Onset Of Genomic Instability Research Articles

Abstract 5650: RP-6306, a novel PKMYT1 inhibitor, demonstrates synthetic lethality as monotherapy and in combination with gemcitabine in CCNE1 amplified cancer cells

Abstract Cyclin E1, the protein product of the CCNE1 gene, complexes with CDK2 and is a key regulator of the G1-S transition in cycling cells. CCNE1 amplification has been associated with increased replication stress and genomic instability associated with tumorigenesis. The serine-threonine protein kinase family member PKMYT1 negatively regulates the G2-Mitosis transition by phosphorylating and inactivating CDK1. The aim of the current study was to evaluate the impact of RP-6306, a novel and selective PKMYT1 inhibitor, on the CCNE1 amplified human breast cancer cell line, HCC1569. RP-6306 is a highly potent PKMYT1 inhibitor that displays single digit nM potency in an in vitro enzyme assay. RP-6306 dose-dependently inhibited the phosphorylation of CDK1 on Thr14 in HCC1569 cells and had no impact on the Tyr15 phospho-site of CDK1 that is regulated by family member Wee1. Cell-based assays showed increased phosphorylation of replication stress and pre-mitotic entry biomarkers in RP-6306 treated HCC1569 cells. Micronuclei and Caspase-3 were detected in a dose-dependent manner in HCC1569 cells treated with RP-6306 indicating the onset of genomic instability and apoptosis in these cells. Growth assays confirmed irreparable damage and proliferation defects in cells treated with RP-6306. Experiments to evaluate the combination of RP-6306 with gemcitabine, an S-phase specific pyrimidine analog that inhibits DNA synthesis showed profound synergistic growth defects in HCC1569 cells. In vivo, RP-6306 inhibition of Thr14 phosphorylation of CDK1 in HCC1569 tumors was directly proportional to free circulating plasma levels and resulted in significant inhibition of tumor growth in a dose and time dependent manner. In combination with gemcitabine, RP-6306 demonstrated tumor regression and superior efficacy compared to single agent treatment of either agent alone in multiple CCNE1 amplified models, including HCC1569 and OVCAR3. Our studies show that inhibition of PKMYT1 kinase activity impairs the growth of CCNE1 amplified cancer cell lines both in vitro and in vivo and stands to benefit cancer patients with CCNE1 amplification. A Phase I clinical trial (NCT04855656- Mythic Study) is currently underway to evaluate RP-6306 in patients with advanced solid tumors. Citation Format: Jimmy Fourtounis, John Martino, Rino Stocco, Prasamit Baruah, Nicole Duffy, David Gallo, Sarah Fournier, JingJing Li, Li Li, Elia Aguado, Adam Petrone, Anne Roulston, Yael Mamane, Stephen Morris, Janek Szychowski, Robert Papp, Mike Zinda, C. Gary Marshall. RP-6306, a novel PKMYT1 inhibitor, demonstrates synthetic lethality as monotherapy and in combination with gemcitabine in CCNE1 amplified cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5650.

From cellular morphology to molecular and epigenetic anomalies of myelodysplastic syndromes.

Myelodysplastic syndromes (MDSs) are a myeloid neoplasm with a propensity for natural evolution or transformation to acute leukemias (AL) over time. Mechanisms for MDS transformation to AL remain poorly understood but are related to genomic instability, which affects the production of the different cell lineages. Genomic instability is also generated by dysfunctional telomeres. Indeed telomeres, the protective ends of chromosomes are the backbone of genome stability. Nuclear telomere remodeling is an early indicator of nuclear remodeling preceding the onset of genomic instability and MDS. This review aims to revisit the pathogenesis and pathophysiology of MDS from morphology and cytogenetics to molecular and epigenetic mechanisms. Furthermore, this review will highlight and discuss recent breakthroughs in dysfunctional telomeres and nuclear telomere architecture roles in the pathogenesis and physiopathology of MDS in the global context of genomic instability.

Acute telomere deprotection prevents ongoing BFB cycles and rampant instability in p16INK4a-deficient epithelial cells.

Telomere dysfunction drives chromosome instability through endless breakage-fusion-bridge (BFB) cycles that promote the formation of highly rearranged genomes. However, reactivation of telomerase or ALT-pathway is required for genome stabilisation and full malignant transformation. To allow the unrestricted proliferation of cells at risk of transformation, we have established a conditional system of telomere deprotection in p16INK4a-deficient MCF-10A cells with modified checkpoints. After sustained expression of a dominant negative form of the shelterin protein TRF2 (TRF2ΔBΔM), cells with telomere fusion did progress to anaphase but no signs of ongoing BFB cycles were observed, thus anticipating proliferation defects. Indeed, 96 h TRF2ΔBΔM expression resulted in noticeable growth proliferation defects in the absence of cell cycle disturbances. Further transient periods of 96 h telomere uncapping did not result in cell cycle disturbances either. And reduction of the telomere damage to short acute deprotection periods did not in any case engender cells with a reorganised karyotype. Strikingly, the growth arrest imposed in cells showing dysfunctional telomeres was not accompanied by an activation of the DNA damage response at cellular level, or by the presence of visible markers of senescence or apoptosis. We propose that the deprotection of many telomeres simultaneously, even for a short time, results in a local activation of the cellular stress response which consequently triggers gradual cell withdrawal from cell cycle, restraining the onset of genomic instability.

Gastric cancer and related epigenetic alterations.

Gastric cancer, a malignant and highly proliferative condition, has significantly affected a large population around the globe and is known to be caused by various factors including genetic, epigenetic, and environmental influences. Though the global trend of these cancers is declining, an increase in its frequency is still a threat because of changing lifestyles and dietary habits. However, genetic and epigenetic alterations related to gastric cancers also have an equivalent contribution towards carcinogenic development. DNA methylation is one of the major forms of epigenetic modification which plays a significant role in gastric carcinogenesis. Methylation leads to inactivation of some of the most important genes like DNA repair genes, cell cycle regulators, apoptotic genes, transcriptional regulators, and signalling pathway regulators; which subsequently cause uncontrolled proliferation of cells. Mutations in these genes can be used as suitable prognostic markers for early diagnosis of the disease, since late diagnosis of gastric cancers has a huge negative impact on overall patient survival. In this review, we focus on the important epigenetic mutations that contribute to the development of gastric cancer and the molecular pathogenesis underlying each of them. Methylation, acetylation, and histone modifications play an integral role in the onset of genomic instability, one of the many contributory factors to gastric cancer. This article also covers the constraints of incomplete knowledge of epigenetic factors influencing gastric cancer, thus throwing light on our understanding of the disease.

Apc and p53 interaction in DNA damage and genomic instability in hepatocytes.

Disruption of Apc within hepatocytes activates Wnt signaling, perturb differentiation and ultimately lead to neoplasia. Apc negatively regulates Wnt signaling but is also involved in organizing the cytoskeleton and may play a role in chromosome segregation. In vitro studies have implicated Apc in the control of genomic stability. However, the relevance of this data has been questioned in vivo as Apc is lost earlier than the onset of genomic instability. Here, we analyse the relationship between immediate loss of Apc and the acquisition of genomic instability in hepatocytes. We used Cre-lox technology to inactivate Apc and in combination with p53 in vivo, to define the consequences of gene loss upon cell-cycle regulation, proliferation, death and aneuploidy. We show that whilst Apc loss leads to increased proliferation, it also leads to increased apoptosis, the accumulation of p53, p21 and markers of DSBs and DNA repair. Flow cytometry revealed an increased 4N DNA content, consistent with a G2 arrest. Levels of anaphase bridges were also elevated, implicating failed chromosome segregation. This was accompanied by an increase in centrosome number which demonstrates a role for Apc in maintaining euploidy.To address the role of p53 in these processes, we analyzed combined loss of Apc and p53, which led to a further increase in proliferation, cell death, DNA damages and repair and a bypass of G2 arrest than was observed with Apc loss. However we observed only a marginal effect on anaphase bridges and centrosome number which could be due to increased cell death. Our data therefore establishes, in an in vivo setting, that APC loss leads to a DNA damage signature and genomic instability in the liver and that additional loss of p53 leads to an increase in the DNA damage signal but not to an immediate increase in the genomic instability phenotype.

3D nuclear organization and genomic instability in cancer.

To understand the genetic changes that occur at tumor initiation and during tumor progression, we focus on changes in nuclear architecture that promote the onset of genomic instability [1,2]. To determine changes in nuclear organization, we measure the 3D nuclear organization of telomeres, the ends of chromosomes. The measurements of telomeres allow one to trace the positions of chromosomes in interphase nuclei and, by using a fluorescent telomere-specific probe, all telomeres can be visualized in a single image. During the past years, we have defined the organization of telomeres in nuclei of normal, immortalized and tumor cells. We have developed quantitative software that enables us to measure the three-dimensional (3D) organization of telomeres [3,4]. The parameters we measure include: number of telomeres, sizes of telomeres, nuclear distribution of telomeres, and the presence of telomeric aggregates. The latter are clusters of telomeres that are absent from normal cells. More recently, we started to automate the 3D image acquisition and analysis and we are able to scan 15 000 cells per hour [5]. We observed changes in the nuclear organization of telomeres as a result of conditional c-Myc deregulation dependent on a functional myc box II [6,7]. We found Epstein-Barr Virus-induced changes in 3D telomere organization and resulting genomic instability [8]. Encouraged by these findings, we focused on tumor initiation and progression in patient samples and observed cancer-associated 3D nuclear telomere changes in lymphoid and solid tumors [9-12]. Moreover, the use of 3D nuclear telomere profiling permitted, for the first time, the identification of patient (and tumor) subpopulations that were not detectable up to that point. For example, we blindly defined three distinct subpopulations that correlated with short-term, intermediate and long-term survival in glioblastoma [11]. Using the same 3D imaging approach, we defined subpopulations in myelodysplastic syndromes and acute myeloid leukemias [12]. Additional studies are currently ongoing. We provided evidence that genomic instability is a result of these nuclear changes. Dynamic nuclear alterations directly result from 3D telomere aberrations [1,2,6,13-15]. These genomic changes include aneuploidy, Robertsonian fusions, breakage-bridge fusion (BBF) cycles with resulting terminal deletions and unbalanced translocations and continued rounds of BBF cycles. While these changes can be followed during cancer progression in patients, their true origin can only be examined in conditional expression studies or longitudinally in mouse models. Using conditional c-Myc deregulation, we demonstrated that changes in 3D telomere profiles precede the onset and propagation of genomic instability [6,13]. In Hodgkin’s lymphoma, in collaboration with Dr. Hans Knecht, we showed that mono-nucleated H cells become multinucleated Reed Sternberg (RS) cells through telomere dysfunction as measured by 3D nuclear profiles [10,16]. These changes coincide with localized shelterin dysfunction, aberrant centrosome duplication as well as spindle formation and significantly elevated levels of DNA damage foci [10,16]. Spectral karyotyping (SKY) and super resolution 3D imaging confirmed the dynamics and complexity of these genetic changes in which RS cells are the end-stage cells generated through multiple defects traced back to the H cells and propagated from there on [15]. Most recently, we have reported that Hodgkin’s patients with recurrent/non-recurrent disease display distinct 3D telomeric profiles [17]. Ongoing studies focus on a variety of cancers where clinicians currently lack the ability to define the risk of an individual patient to progress, the ability of early detection or of monitoring of disease progression. In conclusion, 3D telomere profiling provides a platform technology able to determine normal and aberrant nuclear organization that is a measure of genomic instability and cancer.

Inflammatory response to isocyanates and onset of genomic instability in cultured human lung fibroblasts

Lungs comprise the primary organ exposed to environmental toxic chemicals, resulting in diverse respiratory ailments and other disorders, including carcinogenesis. Carcinogenesis is a multi-stage phenomenon, which involves a series of genetic alterations that begin with genomic instability provoked by certain factors such as inflammation and DNA damage and end with the development of cancer. Isocyanates such as methyl isocyanate are the chief metabolic intermediates in many industrial settings with diverse applications; exposure to them can lead to severe hypersensitive, mutagenic and genotoxic alterations. We examined the molecular mechanisms underlying isocyanate-mediated inflammatory responses and their probable role in the onset of genomic instability in cultured IMR-90 human lung fibroblasts. The isocyanates induced inflammation, resulting in extensive DNA damage, evidenced by increases in ATM, ATR, gammaH2AX, and p53 expression levels. The apoptotic index also increased. Chromosomal anomalies in treated cells included over-expression of centrosome protein and variable amplification of inter-simple sequence repeats, further demonstrating isocyanate-induced genomic instability. This information could be useful in the design of new approaches for risk assessment of potential industrial disasters.

APC mutations lead to cytokinetic failures in vitro and tetraploid genotypes in Min mice

Previous research has proposed that genomic instability contributes to cancer progression, with its initiation linked to tetraploid cell formation (Duesberg, P., and R. Li. 2003. Cell Cycle. 2:202–210; Ganem, N.J., Z. Storchova, and D. Pellman. 2007. Curr. Opin. Genet. Dev. 17:157–162). However, there is little direct evidence linking cancer-causing mutations with such events, and it remains controversial whether genomic instability is a cause or an effect of cancer. In this study, we show that adenomatous polyposis coli (APC) mutations found in human colorectal cancers dominantly inhibit cytokinesis by preventing mitotic spindle anchoring at the anaphase cortex and, thus, blocking initiation of the cytokinetic furrow. We find that dividing crypt cells in the small intestines of APCMin/+ mice exhibit similar mitotic defects, including misoriented spindles and misaligned chromosomes. These defects are observed in normal crypt cells with wild-type levels of β-catenin and, importantly, are associated with tetraploid genotypes. We provide direct evidence that the dominant activity of APC mutants induces aneuploidy in vivo. Our data support a model whereby tetraploid cells represent a first step in the onset of genomic instability and colorectal cancer.

The multi-step process of human skin carcinogenesis: A role for p53, cyclin D1, hTERT, p16, and TSP-1

As proposed by Hanahan and Weinberg (2000. Cell 100, 57–70) carcinogenesis requires crucial events such as (i) genomic instability, (ii) cell cycle deregulation, (iii) induction of a telomere length maintenance mechanism, and (iv) an angiogenic switch. By comparing the expression of p53, cyclin D1, p16, hTERT, and TSP-1 in spontaneously regressing keratoacanthoma (KA) as a paradigm of early neoplasia, with malignant invasive cutaneous squamous cell carcinoma (SCC) as a paradigm of advanced tumour development, we are now able to assign the changes in the expression of these proteins to specific stages and allocate them to defined roles in the multi-step process of skin carcinogenesis. We show that mutational inactivation of the p53 gene, and with that the onset of genomic instability is the earliest event. Individual p53-positive cells are already seen in “normal” skin, and 3/5 actinic keratoses (AKs), 5/22 KAs, and 13/23 SCCs contain p53-positive patches. Cell cycle deregulation was indicated by the overexpression of the cell cycle regulator cyclin D1, as well as by the loss of the cell cycle inhibitor p16. Interestingly, overexpression of cyclin D1 – observed in 80% of KAs and SCCs, respectively – showed a cell cycle-independent function in HaCaT cell transplants on nude mice. Cyclin D1 overexpression was associated with a massive inflammatory response, finally leading to tissue destruction. Loss of the cell cycle inhibitor p16, on the other hand, correlated with SCCs. Thus, it is tempting to suggest that overexpression of cyclin D1 is an early change that in addition to growth stimulation leads to an altered epithelial–mesenchymal interaction, while functional p16 is able to control this deregulated growth and needs to be eliminated for malignant progression. Another requirement for uncontrolled growth is the inhibition of telomere erosion by up-regulating telomerase activity. As measured by hTERT protein expression, all of the KAs and SCCs studied were positive, with a similar distribution of the protein in both groups and an expression pattern resembling that of normal epidermis. Thus, telomerase may not need to be increased significantly in skin carcinomas. Finally, we show that the angiogenesis inhibitor TSP-1 is strongly expressed in most KAs, and mainly by the tumour cells, while in SCCs the generally weak expression is restricted to the tumour–stroma. Furthermore, we provide evidence that the loss of a copy of chromosome 15 is responsible for reduced TSP-1 expression and thereby this aberration contributes to tumour vascularisation (i.e. the angiogenic switch) required for malignant growth.

The onset of genomic instability in sporadic colorectal polyps

The onset of genomic instability in sporadic colorectal polyps