after zona pellucida removal, washed once in nuclease free water and directly lysed and cDNA prepared according to the manufacturers instructions. Meanwhile, control and knockout MII oocytes were also in vitro fertilised with Kdm4a knockout sperm to produce control (+/-) and maternal mutant (-/-) embryos, and cultured in KSOM EmbryoMax medium (Sigma). 16 embryos were staged each day and harvested according to control embryos. Healthiest mutants were chosen for comparison with minimal secondary effects arising from dead/dying embryos. Similar to oocytes, individual cDNA were prepared and amplified according to manufacturers instructions in nuclease free conditions. Conclusions: Our study represents a detailed analysis of differentially expressed genes in oocytes and embryos lacking maternal and endogenous Kdm4a, with sixteen biological replicates, generated by SMARTSeq v4 paired end RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles between the samples at each developmental stage. Our results show that there is a consistent downrgulation of zygotic genome activation (ZGA) genes in the mutant 2-cell embryos. Mutant 4 and 8-cell embryos have significant upregulation of minor ZGA genes giving us robust statistical significance. We conclude that Kdm4a is required for proper gene activation during maternal-to zygotic transition in conjuction with a permissive chromatin landscape.

2020-01-30 | GSE129731 | GEO

Identification of Kdm4a, b and c target genes in MLL-AF9 transformed mouse GMPs (L-GMP) [gene expression]

Project description:In this study we identify genes, that are deregulated in Kdm4a, b and c triple knockout L-GMP cells compared WT L-GMP cells.

2016-06-02 | GSE81298 | GEO