Presence Of Genomic Instability Research Articles

Clinical translation for targeting DNA damage repair in non-small cell lung cancer: a review.

Despite significant advancements in screening, diagnosis, and treatment of non-small cell lung cancer (NSCLC), it remains the primary cause of cancer-related deaths globally. DNA damage is caused by the exposure to exogenous and endogenous factors and the correct functioning of DNA damage repair (DDR) is essential to maintain of normal cell circulation. The presence of genomic instability, which results from defective DDR, is a critical characteristic of cancer. The changes promote the accumulation of mutations, which are implicated in cancer cells, but these may be exploited for anti-cancer therapies. NSCLC has a distinct genomic profile compared to other tumors, making precision medicine essential for targeting actionable gene mutations. Although various treatment options for NSCLC exist including chemotherapy, targeted therapy, and immunotherapy, drug resistance inevitably arises. The identification of deleterious DDR mutations in 49.6% of NSCLC patients has led to the development of novel target therapies that have the potential to improve patient outcomes. Synthetic lethal treatment using poly (ADP-ribose) polymerase (PARP) inhibitors is a breakthrough in biomarker-driven therapy. Additionally, promising new compounds targeting DDR, such as ATR, CHK1, CHK2, DNA-PK, and WEE1, had demonstrated great potential for tumor selectivity. In this review, we provide an overview of DDR pathways and discuss the clinical translation of DDR inhibitors in NSCLC, including their application as single agents or in combination with chemotherapy, radiotherapy, and immunotherapy.

Mammalian Resilience Revealed by a Comparison of Human Diseases and Mouse Models Associated With DNA Helicase Deficiencies.

Maintaining genomic integrity is critical for sustaining individual animals and passing on the genome to subsequent generations. Several enzymes, such as DNA helicases and DNA polymerases, are involved in maintaining genomic integrity by unwinding and synthesizing the genome, respectively. Indeed, several human diseases that arise caused by deficiencies in these enzymes have long been known. In this review, the author presents the DNA helicases associated with human diseases discovered to date using recent analyses, including exome sequences. Since several mouse models that reflect these human diseases have been developed and reported, this study also summarizes the current knowledge regarding the outcomes of DNA helicase deficiencies in humans and mice and discusses possible mechanisms by which DNA helicases maintain genomic integrity in mammals. It also highlights specific diseases that demonstrate mammalian resilience, in which, despite the presence of genomic instability, patients and mouse models have lifespans comparable to those of the general population if they do not develop cancers; finally, this study discusses future directions for therapeutic applications in humans that can be explored using these mouse models.

The Presence of Genomic Instability in Cerebrospinal Fluid in Patients with Meningeal Metastasis

PurposeThis study aimed to explore the genomic instability in cerebrospinal fluid (CSF) in patients with meningeal metastasis (MM).Material and MethodsWe collected the blood and CSF samples of 15 MM patients and one brain parenchymal metastasis (BPM) patient. A panel of 543 cancer-related genes was conducted to analyze the status of genomic instability in CSF and plasma cell-free DNA (cfDNA) of all patients. Subsequently, nine patients underwent low-depth whole-genome sequencing (WGS) analysis to verify the existence of genomic instability, followed by genomic scoring by the application of aneuploidy scores. Diagnosis-specific graded prognostic assessment (DS-GPA) score was utilized to assess the clinical status of MM patients.ResultsThere was significant difference in gene mutation between CSF cfDNA and plasma cfDNA in MM patients. Among them, 12 MM patients developed genomic instability in their CSF cfDNA, while the remaining 3 had stable genetic profile. Besides, BPM patients showed genomic stability in his CSF and paraffin-embedded tissue sections. No genomic instability was noticed in plasma cfDNA of all patients. Sensitive mutations on EGFR, ERBB2, ALK and KRAS genes and increased gene copy numbers of MET and ERBB2 were detected in 10 MM patients with genomic instability, as well as the EGFR gene mutation in one MM case with genomic stability. Additionally, MM patients with genomic instability had lower overall survival and higher aneuploidy scores and tumor mutation burden compared with those with genomic stability. Moreover, MM patients with higher DS-GPA scores benefited from better survival.ConclusionGenomic instability existed in the CSF cfDNA rather than plasma cfDNA of MM patients, which might be the underlying cause of the differences in MM.

Intratumour heterogeneity in endometrial serous carcinoma assessed by targeted sequencing and multiplex ligation-dependent probe amplification: a descriptive study.

Endometrial serous carcinoma (ESC) represents the most aggressive subtype of endometrial carcinoma (EC). According to The Cancer Genome Atlas (TCGA), ESC exhibits a genomic profile characterised by frequent TP53 mutations and somatic copy-number alterations (SCNA). Several studies have suggested the role of intratumour heterogeneity (ITH) in tumour progression and therapy resistance, highlighting ITH as a challenge for personalised medicine. ITH is described as the co-existence of clonal and subclonal cellular populations within a single tumour. To date, the extent and prevalence of ITH in ESC have not been fully evaluated. The aim of this study was to address ITH analysis in ESC. We performed a descriptive integrated molecular approach using targeted sequencing and multiplex ligation-dependent probe amplification (MLPA) to identify mutations and SCNA patterns, respectively. Eight ESC were examined, selecting three tumour regions per case and their corresponding normal tissue. For targeted sequencing a gene panel of 40 genes based on TCGA and other survey data was performed. For MLPA different probe mixes were used to detect SCNA in 106 genes. Analysis of mutations and SCNA were performed in each sample and comparative analysis of the three tumour regions was also conducted. Targeted sequencing showed that mutations in TP53, PIK3CA and PPP2R1A were ubiquitous in all tumour regions. Moreover, MLPA results demonstrated a high frequency of SCNA, according to the already known presence of genomic instability in ESC. Unlike the homogeneous distribution of somatic mutations, SCNA exhibited ITH affecting targetable genes such as ERBB2. Our study suggests that somatic gene copy-number alterations are the main source of ITH in ESC.

Regional signals in the planarian body guide stem cell fate in the presence of genomic instability.

Cellular fate decisions are influenced by their topographical location in the adult body. For instance, tissue repair and neoplastic growth are greater in anterior than in posterior regions of adult animals. However, the molecular underpinnings of these regional differences are unknown. We identified a regional switch in the adult planarian body upon systemic disruption of homologous recombination with RNA-interference of Rad51 Rad51 knockdown increases DNA double-strand breaks (DSBs) throughout the body, but stem cells react differently depending on their location along the anteroposterior axis. In the presence of extensive DSBs, cells in the anterior part of the body resist death, whereas cells in the posterior region undergo apoptosis. Furthermore, we found that proliferation of cells with DNA damage is induced in the presence of brain tissue and that the retinoblastoma pathway enables overproliferation of cells with DSBs while attending to the demands of tissue growth and repair. Our results implicate both autonomous and non-autonomous mechanisms as key mediators of regional cell behavior and cellular transformation in the adult body.

The mini-driver model of polygenic cancer evolution.

Much of cancer genetics research has focused on the identification of the most-important somatic mutations ('major drivers') that cause tumour growth. However, many mutations found in cancer might not be major drivers or 'passenger' mutations, but instead might have relatively weak tumour-promoting effects. Our aim is to highlight the existence of these mutations (termed 'mini drivers' herein), as multiple mini-driver mutations might substitute for a major-driver change, especially in the presence of genomic instability or high mutagen exposure. The mini-driver model has clinical implications: for example, the effects of therapeutically targeting such genes may be limited. However, the main importance of the model lies in helping to provide a complete understanding of tumorigenesis, especially as we anticipate that an increasing number of mini-driver mutations will be found by cancer genome sequencing.

Micronucleus frequency in peripheral blood lymphocytes and frailty status in elderly. A lack of association with clinical features

Frailty is a condition of vulnerability that carries an increased risk of poor outcome in elder adults. Frail individuals show fatigue, weight loss, muscle weakness, and a reduced physical function, and are known to frequently experience disability, social isolation, and institutionalization. Identifying frail people is a critical step for geriatricians to provide timely geriatric care and, eventually, to improve the quality of life in elderly. The aim of the present study is to investigate the association between frailty status and micronucleus (MN) frequency, a known marker of genomic instability, in a sample of elder adults. Several clinical features were evaluated and their possible association with MN frequency was tested. Criteria proposed by Fried were used to identify frail subjects. Overall, 180 elder adults entered the study, 93 of them (51.7%) frail. No association between MN frequency and frailty status was found under the specific conditions tested in this study (mean ratio=1.06; 95% CI 0.96–1.18). The inclusion of MN frequency in the Fried’s frailty scale minimally improved the classification of study subjects according to the multidimensional prognostic index (MPI). The presence of genomic instability in the ageing process and in most chronic diseases, demands further investigation on this issue.

ASTRO 2013

ASTRO 2013

Molecular events in germ cell tumours: linking chromosome‐12 gain, acquisition of pluripotency and response to cisplatin

Germ cell tumours (GCTs) represent the leading cause of cancer-related morbidity and mortality in young men aged 18-35 years. Transformation of the cell of origin results in tumours with several unique properties. GCTs are characterized by gain of the short arm of chromosome 12 in almost all cases, a frequency of genomic alteration not seen in any other solid tumours. GCTs are truly pluripotent, giving rise to cells of somatic and extra-embryonic lineages, which results in tumours with a spectrum of differentiation that rivals that seen in normal embryogenesis and development. Despite the presence of genomic instability and many oncogenic changes, GCTs are highly curable, even in the metastatic setting, due to their extreme sensitivity to cisplatin-based chemotherapy. In this review we highlight some of the molecular events associated with the genesis, differentiation and chemotherapeutic response of these tumours, and discuss how these alterations are linked with biological features unique to germ cells.

Genomic instability in the breast microenvironment? A critical evaluation of the evidence

Tumor-associated stroma plays an active role in breast pathogenesis, with alterations in cell signaling, proliferation and angiogenesis contributing to successful tumorigenesis. Although epigenetic modifications to DNA, as well as changes in RNA and protein expression have been identified in tumor-associated stroma, there is considerable debate regarding the presence of chromosomal alterations, detected as loss of heterozygosity/allelic imbalance events in histologically normal stromal cells adjacent to the breast carcinomas. Previous studies have detected loss of heterozygosity/allelic imbalance at varying distances from the tumor margin, and patterns of chromosomal change have been linked to tumor grade and lymph node status. By contrast, recent reports challenge the presence of genomic instability in stromal cells of the breast tumor microenvironment, leading to the speculation that the loss of heterozygosity/allelic imbalance studies, based almost exclusively on microsatellite-based profiling of formalin-fixed, paraffin-embedded tissues, do not accurately measure the true genomic content of the tumor microenvironment but rather are a reflection of technological artifact. In this perspective, we present evidence surrounding the debate and critically evaluate arguments, both pros and cons, over the presence or absence of genomic instability tumor-associated stroma.

A stochastic carcinogenesis model incorporating multiple types of genomic instability fitted to colon cancer data

A generalization of the two-mutation stochastic carcinogenesis model of Moolgavkar, Venzon and Knudson and certain models constructed by Little [Little, M.P. (1995). Are two mutations sufficient to cause cancer? Some generalizations of the two-mutation model of carcinogenesis of Moolgavkar, Venzon, and Knudson, and of the multistage model of Armitage and Doll. Biometrics 51, 1278–1291] and Little and Wright [Little, M.P., Wright, E.G. (2003). A stochastic carcinogenesis model incorporating genomic instability fitted to colon cancer data. Math. Biosci. 183, 111–134] is developed; the model incorporates multiple types of progressive genomic instability and an arbitrary number of mutational stages. The model is fitted to US Caucasian colon cancer incidence data. On the basis of the comparison of fits to the population-based data, there is little evidence to support the hypothesis that the model with more than one type of genomic instability fits better than models with a single type of genomic instability. Given the good fit of the model to this large dataset, it is unlikely that further information on presence of genomic instability or of types of genomic instability can be extracted from age-incidence data by extensions of this model.

RET oncogene amplification in thyroid cancer: Correlations with radiation-associated, high-grade malignancy, and genomic instability

Abstract. RET oncogene rearrangement is a well-known molecular alteration observed in papillary thyroid cancer (PTC). RET rearrangement is the commonest oncogenic alterations in Chernobyl-related PTC; nearly all to RET/PTC1 or RET/PTC3, resulting from paracentric inversion of chromosome 10. Other less common variants, usually forming as a result of interchromosomal translocation, occur in an extremely limited number of cases. Most often such translocations have been found in radiation-induced PTC. Here, we report the presence of RET oncogene amplification, a new type of RET cytogenetic alteration, in human thyroid cancers. RET amplification was correlated with radiation-associated, high-grade malignant potency, and p53 overexpression, suggesting genomic instability. We also examined p53-binding protein 1 (53BP1) expressions with immunostaining to clarify the presence of genomic instability in thyroid cancers. In thyroid tumors, the level of 53BP1-focus formation was associated with malignant transformation and high-grade malignant potency as well as RET amplification. RET amplification might be induced by a high level of genomic instability with progression of thyroid carcinogenesis and, subsequently, be associated with radiation-induced and/or high-grade malignant cases.

Molecular alterations of E-cadherin gene: possible role in human bladder carcinogenesis.

E-cadherin is a transmembrane glycoprotein which mediates a calcium dependent homophilic interaction among epithelial cells. The altered expression and gene mutations of E-cadherin adhesion molecule have been frequently observed in various tumors. Several invasive carcinomas showed cell-cell adhesion loss although the tumor cells expressed considerable amounts of E-cadherin protein. The purpose of this study was to evaluate the role of E-cadherin gene alterations in genesis and progression of bladder carcinoma by mutation analysis of coding region, expression analysis and microsatellite instability at E-cadherin chromosome locus. We analyzed 30 bladder carcinoma (28 transitional and 2 squamous cell carcinoma) at different stage and grade. The mutation analysis showed that in one case there was a presence of a point mutation at codon 846 that consisted of a G (AGC) to C (ACC) transversion resulting in the replacement of R to T. In another sample the sequence analysis revealed a same-sense mutation at the codon 785 (AAC - AAT). The study of E-cadherin mRNA by Northern blot analysis showed that there were no differences of mRNA levels between tumor and normal mucosa samples. We noted that invasive and anaplastic tumors showed a trend to loss of expression, even if we did not find any statistically significant differences. The microsatellite analysis showed the presence of genomic instability in proximity of the E-cadherin gene. Nine out of 30 (30%) specimens presented molecular alterations in at least one out of 2 loci (D16S260 and D16S301) analyzed. The comparison between microsatellite mutations and clinical-histopathological parameters revealed a higher number of alterations in invasive respect to superficial tumors (p=0.014). On the other hand, there were no statistical differences regarding the correlation with pathological grade. These observations, which, nevertheless, need to be confirmed in a larger number of patients, suggest that alterations of E-cadherin gene may be related to pathobiology of bladder cancer development and clinical progression.

Evaluation of cytophotometric DNA content abnormalities in premalignant and preinvasive breast lesions

Progression of breast neoplasia is characterized by a variety of causal and nonspecific molecular, karyotypic, and cellular level genetic alterations. These include allelic losses, chromosomal rearrangements, and aneusomies, as well as widely divergent clonal DNA content aberrations. Establishment of the sequence and the pathologic significance of individual changes has been challenging owing to disease heterogeneity, protracted natural history, and difficulties in sampling and localizing precursor lesions. These limitations have driven attempts at cytophotometric evaluation of premalignant/preinvasive proliferations using histologic (i.e., in situ) microdissection of intact paraffin-embedded tissue sections. Using image cytophotometric measurements in preserved sections, clonal DNA content abnormalities are identified in up to three-fourths of preinvasive breast carcinomas. The incidence of DNA aneuploidy is grade-dependent and similar in degree to invasive lesions. Comparison of ploidy determinations between preinvasive and corresponding invading populations, however, suggests host tissue permeation is accompanied by measurable DNA content shifts in many cases. Image cytophotometric DNA content abnormalities are also detectable in florid/atypical proliferative lesions, albeit less frequently (∼25% of cases) and to a lesser extent (i.e., near diploid) than cytologically malignant lesions. Although the sensitivity of cytophotometric ploidy assessments in tissue sections is limited by nuclear sectioning, the presence of genomic instability in premalignant lesions is supported by evidence of individual chromosome aneuploidy, demonstrated by interphase cytogenetics with fluorescent centromere-specific probes. These data suggest cytophotometrically detectable DNA content anomalies may precede unequivocal morphologic transformation in breast neoplasia. Further, clonal DNA content heterogeneity in breast carcinoma may accompany biologically critical steps in neoplastic progression of breast tumors.

Pathological and biological relevance of cytophotometric DNA content to breast carcinoma genetic progression

Correlating cytophotometrically detectable genetic alterations to events of known biological and pathological significance in breast carcinoma has been challenging, in large part owing to the difficulty in isolating and analyzing premalignant (i.e., hyperplastic) or preinvasive (i.e., in situ carcinoma) lesions. This problem may be addressed by using histologically directed evaluation of intact, paraffin-embedded tissue sections. Using image cytophotometry in preserved sections, we have identified clonal DNA content abnormalities (i.e., aneuploidy) in up to three-fourths of preinvasive breast carcinomas. Moreover, comparison of ploidy determinations between residual in situ and corresponding invading neoplastic populations suggests that host invasion is accompanied by measurable DNA content shifts in many cases. Image cytophotometric DNA content abnormalities are also detectable in florid/atypical proliferative lesions, albeit less frequently (-25% of cases) and to a lesser extent (i.e., near-diploid) than in situ carcinomas. Taken together, these findings imply an association between clonal DNA content aberrations and histologic disease progression. Although the sensitivity of cytophotometric ploidy assessments in tissue sections is limited by nuclear sectioning artifact and overlap, the presence of genomic instability in precursor lesions is supported by evidence of individual chromosome aneuploidy, which can be demonstrated in tissue sections by interphase cytogenetics with fluorescent, centromere-specific probes. Further, presence of intra-tumoral clonal DNA content heterogeneity is confirmed by cytogenetic studies showing co-existing near-diploid chromosome number modes in many tumors with hyperdiploid stemlines. Karyotypic stemline analyses imply polyploidization events are an important mechanism of clonal evolution leading to genetic heterogeneity.(ABSTRACT TRUNCATED AT 250 WORDS)