Inferring genes that escape X-Chromosome inactivation reveals important contribution of variable escape genes to sex-biased diseases.

The X Chromosome plays an important role in human development and disease. However, functional genomic and disease association studies of X genes greatly lag behind autosomal gene studies, in part owing to the unique biology of X-Chromosome inactivation (XCI). Because of XCI, most genes are only expressed from one allele. Yet, ∼30% of X genes "escape" XCI and are transcribed from both alleles, many only in a proportion of the population. Such interindividual differences are likely to be disease relevant, particularly for sex-biased disorders. To understand the functional biology for X-linked genes, we developed X-Chromosome inactivation for RNA-seq (XCIR), a novel approach to identify escape genes using bulk RNA-seq data. Our method, available as an R package, is more powerful than alternative approaches and is computationally efficient to handle large population-scale data sets. Using annotated XCI states, we examined the contribution of X-linked genes to the disease heritability in the United Kingdom Biobank data set. We show that escape and variable escape genes explain the largest proportion of X heritability, which is in large part attributable to X genes with Y homology. Finally, we investigated the role of each XCI state in sex-biased diseases and found that although XY homologous gene pairs have a larger overall effect size, enrichment for variable escape genes is significantly increased in female-biased diseases. Our results, for the first time, quantitate the importance of variable escape genes for the etiology of sex-biased disease, and our pipeline allows analysis of larger data sets for a broad range of phenotypes.

Dosage compensation and gene expression on the mammalian X chromosome: one plus one does not always equal two.

Counting chromosomes is not just simple math. Although normal males and females differ in sex chromosome content (XY vs. XX), X chromosome imbalance is tolerated because dosage compensation mechanisms have evolved to ensure functional equivalence. In mammals this is accomplished by two processes--X chromosome inactivation that silences most genes on one X chromosome in females, leading to functional X monosomy for most genes in both sexes, and X chromosome upregulation that results in increased gene expression on the single active X in males and females, equalizing dosage relative to autosomes. This review focuses on genes on the X chromosome, and how gene content, organization and expression levels can be influenced by these two processes. Special attention is given to genes that are not X inactivated, and are not necessarily fully dosage compensated. These genes that "escape" X inactivation are of medical importance as they explain phenotypes in individuals with sex chromosome aneuploidies and may impact normal traits and disorders that differ between men and women. Moreover, escape genes give insight into how X chromosome inactivation is spread and maintained on the X.

Loss of PTEN promotes tumor development in malignant melanoma.

Loss of tumor suppressor genes on chromosome 10 plays an important role in the development of 30-60% of melanomas; however, the identity of these genes and the mechanisms by which loss of these genes leads to tumor formation remain uncertain. The phosphatase and tensin homologue deleted from chromosome 10 (PTEN) is one of the genes on chromosome 10 whose of which the loss or inactivation may play an important role in melanoma tumorigenesis, but functional studies directly demonstrating PTEN involvement in melanomas are necessary to confirm this role. To determine the biological importance of PTEN loss in melanomas, we established a novel model in which an intact chromosome 10 was transferred into melanoma cells lacking PTEN protein to express the protein at normal physiological levels and to measure the consequent effects on melanoma tumorigenesis. PTEN expression in these cells retarded tumor development in mice unless, by analogy with loss of heterozygosity, the PTEN gene was deleted or inactivated during tumor formation. Mechanistically, PTEN loss led to the activation of Akt, which consequently down-regulated the apoptotic pathway of melanoma cells. In contrast, expression of PTEN attenuated Akt activation, thereby increasing sensitivity to apoptotic stimuli in cell culture and in vivo in animal models. This model demonstrated that PTEN loss is critical for melanoma tumorigenesis and allowed a dissection of the underlying mechanism by which PTEN loss facilitated melanoma tumor development. In summary, loss of PTEN reduces apoptosis and promotes cell survival, thereby favoring melanoma tumor formation. Thus, these observations provide an etiological basis for PTEN loss during the genesis of sporadic melanomas.

Deregulated Akt3 activity promotes development of malignant melanoma.

Malignant melanoma is the skin cancer with the most significant impact on man, carrying the highest risk of death from metastasis. Both incidence and mortality rates continue to rise each year, with no effective long-term treatment on the horizon. In part, this reflects lack of identification of critical genes involved and specific therapies targeted to correct these defects. We report that selective activation of the Akt3 protein promotes cell survival and tumor development in 43 to 60% of nonfamilial melanomas. The predominant Akt isoform active in melanomas was identified by showing that small interfering RNA (siRNA) against only Akt3, and not Akt1 or Akt2, lowered the amount of phosphorylated (active) Akt in melanoma cells. The amount of active Akt3 increased progressively during melanoma tumor progression with highest levels present in advanced-stage metastatic melanomas. Mechanisms of Akt3 deregulation occurred through a combination of overexpression of Akt3 accompanying copy number increases of the gene and decreased PTEN protein function occurring through loss or haploinsufficiency of the PTEN gene. Targeted reduction of Akt3 activity with siRNA or by expressing active PTEN protein stimulated apoptotic signaling, which reduced cell survival by increasing apoptosis rates thereby inhibiting melanoma tumor development. Identifying Akt3 as a selective target in melanoma cells provides new therapeutic opportunities for patients in the advanced stages of this disease.