Overlapping Probabilities of Top Ranking Gene Lists, Hypergeometric Distribution, and Stringency of Gene Selection Criterion

The treatment of breast cancer has benefitted tremendously from the generation of estrogen receptor-a (ERa)-targeted therapies, but disease relapse continues to pose a challenge due to intrinsic or acquired drug resistance. In an effort to delineate potential predictive biomarkers of therapy responsiveness, multiple groups have identified several uncharacterized cofactors and interacting partners of ERa, including Split Ends (SPEN), a transcriptional corepressor. Here, we demonstrate a role for SPEN in ERa-expressing breast cancers. SPEN nonsense mutations were detectable in the ERa-expressing breast cancer cell line T47D and corresponded to undetectable protein levels. Further analysis of 101 primary breast tumors revealed that 23% displayed loss of heterozygosity at the SPEN locus and that 3% to 4% harbored somatically acquired mutations. A combination of in vitro and in vivo functional assays with microarray-based pathway analyses showed that SPEN functions as a tumor suppressor to regulate cell proliferation, tumor growth, and survival. We also found that SPEN binds ERa in a ligand-independent manner and negatively regulates the transcription of ERa targets. Moreover, we demonstrate that SPEN overexpression sensitizes hormone receptor-positive breast cancer cells to the apoptotic effects of tamoxifen, but has no effect on responsiveness to fulvestrant. Consistent with these findings, two independent datasets revealed that high SPEN protein and RNA expression in ERa-positive breast tumors predicted favorable outcome in patients treated with tamoxifen alone. Together, our data suggest that SPEN is a novel tumor-suppressor gene that may be clinically useful as a predictive biomarker of tamoxifen response in ERa-positive breast cancers. Cancer Res; 75(20); 4351-63. Ó2015 AACR.

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“…S6B-S6E; ref. 28). Interestingly, no such enrichment was observed with the lists of downregulated genes in MCF-7-shRNA-SPEN cells.…”

Section: Transcriptional Regulation Of the Era Targets By Spenmentioning

confidence: 84%

The Estrogen Receptor Cofactor SPEN Functions as a Tumor Suppressor and Candidate Biomarker of Drug Responsiveness in Hormone-Dependent Breast Cancers

et al. 2015

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“…Differentially modeled (remodeled for WT or mismodeled for chdC nulls) genes were identified by cross-comparison of paired read midpoint position and peak value date, and selected only if they reproducibly contained three nonmatching nucleosomes (differing in either nucleosome position or peak height) within 1000 bp 3 ′ to the ATG start site, for two independent biological replicates. The significance of the overlap between gene lists was determined using the hypergeometric distribution (Fury et al 2006). RNA extraction and RNA sequencing RNA was isolated from WT and chdC-null cells strains using TRIzol (Invitrogen) and following the manufacturer's instructions.…”

Section: Data Analysis For Nucleosome Positioningmentioning

confidence: 99%

Regulation of nucleosome positioning by a CHD Type III chromatin remodeler and its relationship to developmental gene expression inDictyostelium

et al. 2017

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Nucleosome placement and repositioning can direct transcription of individual genes; however, the precise interactions of these events are complex and largely unresolved at the whole-genome level. The Chromodomain-Helicase-DNA binding (CHD) Type III proteins are a subfamily of SWI2/SNF2 proteins that control nucleosome positioning and are associated with several complex human disorders, including CHARGE syndrome and autism. Type III CHDs are required for multicellular development of animals and Dictyostelium but are absent in plants and yeast. These CHDs can mediate nucleosome translocation in vitro, but their in vivo mechanism is unknown. Here, we use genome-wide analysis of nucleosome positioning and transcription profiling to investigate the in vivo relationship between nucleosome positioning and gene expression during development of wild-type (WT) Dictyostelium and mutant cells lacking ChdC, a Type III CHD protein ortholog. We demonstrate major nucleosome positional changes associated with developmental gene regulation in WT. Loss of chdC caused an increase of intragenic nucleosome spacing and misregulation of gene expression, affecting ∼50% of the genes that are repositioned during WT development. These analyses demonstrate active nucleosome repositioning during Dictyostelium multicellular development, establish an in vivo function of CHD Type III chromatin remodeling proteins in this process, and reveal the detailed relationship between nucleosome positioning and gene regulation, as cells transition between developmental states.

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“…The significance of overlap between differentially methylated CpG sets was verified by means of the hypergeometric test. 35 Kruskall-Wallis statistics were used to compare the methylation profiles determined for murine samples. A search of the single-nucleotide polymorphism (SNP) database available at the University of California, Santa Cruz genome annotation database identified 18 SNPs in total (http://hgdownload.cse.ucsc.edu/ goldenPath/hg19/database; dbSNP build 131).…”

Section: Sequence Data Analysismentioning

confidence: 99%

Loss of imprinting at the 14q32 domain is associated with microRNA overexpression in acute promyelocytic leukemia

Manodoro¹,

Marzec

Chaplin³

et al. 2014

Blood

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Key Points• Loss of imprinting occurs at the 14q32 domain in APL.• DNA methylation at the CTCF binding sites correlates with the overexpression of 14q32 miRNAs.Distinct patterns of DNA methylation characterize the epigenetic landscape of promyelocytic leukemia/retinoic acid receptor-a (PML-RARa)-associated acute promyelocytic leukemia (APL). We previously reported that the microRNAs (miRNAs) clustered on chromosome 14q32 are overexpressed only in APL. Here, using high-throughput bisulfite sequencing, we identified an APL-associated hypermethylation at the upstream differentially methylated region (DMR), which also included the site motifs for the enhancer blocking protein CCCTC-binding factor (CTCF). Comparing the profiles of diagnostic/ remission paired patient samples, we show that hypermethylation was acquired in APL in a monoallelic manner. The cytosine guanine dinucleotide status of the DMR correlated with expression of the miRNAs following a characteristic position-dependent pattern. Moreover, a signature of hypermethylation was also detected in leukemic cells from an established transgenic PML-RARA APL mouse model at the orthologous region on chromosome 12, including the CTCF binding site located upstream from the mouse miRNA cluster. These results, together with the demonstration that the region does not show DNA methylation changes during myeloid differentiation, provide evidence that 14q32 hypermethylation is implicated in the pathogenesis of APL. We propose a model in which loss of imprinting at the 14q32 domain leads to overexpression of the miRNAs in APL. (Blood. 2014;123(13):2066-2074 IntroductionAcute promyelocytic leukemia (APL) is a subclass of acute myeloid leukemia (AML) characterized by the balanced reciprocal translocation t(15;17)(q22;q11-12) resulting in the fusion between the promyelocytic leukemia gene (PML) and the retinoic acid receptor-a (RARA) gene. 1 The chimeric protein PML-RARa leads to a block of myeloid cell differentiation through constitutive repression of retinoic acid responsive genes.2 This is consistent with the typical accumulation of abnormal hematopoietic progenitor cells blocked at the promyelocyte stage. Accordingly, PML-RARa has been shown to induce APL in transgenic mice. 3 However, deregulation of the retinoic acid pathway is insufficient to initiate APL, 4 and several studies have shown additional genetic and epigenetic processes that accompany the expression of the PML-RARa protein, 5,6 also involving master transcription regulators 7 and modulators of chromatin structure. 8,9 MicroRNAs (miRNAs) are single-stranded small noncoding RNAs (sncRNAs) that negatively regulate the expression of target genes.10 They have been extensively associated with cancer as regulators of cell proliferation, differentiation, and apoptosis. 11 We have previously reported a signature of overexpressed miRNAs in APL.12 These miRNAs are clustered in the DLK1-DIO3 imprinted domain on chromosome 14q32, 13,14 and their specific upregulation in primary APL cells was also confirmed by other ...

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Overlapping Probabilities of Top Ranking Gene Lists, Hypergeometric Distribution, and Stringency of Gene Selection Criterion

Cited by 98 publications

References 12 publications

The Estrogen Receptor Cofactor SPEN Functions as a Tumor Suppressor and Candidate Biomarker of Drug Responsiveness in Hormone-Dependent Breast Cancers

The Estrogen Receptor Cofactor SPEN Functions as a Tumor Suppressor and Candidate Biomarker of Drug Responsiveness in Hormone-Dependent Breast Cancers

Regulation of nucleosome positioning by a CHD Type III chromatin remodeler and its relationship to developmental gene expression inDictyostelium

Loss of imprinting at the 14q32 domain is associated with microRNA overexpression in acute promyelocytic leukemia

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