An integrative approach to assess X-chromosome inactivation using allele-specific expression with applications to epithelial ovarian cancer

AbstractX chromosome inactivation (XCI) is a key epigenetic gene expression regulatory process, which may play a role in women’s cancer. In particular tissues, some genes are known to escape XCI, yet patterns of XCI in ovarian cancer (OC) and their clinical associations are largely unknown. To examine XCI in OC, we integrated germline genotype with tumor copy number, gene expression and DNA methylation information from 99 OC patients. Approximately 10% of genes showed different XCI status (either escaping or being subject to XCI) compared with the studies of other tissues. Many of these genes are known oncogenes or tumor suppressors (e.g. DDX3X, TRAPPC2 and TCEANC). We also observed strong association between cis promoter DNA methylation and allele-specific expression imbalance (P = 2.0 × 10−10). Cluster analyses of the integrated data identified two molecular subgroups of OC patients representing those with regulated (N = 47) and dysregulated (N = 52) XCI. This XCI cluster membership was associated with expression of X inactive specific transcript (P = 0.002), a known driver of XCI, as well as age, grade, stage, tumor histology and extent of rl disease following surgical debulking. Patients with dysregulated XCI (N = 52) had shorter time to recurrence (HR = 2.34, P = 0.001) and overall survival time (HR = 1.87, P = 0.02) than those with regulated XCI, although results were attenuated after covariate adjustment. Similar findings were observed when restricted to high-grade serous tumors. We found evidence of a unique OC XCI profile, suggesting that XCI may play an important role in OC biology. Additional studies to examine somatic changes with paired tumor-normal tissue are needed.

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Diverse mechanisms for epigenetic imprinting in mammals

10.1101/2021.04.30.442087 ◽

2021 ◽

Author(s):

Daniel Andergassen ◽

Zachary D Smith ◽

John L Rinn ◽

Alexander Meissner

Keyword(s):

Genomic Imprinting ◽

X Chromosome ◽

Gene Clusters ◽

Endogenous Retrovirus ◽

X Chromosome Inactivation ◽

Polycomb Group ◽

Chromosome Inactivation ◽

Epigenetic Mechanisms ◽

Specific Expression ◽

Allele Specific

Genomic imprinting and X chromosome inactivation (XCI) require epigenetic mechanisms to direct allele-specific expression. Despite their critical roles in embryonic development, how universal epigenetic regulators coordinate these specific tasks from single locus to chromosome-scale remains understudied. Here, we systematically disrupted multiple essential epigenetic pathways within polymorphic F1 zygotes to examine postimplantation effects on canonical and non-canonical genomic imprinting as well as X chromosome inactivation. We find that DNA methylation and Polycomb group repressors are both indispensable for autosomal imprinting, albeit at distinct gene sets. Moreover, the extraembryonic ectoderm relies on a broader spectrum of unique imprinting mechanisms, including non-canonical targeting of maternal endogenous retrovirus (ERV) driven promoters by G9a. We further utilize our data to identify Polycomb dependent and independent gene clusters on the imprinted X chromosome, which appears to reflect distinct domains of Xist-mediated suppression. Our data has allowed us to assemble a comprehensive inventory of the epigenetic mechanisms utilized in eutherian mammals to maintain parent-specific imprinting, including an expanded view of the placental lineage that comprises multiple unique pathways.

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Abstract 2420: Integrative analyses of gene expression, DNA methylation, genotype and copy number alterations characterize X-chromosome inactivation in ovarian cancer

10.1158/1538-7445.am2017-2420 ◽

2017 ◽

Author(s):

Stacey J. Winham ◽

Nicholas B. Larson ◽

Sebastian M. Armasu ◽

Zachary C. Fogarty ◽

Melissa C. Larson ◽

...

Keyword(s):

Gene Expression ◽

Ovarian Cancer ◽

Dna Methylation ◽

X Chromosome ◽

Copy Number ◽

X Chromosome Inactivation ◽

Chromosome Inactivation ◽

Copy Number Alterations ◽

Integrative Analyses

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A Functional Chromatin Domain Does Not Resist X Chromosome Inactivation: Silencing of cLys Correlates with Methylation of a Dual Promoter-Replication Origin

Molecular and Cellular Biology ◽

10.1128/mcb.22.13.4667-4676.2002 ◽

2002 ◽

Vol 22 (13) ◽

pp. 4667-4676 ◽

Cited By ~ 11

Author(s):

Suyinn Chong ◽

Joanna Kontaraki ◽

Constanze Bonifer ◽

Arthur D. Riggs

Keyword(s):

X Chromosome ◽

Copy Number ◽

Cpg Island ◽

Regulatory Elements ◽

X Chromosome Inactivation ◽

Chromosome Inactivation ◽

Chromatin Domain ◽

Specific Expression ◽

Position Effects ◽

Chicken Lysozyme

ABSTRACT To investigate the molecular mechanism(s) involved in the propagation and maintenance of X chromosome inactivation (XCI), the 21.4-kb chicken lysozyme (cLys) chromatin domain was inserted into the Hprt locus on the mouse X chromosome. The inserted fragment includes flanking matrix attachment regions (MARs), an origin of bidirectional replication (OBR), and all the cis-regulatory elements required for correct tissue-specific expression of cLys. It also contains a recently identified and widely expressed second gene, cGas41. The cLys domain is known to function as an autonomous unit resistant to chromosomal position effects, as evidenced by numerous transgenic mouse lines showing copy-number-dependent and development-specific expression of cLys in the myeloid lineage. We asked the questions whether this functional chromatin domain was resistant to XCI and whether the X inactivation signal could spread across an extended region of avian DNA. A generally useful method was devised to generate pure populations of macrophages with the transgene either on the active (Xa) or the inactive (Xi) chromosome. We found that (i) cLys and cGas41 are expressed normally from the Xa; (ii) the cLys chromatin domain, even when bracketed by MARs, is not resistant to XCI; (iii) transcription factors are excluded from lysozyme enhancers on the Xi; and (iv) inactivation correlates with methylation of a CpG island that is both an OBR and a promoter of the cGas41 gene.

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Re: Association Between Nonrandom X-Chromosome Inactivation and BRCA1 Mutation in Germline DNA of Patients With Ovarian Cancer

JNCI Journal of the National Cancer Institute ◽

10.1093/jnci/91.17.1507b ◽

1999 ◽

Vol 91 (17) ◽

pp. 1507-1508

Author(s):

J. Boyd ◽

S. A. Narod

Keyword(s):

Ovarian Cancer ◽

X Chromosome ◽

Brca1 Mutation ◽

X Chromosome Inactivation ◽

Chromosome Inactivation

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Single Cell Expression Data Reveal Human Genes that Escape X-Chromosome Inactivation

10.1101/079830 ◽

2016 ◽

Cited By ~ 2

Author(s):

Kerem Wainer-Katsir ◽

Michal Linial

Keyword(s):

X Chromosome ◽

Direct Method ◽

Single Cells ◽

X Chromosome Inactivation ◽

Chromosome Inactivation ◽

P Value ◽

Expression Data ◽

Rna Seq ◽

Specific Expression ◽

Biallelic Expression

ABSTRACTSex chromosomes pose an inherent genetic imbalance between genders. In mammals, one of the female’s X-chromosomes undergoes inactivation (Xi). Indirect measurements estimate that about 20% of Xi genes completely or partially escape inactivation. The identity of these escapee genes and their propensity to escape inactivation remain unsolved. A direct method for identifying escapees was applied by quantifying differential allelic expression from single cells. RNA-Seq fragments were assigned to informative SNPs which were labeled by the appropriate parental haplotype. This method was applied for measuring allelic specific expression from Chromosome-X (ChrX) and an autosomal chromosome as a control. We applied the protocol for measuring biallelic expression from ChrX to 104 primary fibroblasts. Out of 215 genes that were considered, only 13 genes (6%) were associated with biallelic expression. The sensitivity of escapees' identification was increased by combining SNP mapping for parental diploid genomes together with RNA-Seq from clonal single cells (25 lymphoblasts). Using complementary protocols, referred to as strict and relaxed, we confidently identified 25 and 31escapee genes, respectively. When pooled versions of 30 and 100 cells were used, <50% of these genes were revealed. We assessed the generality of our protocols in view of an escapee catalog compiled from indirect methods. The overlap between the escapee catalog and the genes’ list from this study is statistically significant (P-value of E-07). We conclude that single cells’ expression data are instrumental for studying X-inactivation with an improved sensitivity. Finally, our results support the emerging notion of the non-deterministic nature of genes that escape X-chromosome inactivation.

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