Quantitative Profiling of Chromatome Dynamics Reveals a Novel Role for HP1BP3 in Hypoxia-induced Oncogenesis

Abstract

In contrast to the intensely studied genetic and epigenetic changes that induce host cell transformation to initiate tumor development, those that promote the malignant progression of cancer remain poorly defined. As emerging evidence suggests that the hypoxic tumor microenvironment could re-model the chromatin-associated proteome (chromatome) to induce epigenetic changes and alter gene expression in cancer cells, we hypothesized that hypoxia-driven evolution of the chromatome promotes malignant changes and the development of therapy resistance in tumor cells. To test this hypothesis, we isolated chromatins from tumor cells treated with varying conditions of normoxia, hypoxia, and re-oxygenation and then partially digested them with DNase I and analyzed them for changes in euchromatin-and heterochromatinassociated proteins using an iTRAQ-based quantitative proteomic approach. We identified a total of 1446 proteins with a high level of confidence, including 819 proteins that were observed to change their chromatin association topology under hypoxic conditions. These hypoxia-sensitive proteins included key mediators of chromatin organization, transcriptional regulation, and DNA repair. Furthermore, our proteomic and functional experiments revealed a novel role for the chromatin organizer protein HP1BP3 in mediating chromatin condensation during hypoxia, leading to increased tumor cell viability, radio-resistance, chemo-resistance, and self-renewal. Taken together, our findings indicate that HP1BP3 is a key mediator of tumor progression and cancer cell acquisition of therapy-resistant traits, and thus might represent a novel therapeutic target in a range of human malignancies. Molecular &

ERO1α promotes hypoxic tumour progression and is associated with poor prognosis in pancreatic cancer

“…In pancreatic tumours, HIF-1α expression in a CD133+ stem cell-like population has been shown to promote EMT (21), and mutations in HIF-1α itself are key drivers of a variety of cancer types including PDA (22). These data are consistent with the emerging consensus that hypoxiainduced metabolic reprogramming is a hallmark feature of solid tumours including PDA (23), a key event driving the epigenetic changes that promote early invasion and metastasis (24)(25)(26), and a crucial determinant of immunosuppressive phenotypes that limit the effectiveness of many cancer therapies (27,28). Despite substantial research progress, the molecular mechanisms that underpin hypoxia-induced effects on tumour development remain poorly understood, hence pancreatic cancer prognosis has failed to improve significantly for many years and treatment options for this disease remain extremely limited.…”

“…Cell were then washed with cold PBS and lysed using 8M Urea buffer containing cOmplete TM EASYpack protease inhibitor cocktail (Sigma Aldrich, USA). In-solution digestion was performed as previously described (26). Extracted peptides were subjected to fractionation on an XBridge TM BEH C18 column (4.6 ×250 mm; Waters Corporation, Milford, MA, USA) and analysed by liquid chromatography-tandem mass spectrometry (LC-MS/MS).…”

Uncovering Neurodegenerative Protein Modifications via Proteomic Profiling

“…Despite this ability to yield useful data on the molecular pathology of neurodegeneration, use of these techniques is complicated by the extreme complexity of CNS tissues, which restricts the characterization of low-abundance proteins (Choudhary & Grant, 2004). Another drawback is the relative expense of the stable isotope labeling reagents and instrumentation required, which necessitates the pooling of samples from multiple individual subjects (Datta, Chen, & Sze, 2014;Datta et al, 2011Datta et al, , 2010Datta, Qian, et al, 2014;Dutta, Yan, Lim, Tam, & Sze, 2014). Yet another challenge associated with the use of quantitative proteomics to analyze brain tissues is the inability to assign the identified and characterized proteins to specific cell types in the affected tissues.…”

Multifaceted control of DNA repair pathways by the hypoxic tumor microenvironment

“…A recent quantitative proteomic study of the chromatin-associated proteome identified a large number of proteins that changed their chromatin association under hypoxia, including over 100 proteins involved in chromatin and transcription modulation, which likely represent factors mediating epigenetic changes as well as those responding to the changes [88]. The most commonly reported global histone changes under hypoxia involve histone H3 lysine 4 and lysine 9 di- and tri-methylation (H3K4me2, H3K4me3, H3K9me2, and HeK9me3).…”