Disruption In Cancer Research Articles

DIPG-45. ELONGIN B REGULATES H3K27M CHROMATIN INCORPORATION TO PROMOTE MALIGNANCY IN DIFFUSE MIDLINE GLIOMA

Abstract Chromatin dysregulation is both a cause and consequence of aberrant RNA Polymerase II (Pol2) transcription in cancer. Some of the most striking examples of chromatin disruption in cancer include somatic mutations in genes encoding histone H3 (H3.3/H3.1K27M) observed in ~80% of diffuse midline glioma (DMG). H3K27M mutant histones act in a dominant manner to disrupt chromatin regulation and Pol2-dependent transcription in DMG. How H3K27M impinges on the Pol2 transcriptional machinery and whether aberrant Pol2 transcription can reciprocally induce chromatin dysregulation in DMG remain open questions. We conducted epigenome-focused CRISPR dropout screens and identified multiple regulators of Pol2 elongation, including Elongin B and C (ELOB/ELOC) as DMG genetic dependencies. Follow-up studies confirm that knockout (KO) of ELOB inhibits DMG proliferation in neurosphere culture and abrogates DMG tumorigenesis in orthotopic xenografts. Additional chromatin profiling studies reveal that ELOB binding sites are enriched in H3K27M mutant histones, suggesting that ELOB works together with H3K27M to promote malignant gene expression in DMG. Indeed, reciprocal knockout studies suggest that while ELOB chromatin binding patterns were not altered by H3K27M KO, ELOB KO significantly reduced H3K27M chromatin incorporation at thousands of genomic loci. Further RNAseq and PROseq analyses reveal that ELOB KO alters Pol2 transcription resulting in the up-regulation of genes associated with neuronal and muscle differentiation and the repression of glial stem cell genes. Together, these findings suggest that H3K27M chromatin binding patterns and aberrant gene regulation in DMG are, in part, dictated by ELOB and the Pol2 elongation machinery. Finally, analyses of patient datasets indicate that ELOB complex genes are overexpressed in high grade glioma and DMG and correlate with decreased patient survival. Collectively, these studies suggest that a functional interaction between ELOB and H3K27M mutant histones induces DMG-specific aberrations in chromatin and gene regulation to drive malignancy.

Alteration of membrane potential of head and neck cancer cells using a piezoelectric nanofiber interface.

Membrane potential (Vmem) is an electrical property associated with any cell, specific to its origin and function. These transmembrane voltage gradients have been established to control not only neural signaling via gap junctions, but also cell proliferation, migration, differentiation, and orientation in both excitable and non-excitable cells. The bioelectric state of cancer cells is different from that of healthy cells, causing a disruption in cell signaling pathways, affecting all three processes of carcinogenesis - initiation, promotion, and progression. More positively charged or depolarized Vmem correspond to more undifferentiated, proliferative, and stem-like cells. Understanding of the underlying bioelectric mechanisms and their disruption in cancer can be advanced by developing molecular tools capable of measuring and altering Vmem. Current gold standards include bio actuators, patch clamps, conductive polymers, and treatment with pharmacological drugs such as ivermectin. Biocompatible piezoelectric (PE) materials can alter the Vmem of cells by contact, without the use of transgenes. Here we introduce a PE polyvinylidene fluoride-trifluoroethylene (PVDF-TrFE) biomaterial interface capable of generating quantified electrical stimuli in response to mechanical deformation, thus altering resting Vmem of cells. PVDF-TrFE nanofibers seeded with Cal27 - oral squamous carcinoma cells (OSCC) were subjected to 1 cm mechanical stretch deformations at a frequency of 1 Hz for 3 minutes every 24 h. Results indicated significant increase in cell proliferation for treatment groups on days 3, 5, and 7 of culture as compared to controls. This platform can be further evolved to alter Vmem of cancer spheroids in 3D to better mimic the bioelectric state of cells in the tumor microenvironment (TME) and study subsequent alterations in signaling pathways.

MYC Ran Up the Clock: The Complex Interplay between MYC and the Molecular Circadian Clock in Cancer.

The MYC oncoprotein and its family members N-MYC and L-MYC are known to drive a wide variety of human cancers. Emerging evidence suggests that MYC has a bi-directional relationship with the molecular clock in cancer. The molecular clock is responsible for circadian (~24 h) rhythms in most eukaryotic cells and organisms, as a mechanism to adapt to light/dark cycles. Disruption of human circadian rhythms, such as through shift work, may serve as a risk factor for cancer, but connections with oncogenic drivers such as MYC were previously not well understood. In this review, we examine recent evidence that MYC in cancer cells can disrupt the molecular clock; and conversely, that molecular clock disruption in cancer can deregulate and elevate MYC. Since MYC and the molecular clock control many of the same processes, we then consider competition between MYC and the molecular clock in several select aspects of tumor biology, including chromatin state, global transcriptional profile, metabolic rewiring, and immune infiltrate in the tumor. Finally, we discuss how the molecular clock can be monitored or diagnosed in human tumors, and how MYC inhibition could potentially restore molecular clock function. Further study of the relationship between the molecular clock and MYC in cancer may reveal previously unsuspected vulnerabilities which could lead to new treatment strategies.

Bispecific anti-OX40/5T4 antibodies for cancer treatment.

OX40 and 5T4 are molecules that play a role in T-cell expansion and cytoskeleton's disruption in cancer, respectively. US2019161555 patent describes a bispecific antibody that targets OX40/5T4 with the potential application of cancer treatment. The method of analysis of the US201916155 patent consisted of claim's analysis, as well as the chemical/biological information's analysis of the bispecific antibody. The patent includes independent claims related to bispecific antibodies that bind to OX40/5T4, DNA encoding the antibodies, a vector that harbors the DNA, a host cell that contains the vector, a pharmaceutical composition containing a pharmaceutically effective amount of the antibodies, medical use of the antibodies, use of the antibodies in the treatment or prevention of neoplastic disordersand a method of treating neoplastic disorders. Bispecific antibodies that target OX40/5T4 can activate IL-2 secretion in CD4+ T cells.

Architecture of autoinhibited and active BRAF-MEK1-14-3-3 complexes.

RAF family kinases are RAS-activated switches that initiate signaling through the MAP kinase cascade to control cellular proliferation, differentiation and survival1–3. RAF activity is tightly regulated, and inappropriate activation is a frequent cause of cancer4–6. At present, the structural basis for RAF regulation is poorly understood. Here we describe autoinhibited and active state structures of full-length BRAF in complexes with MEK1 and a 14-3-3 dimer, determined using cryo electron microscopy (cryo-EM). A 4.1Å resolution cryo-EM reconstruction reveals an inactive BRAF/MEK1 complex restrained in a cradle formed by the 14-3-3 dimer, which binds the phosphorylated S365 and S729 sites that flank the BRAF kinase domain. The BRAF cysteine-rich domain (CRD) occupies a central position that stabilizes this assembly, but the adjacent RAS-binding domain (RBD) is poorly ordered and peripheral. The 14-3-3 cradle maintains autoinhibition by sequestering the membrane-binding CRD and blocking dimerization of the BRAF kinase domain. In the active state, these inhibitory interactions are released and a single 14-3-3 dimer rearranges to bridge the C-terminal pS729 binding sites of two BRAFs, driving formation of an active, back-to-back BRAF dimer. Our structural snapshots provide a foundation for understanding normal RAF regulation and its mutational disruption in cancer and developmental syndromes.

Protein interaction disruption in cancer

BackgroundMost methods that integrate network and mutation data to study cancer focus on the effects of genes/proteins, quantifying the effect of mutations or differential expression of a gene and its neighbors, or identifying groups of genes that are significantly up- or down-regulated. However, several mutations are known to disrupt specific protein-protein interactions, and network dynamics are often ignored by such methods. Here we introduce a method that allows for predicting the disruption of specific interactions in cancer patients using somatic mutation data and protein interaction networks.MethodsWe extend standard network smoothing techniques to assign scores to the edges in a protein interaction network in addition to nodes. We use somatic mutations as input to our modified network smoothing method, producing scores that quantify the proximity of each edge to somatic mutations in individual samples.ResultsUsing breast cancer mutation data, we show that predicted edges are significantly associated with patient survival and known ligand binding site mutations. In-silico analysis of protein binding further supports the ability of the method to infer novel disrupted interactions and provides a mechanistic explanation for the impact of mutations on key pathways.ConclusionsOur results show the utility of our method both in identifying disruptions of protein interactions from known ligand binding site mutations, and in selecting novel clinically significant interactions.Supporting website with software and data: https://www.cs.cmu.edu/~mruffalo/mut-edge-disrupt/.

Correction to: Epigenetic Basis of Circadian Rhythm Disruption in Cancer.

The Chapter was inadvertently published with incorrect figure (Fig. 1). The same has been corrected in the chapter.

Sulforaphane metabolites cause apoptosis via microtubule disruption in cancer.

Sulforaphane (SFN) inhibited growth in many cancers, but its half-life is 2 h in circulation. However, its metabolites, sulforaphane-cysteine (SFN-Cys) and sulforaphane-N-acetyl-cysteine (SFN-NAC) had longer half-lives and decreased the cell viability in both dose- and time-dependent manners in human prostate cancer. Flow cytometry assay revealed that these two SFN metabolites induced apoptosis with the features such as vacuolization, disappeared nuclear envelope, nuclear agglutination and fragmentation via transmission electron microscopy observation. Western blot showed that the sustained phosphorylation of ERK1/2 mediated by SFN metabolites caused activation and upregulation of cleaved Caspase 3 and downregulation of α-tubulin. High expression of α-tubulin was demonstrated to be positively correlated with cancer pathological grading. Both co-immunoprecipitation and immunofluorescence staining implicated the interaction between SFN metabolite-induced phosphorylated ERK1/2 and α-tubulin, and Caspase 3 cleavage assay showed that α-tubulin might be the substrate for cleaved Caspase 3. More, the SFN metabolite-mediated reduction of α-tubulin increased the depolymerization and instability of microtubules by microtubule polymerization assay. Reversely, microtubule-associated protein Stathmin-1 phosphorylation was increased via phosphorylated ERK1/2 and total Stathmin-1 was reduced, which might promote over-stability of microtubules. Immunofluorescence staining also showed that SFN metabolites induced the 'nest-like' structures of microtubule distribution resulting from the disrupted and aggregated microtubules, and abnormal nuclear division, suggesting that the disturbance of spindle formation and mitosis turned up. Thus, SFN-Cys and SFN-NAC triggered the dynamic imbalance of microtubules, microtubule disruption leading to cell apoptosis. These findings provided a novel insight into the chemotherapy of human prostate cancer.

Epigenetic Basis of Circadian Rhythm Disruption in Cancer.

Self-sustained and synchronized to environmental stimuli, circadian clocks are under genetic and epigenetic regulation. Recent findings have greatly increased our understanding of epigenetic plasticity governed by circadian clock. Thus, the link between circadian clock and epigenetic machinery is reciprocal. Circadian clock can affect epigenetic features including genomic DNA methylation, noncoding RNA, mainly miRNA expression, and histone modifications resulted in their 24-h rhythms. Concomitantly, these epigenetic events can directly modulate cyclic system of transcription and translation of core circadian genes and indirectly clock output genes. Significant findings interlocking circadian clock, epigenetics, and cancer have been revealed, particularly in breast, colorectal, and blood cancers. Aberrant methylation of circadian gene promoter regions and miRNA expression affected circadian gene expression, together with 24-h expression oscillation pace have been frequently observed.

Integrative analysis reveals disrupted pathways regulated by microRNAs in cancer.

MicroRNAs (miRNAs) are small endogenous regulatory molecules that modulate gene expression post-transcriptionally. Although differential expression of miRNAs have been implicated in many diseases (including cancers), the underlying mechanisms of action remain unclear. Because each miRNA can target multiple genes, miRNAs may potentially have functional implications for the overall behavior of entire pathways. Here, we investigate the functional consequences of miRNA dysregulation through an integrative analysis of miRNA and mRNA expression data using a novel approach that incorporates pathway information a priori. By searching for miRNA-pathway associations that differ between healthy and tumor tissue, we identify specific relationships at the systems level which are disrupted in cancer. Our approach is motivated by the hypothesis that if an miRNA and pathway are associated, then the expression of the miRNA and the collective behavior of the genes in a pathway will be correlated. As such, we first obtain an expression-based summary of pathway activity using Isomap, a dimension reduction method which can articulate non-linear structure in high-dimensional data. We then search for miRNAs that exhibit differential correlations with the pathway summary between phenotypes as a means of finding aberrant miRNA-pathway coregulation in tumors. We apply our method to cancer data using gene and miRNA expression datasets from The Cancer Genome Atlas and compare ∼105 miRNA-pathway relationships between healthy and tumor samples from four tissues (breast, prostate, lung and liver). Many of the flagged pairs we identify have a biological basis for disruption in cancer.

Abstract A01: ER stress disrupts circadian rhythms via miR-211

Abstract The Endoplasmic Reticulum, ER, senses both intracellular and extracellular stimuli that perturb the folding and maturation of secretory proteins that transit the ER. In the context of neoplastic growth, oncogenes such as c-Myc, H-Ras and BRAF trigger ER stress and activate the Unfolded Protein Response (UPR), a cell adaptive signaling pathway composed of three primary signal transducers, PERK, IRE-1 and ATF6. Bmal1 and Clock form a core heterodimeric transcription complex regulates both central and peripheral circadian rhythms. There are multiple lines of evidence suggesting that deregulation of circadian rhythms contribute to neoplastic cell growth, altered cellular metabolism and tumorigenesis. Analogously, UPR signaling contributes to tumor cell survival and tumor growth under conditions of micro-environmental and metabolic stress. However, whether UPR interactively regulates stress with the circadian clock is largely unknown. Herein, we describe the molecular mechanisms whereby UPR signaling integrates with the circadian clock. We provide evidence that ER stress-dependent activation of PERK alters circadian oscillations via micro-RNA 211-dependent suppression of BMAL1 and Clock. We provide evidence that the mechanism of regulation of BMAL1 versus clock is distinct, reflecting novel ability of miR-211 to function in both the nucleus and cytoplasm. We provide additional support for this model through using a mouse model to interrogate the role of PERK signaling in a liver specific response to ER stress. With regard to the impact of PERK signaling and circadian clock disruption in cancer, we assessed PERK-miR-211 signaling in c-Myc and MLL-AF9 driven malignancy. Here, expression of either c-Myc or MLL-AF9 expression was directly associated with activation of PERK-miR-211 and loss of both BMAL1 and Clock expression. We also found that Myc driven human Burkitt's lymphoma has PERK hyperactivation, higher miR-211 expression, and loss of circadian oscillations. As the Bmal1 promoter is hypermethylated in multiple lymphoma cancer cell lines, we hypothesize that this is likely to reflect the action of nuclear miR-211. Consistently, anti-miR211 partially released Bmal1 repression and Inhibition PERK or suppression miR-211 rescued circadian rhythms in lymphoma cells thereby affecting their survival and proliferation. Our data suggested a model where ER stress disrupts peripheral circadian rhythms via PERK-miR211-Bmal1/Clock pathway. Targeting activated ER stress or abnormal miR-211 expression to rescue circadian rhythms could be a new potential therapy for Myc- (perhaps also other oncogenes) driven hematological malignancy. Citation Format: Yiwen Bu, John Alan Diehl. ER stress disrupts circadian rhythms via miR-211. [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer: Mechanisms to Medicines ; 2015 Dec 4-7; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2016;76(6 Suppl):Abstract nr A01.

Abstract B31: Disruption of Folliculin interacting protein-1 modulates Myc-driven metabolism, increasing cell death following metabolic stress

Abstract Folliculin interacting protein-1 (Fnip1) is a cytoplasmic protein originally discovered through its interaction with Folliculin (Flcn), a tumor suppressor mutated in the rare fibrofolliculoma disorder Birt-Hogg Dubé syndrome. Fnip1 and Flcn both interact with the master metabolic regulator AMP kinase (AMPK). Our previous studies have shown that Fnip1 is required for the development of B-cells past the late pre-B stage (Park et al Immunity 2012) and for the development invariant natural killer T (iNKT) cells in the thymus (Park et al PNAS 2014). Fnip1 deficiency also prevented the development of B cell lymphoma in Eµ-Myc transgenic mice. Fnip1 deficient immune cells exhibited hyperactivation of mTORC1 concurrent with increased activation of AMPK. In this study, we examined the potential efficacy of Fnip1 disruption in cancer by disrupting Fnip1 in primary mouse and human B cell lines overexpressing the Myc oncogene. We show that constitutive depletion of Fnip1 in primary pre-B cells, conditional knockdown of Fnip1 in primary mouse mature B cells using the Cre-loxP system, or siRNA-mediated depletion of endogenous FNIP1 from a human B cell line expressing a conditional Myc allele, increase oxidative phosphorylation and Myc-induced glycolysis, which support cell division. Disruption of Fnip1 increases death of primary murine pre-B Eµ-Myc cells and human B cell lines in response to nutrient deprivation and chemotherapeutic drugs in vitro. Mass spectrometric analysis of a human B cell line depleted of Fnip1 reveals significant alterations in metabolites involved in glutaminolysis, glycolysis, antioxidant and serine biosynthesis pathways. These results suggest that inhibition of Fnip1 may provide a novel strategy to increase death of lymphoma cells in response to cytotoxic and metabolic stress. Citation Format: Julita A. Ramirez, Mark Tsang, Heon Park, Daciana Margineantu, Haiwei Gu, Daniel Raftery, David M. Hockenbery, Brian M. Iritani. Disruption of Folliculin interacting protein-1 modulates Myc-driven metabolism, increasing cell death following metabolic stress. [abstract]. In: Proceedings of the AACR Special Conference: Metabolism and Cancer; Jun 7-10, 2015; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Res 2016;14(1_Suppl):Abstract nr B31.

Exome sequencing of pleuropulmonary blastoma reveals frequent biallelic loss of TP53 and two hits in DICER1 resulting in retention of 5p-derived miRNA hairpin loop sequences.

Pleuropulmonary blastoma is a rare childhood malignancy of lung mesenchymal cells that can remain dormant as epithelial cysts or progress to high-grade sarcoma. Predisposing germline loss-of-function DICER1 variants have been described. We sought to uncover additional contributors through whole exome sequencing of 15 tumor/normal pairs, followed by targeted resequencing, miRNA analysis and immunohistochemical analysis of additional tumors. In addition to frequent biallelic loss of TP53 and mutations of NRAS or BRAF in some cases, each case had compound disruption of DICER1: a germline (12 cases) or somatic (3 cases) loss-of-function variant plus a somatic missense mutation in the RNase IIIb domain. 5p-Derived microRNA (miRNA) transcripts retained abnormal precursor miRNA loop sequences normally removed by DICER1. This work both defines a genetic interaction landscape with DICER1 mutation and provides evidence for alteration in miRNA transcripts as a consequence of DICER1 disruption in cancer.

SOX15 and other SOX family members are important mediators of tumorigenesis in multiple cancer types.

SOX genes are transcription factors with important roles in embryonic development and carcinogenesis. The SOX family of 20 genes is responsible for regulating lineage and tissue specific gene expression patterns, controlling numerous developmental processes including cell differentiation, sex determination, and organogenesis. As is the case with many genes involved in regulating development, SOX genes are frequently deregulated in cancer. In this perspective we provide a brief overview of how SOX proteins can promote or suppress cancer growth. We also present a pan-cancer analysis of aberrant SOX gene expression and highlight potential molecular mechanisms responsible for their disruption in cancer. Our analyses indicate the prominence of SOX deregulation in different cancer types and reveal potential roles for SOX genes not previously described in cancer. Finally, we summarize our recent identification of SOX15 as a candidate tumor suppressor in pancreatic cancer and propose several research avenues to pursue to further delineate the emerging role of SOX15 in development and carcinogenesis.

Chronic lymphocytic leukemia: molecular heterogeneity revealed by high-throughput genomics

Chronic lymphocytic leukemia (CLL) has been consistently at the forefront of genetic research owing to its prevalence and the accessibility of sample material. Recently, genome-wide technologies have been intensively applied to CLL genetics, with remarkable progress. Single nucleotide polymorphism arrays have identified recurring chromosomal aberrations, thereby focusing functional studies on discrete genomic lesions and leading to the first implication of somatic microRNA disruption in cancer. Next-generation sequencing (NGS) has further transformed our understanding of CLL by identifying novel recurrently mutated putative drivers, including the unexpected discovery of somatic mutations affecting spliceosome function. NGS has further enabled in-depth examination of the transcriptional and epigenetic changes in CLL that accompany genetic lesions, and has shed light on how different driver events appear at different stages of disease progression and clonally evolve with relapsed disease. In addition to providing important insights into disease biology, these discoveries have significant translational potential. They enhance prognosis by highlighting specific lesions associated with poor clinical outcomes (for example, driver events such as mutations in the splicing factor subunit gene SF3B1) or with increased clonal heterogeneity (for example, the presence of subclonal driver mutations). Here, we review new genomic discoveries in CLL and discuss their possible implications in the era of precision medicine.

PP2A Counterbalances Phosphorylation of pRB and Mitotic Proteins by Multiple CDKs: Potential Implications for PP2A Disruption in Cancer

Protein Phosphatase 2A (PP2A) consists of a collection of heterotrimeric serine/threonine phosphatase holoenzymes that play multiple roles in cell signaling via dephosphorylation of numerous substrates of a large family of serine/threonine kinases. PP2A substrate specificity is mediated by B regulatory subunits of four different families, which selectively recognize diverse substrates by mechanisms that are not well understood. Among the many signaling pathways with critical PP2A functions are several deregulated in cancer cells, and PP2A is a know tumor suppressor. However, the precise composition of the heterotrimeric PP2A complexes with tumor supressor activity is not well understood. This review is centered on the emerging role of the B regulatory subunit B55α and related subfamilly members in the modulation of the phosphorylation state of pocket proteins and mitotic CDK substrates, as well as the implications of PP2A function disruption in cancer in the context of these activities.

The functions and regulation of the PTEN tumour suppressor

The importance of the physiological function of phosphatase and tensin homologue (PTEN) is illustrated by its frequent disruption in cancer. By suppressing the phosphoinositide 3-kinase (PI3K)-AKT-mammalian target of rapamycin (mTOR) pathway through its lipid phosphatase activity, PTEN governs a plethora of cellular processes including survival, proliferation, energy metabolism and cellular architecture. Consequently, mechanisms regulating PTEN expression and function, including transcriptional regulation, post-transcriptional regulation by non-coding RNAs, post-translational modifications and protein-protein interactions, are all altered in cancer. The repertoire of PTEN functions has recently been expanded to include phosphatase-independent activities and crucial functions within the nucleus. Our increasing knowledge of PTEN and pathologies in which its function is altered will undoubtedly inform the rational design of novel therapies.

Molecular Targeted Therapy for Hepatocellular Carcinoma: Bench to Bedside

According to the International Agency for Research on Cancer, approximately 670,000 new cases of hepatocellular carcinoma (HCC) developed in 2005, making it the fifth most common cancer and third most common cause of cancer-related death worldwide. HCC is a complex and heterogeneous tumor with several genomic alterations. There is evidence of aberrant activation of several signaling cascades such as EGFR, Ras/Raf/MEK, PI3K/mTOR, HGF/MET, Wnt, Hedgehog and apoptotic signaling pathway. Recently a multikinase inhibitor, sorafenib, has shown survival benefits in patients with advanced HCC. It has been proposed that signaling pathway disruption in cancer can be grouped in six function capabilities, some of which need to be altered for cancer development: self-sufficiency in growth signals, insensitivity to anti-growth signals, evading apoptosis, limitless replicative potential, sustained angiogenesis and tumor invasion and metastases. The aim is to integrate these concepts into the molecular pathogenesis of HCC. It has also been proposed that there are common disturbances universal to all liver cancers on top of the more specific mechanisms. Based on this basic research, a molecular targeted agent has recently been developed. There have been no effective chemotherapeutic agents for advanced HCC. Sorafenib, an oral multikinase inhibitor, has set a milestone in the management of HCC in that it is the first agent to significantly improve the overall survival in patients with advanced HCC in a double-blind, placebo-controlled, phase III study. Clinical trials testing new agents for first- and second-line agents, as well as in combination with existing treatment options such as transarterial chemoembolization or arterial infusion chemotherapy, are ongoing. The results of these trials are therefore eagerly awaited.

Genomic and Epigenomic Integration Identifies a Prognostic Signature in Colon Cancer

The importance of genetic and epigenetic alterations maybe in their aggregate role in altering core pathways in tumorigenesis. Merging genome-wide genomic and epigenomic alterations, we identify key genes and pathways altered in colorectal cancers (CRC). DNA methylation analysis was tested for predicting survival in CRC patients using Cox proportional hazard model. We identified 29 low frequency-mutated genes that are also inactivated by epigenetic mechanisms in CRC. Pathway analysis showed the extracellular matrix (ECM) remodeling pathway is silenced in CRC. Six ECM pathway genes were tested for their prognostic potential in large CRC cohorts (n = 777). DNA methylation of IGFBP3 and EVL predicted for poor survival (IGFBP3: HR = 2.58, 95% CI: 1.37-4.87, P = 0.004; EVL: HR = 2.48, 95% CI: 1.07-5.74, P = 0.034) and simultaneous methylation of multiple genes predicted significantly worse survival (HR = 8.61, 95% CI: 2.16-34.36, P < 0.001 for methylation of IGFBP3, EVL, CD109, and FLNC). DNA methylation of IGFBP3 and EVL was validated as a prognostic marker in an independent contemporary-matched cohort (IGFBP3 HR = 2.06, 95% CI: 1.04-4.09, P = 0.038; EVL HR = 2.23, 95% CI: 1.00-5.0, P = 0.05) and EVL DNA methylation remained significant in a secondary historical validation cohort (HR = 1.41, 95% CI: 1.05-1.89, P = 0.022). Moreover, DNA methylation of selected ECM genes helps to stratify the high-risk stage 2 colon cancers patients who would benefit from adjuvant chemotherapy (HR: 5.85, 95% CI: 2.03-16.83, P = 0.001 for simultaneous methylation of IGFBP3, EVL, and CD109). CRC that have silenced genes in ECM pathway components show worse survival suggesting that our finding provides novel prognostic biomarkers for CRC and reflects the high importance of integrative analyses linking genetic and epigenetic abnormalities with pathway disruption in cancer.

Histone methylation patterns in human breast cancer

Histone post‐translational modifications regulate gene expression, and their misregulation is linked to cancer development. Histone methylation occurs on lysine residues, established by enzymes that regulate chromatin structure and gene activity. The ability of histone methylation to signal in chromatin depends on the lysine that is targeted and the methylation state (me1, me2, or me3) that is achieved. Methylation on histone H3 lysine 4 (H3K4) correlates with gene activity and the H3K4 methyltransferase MLL is translocated in hematological cancers. The H3K36 methyltransferase NSD1 is fused to NUP98 in leukemia and this histone mark is associated with active genes. The pattern of histone modification disruption in cancer has been largely unexplored. We examined by western blot the levels of H3K4me3 and H3K36me3 in breast cancer cell lines. We show that there are differential levels of histone methylation in several of the cancer cell lines when compared to a normal mammary epithelial cell line. BT549 and SUM102 cells exhibit low levels of H3K4me3 and increased levels of H3K36me3. These cell lines also have a defect in DNA methyltransferase activity resulting in increased levels of DNA methylation. Our data suggests that similar to DNA methylation, these histone marks are coupled to the pathology of breast cancer. Future studies will determine if histone methylation marks are clinically relevant for patient assessment.