Observations on the presence of E domain variants of estrogen receptor-α in the breast tumors

Comprehensive landscape of subtype-specific coding and non-coding RNA transcripts in breast cancer

Molecular classification of breast cancer into clinically relevant subtypes helps improve prognosis and adjuvant-treatment decisions. The aim of this study is to provide a better characterization of the molecular subtypes by providing a comprehensive landscape of subtype-specific isoforms including coding, long non-coding RNA and microRNA transcripts. Isoform-level expression of all coding and non-coding RNAs is estimated from RNA-sequence data of 1168 breast samples obtained from The Cancer Genome Atlas (TCGA) project. We then search the whole transcriptome systematically for subtype-specific isoforms using a novel algorithm based on a robust quasi-Poisson model. We discover 5451 isoforms specific to single subtypes. A total of 27% of the subtype-specific isoforms have better accuracy in classifying the intrinsic subtypes than that of their corresponding genes. We find three subtype-specific miRNA and 707 subtype-specific long non-coding RNAs. The isoforms from long non-coding RNAs also show high performance for separation between Luminal A and Luminal B subtypes with an AUC of 0.97 in the discovery set and 0.90 in the validation set. In addition, we discover 1500 isoforms preferentially co-expressed in two subtypes, including 369 isoforms co-expressed in both Normal-like and Basal subtypes, which are commonly considered to have distinct ER-receptor status. Finally, analyses at protein level reveal four subtype-specific proteins and two subtype co-expression proteins that successfully validate results from the isoform level.

Estrogen receptor α and β in the normal immune system and in lymphoid malignancies

Estrogens regulate various normal and pathophysiological processes including cancers. Cellular signaling by estrogens is mediated by estrogen receptor α (ERα) and β (ERβ), respectively. Binding of agonists to the ERs affects gene transcription. The main endogenous estrogen, 17β-estradiol (E2), binds to both ERα and ERβ with similar affinity. However, the ligand-binding pocket of ERα and ERβ are slightly different which has allowed the development of selective ER ligands. Importantly, while estrogens via ERα stimulate proliferation, signaling via ERβ inhibits proliferation and promotes apoptosis. In both normal and cancer cells the ERs are co-expressed with ER splice variants which may modify the transcriptional activity of the wild-type receptors. Estrogens have prominent effects on immune functions and both ERα and ERβ are expressed in immune cells and lymphoid malignancies. With regard to lymphoid malignancies, most show estrogen influence as several epidemiological studies of lymphoid cancers demonstrate gender differences in incidence and prognosis with males being more affected. In line with these findings, recent results generated by us have shown that ERβ selective agonists inhibit growth and induce apoptosis in human and murine lymphomas in vivo in xenograft experiments. This suggests that ERβ selective agonists in the future may be useful in the treatment of lymphomas.

Quantitative profiles of the mRNAs of ER-alpha and its novel variant ER-alpha36 in breast cancers and matched normal tissues

OBJECTIVE

The novel estrogen receptor-alpha (ER-alpha) variant ER-alpha36 is reported to be functional in the estrogen signaling pathway and is related to tamoxifen resistance in breast cancer. However, ER-alpha36 tends to be a favorable factor for survival in patients without tamoxifen therapy. To investigate the mechanisms behind this paradox, we determined the differences between the transcriptional profiles of ER-alpha36 and full-length ER-alpha (ER-alpha66) in breast cancers and matched normal tissues.

METHODS

We analyzed ER-alpha36 and ER-alpha66 messenger RNA (mRNA) levels in 74 pairs of breast cancers and matched normal tissues using a real-time quantitative polymerase chain reaction (PCR) assay, and correlated the results with their clinicopathological characteristics.

RESULTS

Breast cancers expressed lower ER-alpha36 mRNA levels than matched normal tissues regardless of their ER-alpha66 expression status. Down-regulation of ER-alpha36 mRNA was correlated with local progression, lymph node metastasis, and advanced cancer stage. The level of ER-alpha66 mRNA was lower in ER-alpha negative breast cancers compared with matched normal tissues. No differences in ER-alpha66 mRNA levels were observed during cancer progression.

CONCLUSION

Down-regulation of ER-alpha36 is associated with carcinogenesis and progression of breast cancer.

Oestrogen receptor splice variants in the pathogenesis of disease

The full-length oestrogen receptor (ER) exists in most vertebrates as two separately encoded isoforms. ER splice variants represent truncated or otherwise modified versions of the full-length alpha or beta isoforms of the parent receptor. ERalpha is found on chromosome 6q and encodes a 595 amino acid protein, while ERbeta is found on chromosome 14q and encodes a 530 amino acid protein. These receptors possess differing ligand affinities, are differentially expressed in a tissue-specific fashion and may act antagonistically. Their altered expression has been implicated in the pathophysiology of a diverse range of conditions from cancer progression in hormone-responsive tissues to neurodegenerative disease. Variously co-expressed with full-length ERs, ER splice variants may have a positive or negative influence on transcription either by modifying the effect of the parent receptor or through their own intrinsic activity. To date, the vast majority of studies have used generic primers or antibodies against the full-length receptors and would not distinguish ER-mediated effects associated with various splice variants. Thus the evidence base of the influence of ER splice variants in normal developmental physiology and in the pathogenesis of disease is weak and greater understanding of their role will undoubtedly lead to new therapeutic strategies for disease intervention and treatment. This review aims to compile the current evidence for the presence of ER splice variants in humans, their physiological roles and clinical sequelae.