Epigenetic mechanisms and genome stability

Epigenetic marks are well recognized as heritable chemical modifications of DNA and chromatin that induce chromatin structural changes thereby affecting gene activity. A lesser-known phenomenon is the pervasive effects these marks have on genomic integrity. Remarkably, epigenetic marks and the enzymes that establish them are involved in multiple aspects of maintaining genetic content. These aspects include preserving nucleotide sequences such as repetitive elements, preventing DNA damage, functioning in DNA repair mechanisms and chromatin restoration, and defining chromosomal organization through effects on structural elements such as the centromere. This review discusses these functional aspects of epigenetic marks and their effects on human health and disease

Distinct and overlapping control of 5-methylcytosine and 5-hydroxymethylcytosine by the TET proteins in human cancer cells

BACKGROUND: The TET family of dioxygenases catalyze conversion of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), but their involvement in establishing normal 5mC patterns during mammalian development and their contributions to aberrant control of 5mC during cellular transformation remain largely unknown. We depleted TET1, TET2, and TET3 in a pluripotent embryonic carcinoma cell model and examined the impact on genome-wide 5mC, 5hmC, and transcriptional patterns. RESULTS: TET1 depletion yields widespread reduction of 5hmC, while depletion of TET2 and TET3 reduces 5hmC at a subset of TET1 targets suggesting functional co-dependence. TET2 or TET3 depletion also causes increased 5hmC, suggesting these proteins play a major role in 5hmC removal. All TETs prevent hypermethylation throughout the genome, a finding dramatically illustrated in CpG island shores, where TET depletion results in prolific hypermethylation. Surprisingly, TETs also promote methylation, as hypomethylation was associated with 5hmC reduction. TET function is highly specific to chromatin environment: 5hmC maintenance by all TETs occurs at polycomb-marked chromatin and genes expressed at moderate levels; 5hmC removal by TET2 is associated with highly transcribed genes enriched for H3K4me3 and H3K36me3. Importantly, genes prone to hypermethylation in cancer become depleted of 5hmC with TET deficiency, suggesting that TETs normally promote 5hmC at these loci. Finally, all three TETs, but especially TET2, are required for 5hmC enrichment at enhancers, a condition necessary for expression of adjacent genes. CONCLUSIONS: These results provide novel insight into the division of labor among TET proteins and reveal important connections between TET activity, the chromatin landscape, and gene expression

Acute Depletion Redefines the Division of Labor among DNA Methyltransferases in Methylating the Human Genome

Global patterns of DNA methylation, mediated by the DNA methyltransferases (DNMTs), are disrupted in all cancers by mechanisms that remain largely unknown, hampering their development as therapeutic targets. Combinatorial acute depletion of all DNMTs in a pluripotent human tumor cell line, followed by epigenome and transcriptome analysis, revealed DNMT functions in fine detail. DNMT3B occupancy regulates methylation during differentiation, whereas an unexpected interplay was discovered in which DNMT1 and DNMT3B antithetically regulate methylation and hydroxymethylation in gene bodies, a finding confirmed in other cell types. DNMT3B mediated non-CpG methylation, whereas DNMT3L influenced the activity of DNMT3B toward non-CpG versus CpG site methylation. Altogether, these data reveal functional targets of each DNMT, suggesting that isoform selective inhibition would be therapeutically advantageous

33 UPLIFT (ENGOT-ov67/GOG-3048) a pivotal cohort of upifitamab rilsodotin (XMT-1536; UpRi), a NaPi2b-directed antibody drug conjugate (ADC) in platinum-resistant ovarian cancer

Upifitamab rilsodotin (UpRi), is a first-in-class antibody drug conjugate targeting NaPi2b, a sodium-dependent phosphate transporter protein broadly expressed in solid tumors including high-grade serous epithelial ovarian, fallopian tube and primary peritoneal cancers (OC), and limited expression in healthy tissues. Preliminary antitumor activity from the Phase 1b expansion cohort of heavily pretreated patients with OC has been reported (Richardson et al., SGO 2022). Data through June 2021 demonstrated clinically meaningful activity in patients with recurrent ovarian cancer, with notable activity in patients with NaPi2b-high tumors (TPS ≥75) treated at the optimized dose of 36 mg/m2. Effective and well-tolerated treatments for platinum-resistant ovarian cancer (PROC) remain a substantial unmet medical need. Single agent chemotherapy, which is the standard of care, has limited efficacy (response rate ≤12%) and short duration of response. Based on the encouraging anti-tumor activity of UpRi, UPLIFT was designed to be a single-arm Phase 2 registrational trial for UpRi in PROC. The UPLIFT cohort is enrolling patients with platinum-resistant high grade serous ovarian, fallopian tube and primary peritoneal cancer with up to 4 prior lines of therapy. Prior bevacizumab is required for patients with 1 or 2 prior lines of therapy but is not required for patients with 3–4 prior lines of therapy. Patients may enroll regardless of NaPi2b expression; ≤ Grade 2 peripheral neuropathy is permitted. Primary platinum refractory patients are excluded. UPLIFT will enroll approximately 180 patients globally, including approximately 100 patients with high NaPi2b expression. UpRi will be dosed intravenously at 36 mg/ m2 up to a maximum dose of ~80 mg every 4 weeks. Baseline tumor samples (fresh or archived) will be collected for central analysis of NaPi2b expression. The primary endpoint is ORR in patients with high NaPi2b expression. The cut-off for high NaPi2b expression is Tumor Proportion Score (TPS) ≥75, which was based on data from the Phase 1 expansion cohort. Secondary endpoints include ORR in the overall population, duration of response, and safety. This study is being conducted in collaboration with ENGOT (ENGOT-ov67) and GOG (GOG-3048). Patients will be enrolled globally. NCT03319628 This is a Trial in Progress; therefore, we do not have results/conclusions at this time. This is a Trial in Progress; therefore, we do not have results/conclusions at this time