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CDKN1C (encoding tumor suppressor p57(KIP2)) is a cyclin-dependent kinase (CDK) inhibitor whose family members are often transcriptionally downregulated in human cancer via promoter DNA methylation. In this study, we show that CDKN1C is repressed in breast cancer cells mainly through histone modifications. In particular, we show that CDKN1C is targeted by histone methyltransferase EZH2-mediated histone H3 lysine 27 trimethylation (H3K27me3), and can be strongly activated by inhibition of EZH2 in synergy with histone deacetylase inhibitor. Consistent with the overexpression of EZH2 in a variety of human cancers including breast cancer, CDKN1C in these cancers is downregulated, and breast tumors expressing low levels of CDKN1C are associated with a poor prognosis. We further show that assessing both EZH2 and CDKN1C expression levels as a measurement of EZH2 pathway activity provides a more predictive power of disease outcome than that achieved with EZH2 or CDKN1C alone. Taken together, our study reveals a novel epigenetic mechanism governing CDKN1C repression in breast cancer. Importantly, as a newly identified EZH2 target with prognostic value, it has implications in patient stratification for cancer therapeutic targeting EZH2-mediated gene repression.

The ability of neural stem cells (NSCs) to switch between quiescent and proliferative states is fundamental for adult neurogenesis and regeneration. Microproteins or short open reading frame (sORF)-encoded peptides (SEPs), are highly abundant yet largely understudied, and their role in brain development remains unclear. Here, we demonstrate that two evolutionarily-conserved microprotein paralogs, Simba1 and Simba2, encoded by sORFs CG15715 and CG18081 , respectively, govern the reactivation of Drosophila quiescent NSCs. Both Simba1 and Simba2 function in NSCs and Blood-Brain-Barrier (BBB) glial cells to promote NSC reactivation. Mechanistically, Simba1 and Simba2 act as transcription factors activating the WNT/Wingless signalling pathway during NSC reactivation. We uncover a critical role of Wg signalling molecules in promoting NSC reactivation and the translocation of Wingless from BBB glia to NSCs. Our findings reveal a role for microproteins Simba1/2 in regulating NSC reactivation through Wg signalling. Moreover, our bioinformatic analysis and luciferase assay suggest that ZNF706, the human ortholog of Simba1/2, is required for WNT signaling activation in human cells. The conserved function of Simba1/2/ZNF706 in activating WNT/Wg signalling in Drosophila and humans suggests that this new regulatory paradigm may be applicable to broader cellular processes and disease conditions. Drosophila Microproteins Simba1/2 act in neural stem cells and blood-brain-barrier glia to promote reactivation of neural stem cells via activating WNT/Wingless signaling, while human ortholog ZNF706 is found to have a conserved role in activating WNT pathway.

Metastasis is a significant health issue. The standard mode of care is combination of chemotherapy and targeted therapeutics but the 5-year survival rate remains low. New/better drug targets that can improve outcomes of patients with metastatic disease are needed. Metastasis is a complex process, with each step conferred by a set of genetic aberrations. Mapping the molecular changes associated with metastasis improves our understanding of the etiology of this disease and contributes to the pipeline of targeted therapeutics. Here, phosphoproteomics of a xenograft-derived in vitro model comprising 4 isogenic cell lines with increasing metastatic potential implicated Transient Receptor Potential Vanilloid subtype 4 in breast cancer metastasis. TRPV4 mRNA levels in breast, gastric and ovarian cancers correlated with poor clinical outcomes, suggesting a wide role of TRPV4 in human epithelial cancers. TRPV4 was shown to be required for breast cancer cell invasion and transendothelial migration but not growth/proliferation. Knockdown of Trpv4 significantly reduced the number of metastatic nodules in mouse xenografts leaving the size unaffected. Overexpression of TRPV4 promoted breast cancer cell softness, blebbing, and actin reorganization. The findings provide new insights into the role of TRPV4 in cancer extravasation putatively by reducing cell rigidity through controlling the cytoskeleton at the cell cortex.

While early pharmacogenomic studies have primarily been carried out in Western populations, there has been a notable increase in the number of Asian studies over the past decade. We systematically reviewed all pharmacogenomic studies conducted in Asia published before 2016 to highlight trends and identify research gaps in Asia. We observed that pharmacogenomic research in Asia was dominated by larger developed countries, notably Japan and Korea, and mainly driven by local researchers. Studies were focused on drugs acting on the CNS, chemotherapeutics and anticoagulants. Significantly, several novel pharmacogenomic associations have emerged from Asian studies. These developments are highly encouraging for the strength of regional scientific and clinical community and propound the importance of discovery studies in different populations.

CDKN1C (encoding tumor suppressor p57.sup.KIP2) is a cyclin-dependent kinase (CDK) inhibitor whose family members are often transcriptionally downregulated in human cancer via promoter DNA methylation. In this study, we show that CDKN1C is repressed in breast cancer cells mainly through histone modifications. In particular, we show that CDKN1C is targeted by histone methyltransferase EZH2-mediated histone H3 lysine 27 trimethylation (H3K27me3), and can be strongly activated by inhibition of EZH2 in synergy with histone deacetylase inhibitor. Consistent with the overexpression of EZH2 in a variety of human cancers including breast cancer, CDKN1C in these cancers is downregulated, and breast tumors expressing low levels of CDKN1C are associated with a poor prognosis. We further show that assessing both EZH2 and CDKN1C expression levels as a measurement of EZH2 pathway activity provides a more predictive power of disease outcome than that achieved with EZH2 or CDKN1C alone. Taken together, our study reveals a novel epigenetic mechanism governing CDKN1C repression in breast cancer. Importantly, as a newly identified EZH2 target with prognostic value, it has implications in patient stratification for cancer therapeutic targeting EZH2-mediated gene repression.

The let-23 Receptor/let-60 Ras/mpk-1 MAP kinase signaling pathway induces the formation of the vulva in C. elegans. We show that the lin-31 and lin-1 transcription factors act downstream of mpk-1 MAP kinase. Both proteins can be phosphorylated by MAP kinase in vitro and in vivo. A phophorylation-defective version of LIN-31 blocks vulval induction, and a LIN-31::VP16 chimeric activator promotes vulval induction, suggesting that LIN-31 may act as a transcriptional activator when phosphorylated. LIN-31 WH and LIN-1 Ets also physically associate, and this association is blocked by MAP kinase phosphorylation of LIN-31. Vulval induction is blocked when LIN-1/LIN-31 dissociation is prevented. We also show that LIN-31 only responds to MAP kinase in the vulva, and not in other tissues where MAP kinase is known to function. lin-31 is necessary for the expression of a vulval-specific marker, and ectopic expression of lin-31 is sufficient to induce expression of this marker in another let-23 Receptor-responsive cell type. These results suggest that LIN-31 may act as a tissue-specific effector of the let-23 Receptor/let-60 Ras/mpk-1 MAP kinase signaling pathway, and may contribute to the expression of the vulval-specific response. Little is also known about how the vulval precursor cells acquire their specific developmental competence. We found that lin-31 is down-regulated in P5.p, P6.p, and P7.p, just before these cells divide to generate vulval tissue. Activation of the let-23 Receptor/ let-60 Ras/mpk-1 MAP kinase signaling pathway is both necessary and sufficient for down-regulation of lin-31 in these cells. This down-regulation of LIN-31 is physiologically important for vulval development, as ectopic LIN-31 expression results in the formation of defective vulvae. Through the use of promoter deletions and a transgenic animal assay, a number of cis-acting elements that contribute to lin-31 expression were identified.

The human genome contains more than 200,000 gene isoforms. However, different isoforms can be highly similar, and with an average length of 1.5kb remain difficult to study with short read sequencing. To systematically evaluate the ability to study the transcriptome at a resolution of individual isoforms we profiled 5 human cell lines with short read cDNA sequencing and Nanopore long read direct RNA, amplification-free direct cDNA, PCR-cDNA sequencing. The long read protocols showed a high level of consistency, with amplification-free RNA and cDNA sequencing being most similar. While short and long reads generated comparable gene expression estimates, they differed substantially for individual isoforms. We find that increased read length improves read-to-transcript assignment, identifies interactions between alternative promoters and splicing, enables the discovery of novel transcripts from repetitive regions, facilitates the quantification of full-length fusion isoforms and enables the simultaneous profiling of m6A RNA modifications when RNA is sequenced directly. Our study demonstrates the advantage of long read RNA sequencing and provides a comprehensive resource that will enable the development and benchmarking of computational methods for profiling complex transcriptional events at isoform-level resolution. Competing Interest Statement The authors have declared no competing interest. Footnotes * https://github.com/GoekeLab/sg-nex-data