Specialized replication of heterochromatin domains ensures self-templated chromatin assembly and epigenetic inheritance

Heterochromatin, defined by histone H3 lysine 9 methylation (H3K9me), spreads across large domains and can be epigenetically inherited in a self-propagating manner. Heterochromatin propagation depends upon a read-write mechanism, where the Clr4/Suv39h methyltransferase binds to preexisting trimethylated H3K9 (H3K9me3) and further deposits H3K9me. How the parental methylated histone template is preserved during DNA replication is not well understood. Here, we demonstrate using Schizosaccharomyces pombe that heterochromatic regions are specialized replication domains demarcated by their surrounding boundary elements. DNA replication throughout these domains is distinguished by an abundance of replisome components and is coordinated by Swi6/HP1. Although mutations in the replicative helicase subunit Mcm2 that affect histone binding impede the maintenance of a heterochromatin domain at an artificially targeted ectopic site, they have only a modest impact on heterochromatin propagation via the read-write mechanism at an endogenous site. Instead, our findings suggest a crucial role for the replication factor Mcl1 in retaining parental histones and promoting heterochromatin propagation via a mechanism involving the histone chaperone FACT. Engagement of FACT with heterochromatin requires boundary elements, which position the heterochromatic domain at the nuclear peripheral subdomain enriched for heterochromatin factors. Our findings highlight the importance of replisome components and boundary elements in creating a specialized environment for the retention of parental methylated histones, which facilitates epigenetic inheritance of heterochromatin.

Tissue inhibitors of metalloproteinases are proteolytic targets of matrix metalloproteinase 9

Extracellular proteolysis and turnover are core processes of tissue homeostasis. The predominant matrix-degrading enzymes are members of the Matrix Metalloproteinase (MMP) family. MMPs extensively degrade core matrix components in addition to processing a range of other factors in the extracellular, plasma membrane, and intracellular compartments. The proteolytic activity of MMPs is modulated by the Tissue Inhibitors of Metalloproteinases (TIMPs), a family of four multi-functional matrisome proteins with extensively characterized MMP inhibitory functions. Thus, a well-regulated balance between MMP activity and TIMP levels has been described as critical for healthy tissue homeostasis, and this balance can be chronically disturbed in pathological processes. The relationship between MMPs and TIMPs is complex and lacks the constraints of a typical enzyme-inhibitor relationship due to secondary interactions between various MMPs (specifically gelatinases) and TIMP family members. We illustrate a new complexity in this system by describing how MMP9 can cleave members of the TIMP family when in molar excess. Proteolytic processing of TIMPs can generate functionally altered peptides with potentially novel attributes. We demonstrate here that all TIMPs are cleaved at their C-terminal tails by a molar excess of MMP9. This processing removes the N-glycosylation site for TIMP3 and prevents the TIMP2 interaction with latent proMMP2, a prerequisite for cell surface MMP14-mediated activation of proMMP2. TIMP2/4 are further cleaved producing ∼14 kDa N-terminal proteins linked to a smaller C-terminal domain through residual disulfide bridges. These cleaved TIMP2/4 complexes show perturbed MMP inhibitory activity, illustrating that MMP9 may bear a particularly prominent influence upon the TIMP:MMP balance in tissues.

Abstract 70: Mechanisms of tumor dormancy induction mediated by abrogation of myeloid tgfβ signaling

Persistence in a dormant state of residual tumor cells can occur following extended periods of clinical remission which may last decades. The disseminated tumor cells in distant organ sites eventually gain context dependent metastasis advantage during tumor progression. The mechanisms for dormancy induction or reactivation remain unclear. We found that the abrogation of myeloid TGF-β signaling induced tumor dormancy in breast cancer metastasis models. When given extended time, the TGFβRIImyeKO mice eventually developed similar number of metastatic nodules to that of control mice. We further validated our finding using an inducible system where reintroduction of TβRII diminished the tumor dormancy induction. RNAseq of dormant vs proliferative tumor cells identify 504 differential expressed genes, including those involving cell cycle arrest, IFNg response, MTOR signaling as well as MYC targeted genes. Immune cell profiling showed differential immune composition in micro and macro-tumor microenvironment between WT and TβRIImyeKO lung tissues. Of great interest, abrogation of myeloid specific TGF-β signaling increased the number of CD103+DCs that displayed elevated TNFa production, which in turn increased IFNg+ production in T cells leading to improved innate

and adaptive immunity. Importantly, depletion of CD103 DCs in tumor-bearing TβRIImyeKO mice diminished the dormancy phenotype, which was not observed for the pDC depletion in the WT control mice. These data demonstrate that abrogation of myeloid specific TGF-β signaling improved the immune microenvironment, which induced tumor dormancy. Our data provide mechanistic insight and resources to understand the tumor dormancy.

Citation Format: Abdul Ahad, Feng Leng, Hiroshi Ichise, Justin Gray, Olga Aprelikova, Maura O’Neill, Ronald Holewinski, Vishal N. Kopardé4, Yasuhiro Moriwaki, Christine Hollander, Ronald Germain, Thorkell Andresson, Yang Li. Mechanisms of tumor dormancy induction mediated by abrogation of myeloid tgfβ signaling [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 70.

Functional characterization of a chr13q22.1 pancreatic cancer risk locus reveals long-range interaction and allele-specific effects on DIS3 expression

Genome-wide association studies (GWAS) have identified multiple common susceptibility loci for pancreatic cancer. Here we report fine-mapping and functional analysis of one such locus residing in a 610 kb gene desert on chr13q22.1 (marked by rs9543325). The closest candidate genes, KLF5, KLF12, PIBF1, DIS3 and BORA, range in distance from 265-586 kb. Sequencing three sub-regions containing the top ranked SNPs by imputation P-value revealed a 30 bp insertion/deletion (indel) variant that was significantly associated with pancreatic cancer risk (rs386772267, P = 2.30 × 10-11, OR = 1.22, 95% CI 1.15-1.28) and highly correlated to rs9543325 (r2 = 0.97 in the 1000 Genomes EUR population). This indel was the most significant cis-eQTL variant in a set of 222 histologically normal pancreatic tissue samples (β = 0.26, P = 0.004), with the insertion (risk-increasing) allele associated with reduced DIS3 expression. DIS3 encodes a catalytic subunit of the nuclear RNA exosome complex that mediates RNA processing and decay, and is mutated in several cancers. Chromosome conformation capture revealed a long range (570 kb) physical interaction between a sub-region of the risk locus, containing rs386772267, and a region ∼6 kb upstream of DIS3 Finally, repressor regulatory activity and allele-specific protein binding by transcription factors of the TCF/LEF family were observed for the risk-increasing allele of rs386772267, indicating that expression regulation at this risk locus may be influenced by the Wnt signaling pathway. In conclusion, we have identified a putative functional indel variant at chr13q22.1 that associates with decreased DIS3 expression in carriers of pancreatic cancer risk-increasing alleles, and could therefore affect nuclear RNA processing and/or decay.

A phase I study of gemcitabine plus dasatinib (GD) or gemcitabine plus dasatinib plus cetuximab (GDC) in refractory solid tumors

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Background: Dasatinib (D) is a small molecule tyrosine kinase inhibitor with activity against both bcr-abl and src. Cetuximab (C) is a monoclonal antibody that blocks EGFR. Preclinical models suggest D reverses resistance to G. In addition, src and EGFR pathways interact; synergism of dual blockade by D + C is possible. We evaluated two combination regimens, GD and GDC, in a Phase I dose escalation study. Methods: Patients (pts) with advanced solid tumors were enrolled in cohorts of 3–6 to either GD or GDC. G was dosed in mg/m2 weekly for 3 of 4 weeks, D was dosed in mg PO BID, and C was dosed at 250 mg/m2 weekly after loading dose of C=400; cycle length was 28 days. Dose levels were as follows: 1) G 1000 + D 50 ± C; 2) G 1,000 + D 70 ± C; 3) G 1,000 + D 100 ± C. Standard cycle 1 DLT definitions were used. Eligible pts had advanced solid tumors, adequate organ and marrow function, and no co-morbidities that would increase risk of toxicity. Serum, plasma, and skin biopsy biomarkers were obtained pre- and on treatment. Results: 25 pts have been enrolled, including 21 with pancreatic adenocarcinoma, 3 of whom had received prior G. 21 pts were evaluable for toxicity and 18 for efficacy. Four DLT were observed: Gr 3 ANC with infection (GDC1, n=1), Gr 3 ALT (GD2, n=2), and Gr 5 pneumonitis (GDC2, n=1). Possible treatment-related adverse events in later cycles included: Gr3–4 ANC (n=4), Gr4 colitis (n=1), Gr3 bilirubin (n=2), Gr3 Hgb (n=2), Gr3 Plt (n=2), Gr3 edema/fluid retention syndrome (n=1), and Gr3 vomiting (n=2). One previously untreated pt had a partial response. Eight of 18 pts, 3 of whom had received prior G, had stable disease as best response, median duration = 5 months (range 1–7). Biomarker results are pending. Conclusions: The MTD of the GD arm is G1000/D50BID. Stable disease in previous G-refractory pts was noted. Hematologic toxicities were dose-limiting; later toxicities including hematologic, LFT changes, pneumonitis, and fluid retention were seen. To address these toxicities, once daily dosing of D will be explored, followed by an expanded cohort of G + daily D vs G + bid D in pts with treatment-naïve pancreatic cancer.

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Results of a phase I study of bevacizumab (BV), everolimus (EV), and erlotinib (E) in patients with advanced solid tumors

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Background: BV inhibits vascular endothelial growth factor (VEGF). EV is an mTOR (mammalian target of rapamycin) inhibitor. E inhibits epidermal growth factor receptor (EGFR) tyrosine kinase. VEGF, mTOR, and EGFR inhibitors have anti-tumor and anti-angiogenesis effects alone and in combination in preclinical models. As a combination targeted therapy, we evaluated BV + EV + E in a phase I, pharmacokinetic (PK), biomarker study. Methods: Cycle length was 28 days. Doses: BV 10mg/kg IV q14d. EV 5mg PO QD, escalating to 10mg QD. Once the recommended phase II dose (RPTD) of BV + EV was reached, E was added, starting at 75 mg PO QD. DLT was defined as any treatment-related grade 4 heme or grade 3/4 non-heme event in Cycle 1. Results: 34 pts have been enrolled (18 F, 16 M), 28 evaluable for DLT, 24 for efficacy. Median age is 58y (range 29–73). Dose level 1 (BV 10mg/EV 5mg) had no DLT’s. Dose level 2 (BV 10mg/EV 10mg) had no DLT’s and the cohort was expanded to 13 evaluable pts. E (75mg) was added to BV 10mg/ EV 10mg. 2/6 patients had DLT (grade 3 mucositis and grade 3 rash). The doses were adjusted to BV 5mg/EV 5mg/E 75mg. 3 patients had no DLT and this dose is the MTD and RPTD for the 3-drug combination. 20 more patients are being enrolled at the RPTD for biomarker studies. Other grade ¾ toxicity included: nephrotic syndrome, cardiac ischemia, ventricular thrombus, portacath thrombosis, and bowel perforation. 2 patients had PR: 1 renal and 1 osteosarcoma. 16/24 pts had SD (10–112+ weeks). 5/6 patients with colorectal cancer (CRC) previously progressing on BV had SD (16+ - 112 weeks). One CRC patient had 19% radiologic decrease. Conclusions: BV + EV + E preliminary clinical activity (notably in refractory CRC) and class-related side effects were seen. The MTD is BV 5mg/kg IV q14d + EV 5mg PO QD + E 75mg PO QD. Updated data will be presented.

No significant financial relationships to disclose.