Molecular cytogenetics in solid tumors: laboratorial tool for diagnosis, prognosis, and therapy

Cancer cytogenetics in the era of artificial intelligence: shaping the future of chromosome analysis

Artificial intelligence (AI) has rapidly advanced in the past years, particularly in medicine for improved diagnostics. In clinical cytogenetics, AI is becoming crucial for analyzing chromosomal abnormalities and improving precision. However, existing software lack learning capabilities from experienced users. AI integration extends to genomic data analysis, personalized medicine and research, but ethical concerns arise. In this article, we discuss the challenges of the full automation in cytogenetic test interpretation and focus on its importance and benefits.

ChatGPT as an aid for pathological diagnosis of cancer

Diagnostic workup of cancer patients is highly reliant on the science of pathology using cytopathology, histopathology, and other ancillary techniques like immunohistochemistry and molecular cytogenetics. Data processing and learning by means of artificial intelligence (AI) has become a spearhead for the advancement of medicine, with pathology and laboratory medicine being no exceptions. ChatGPT, an artificial intelligence (AI)-based chatbot, that was recently launched by OpenAI, is currently a talk of the town, and its role in cancer diagnosis is also being explored meticulously. Pathology workflow by integration of digital slides, implementation of advanced algorithms, and computer-aided diagnostic techniques extend the frontiers of the pathologist's view beyond a microscopic slide and enables effective integration, assimilation, and utilization of knowledge that is beyond human limits and boundaries. Despite of it's numerous advantages in the pathological diagnosis of cancer, it comes with several challenges like integration of digital slides with input language parameters, problems of bias, and legal issues which have to be addressed and worked up soon so that we as a pathologists diagnosing malignancies are on the same band wagon and don't miss the train.

Fluorescence in-situ hybridization technique as a diagnostic and prognostic tool in oral squamous cell carcinoma

Background and Objectives:

Early diagnosis and appropriate management are of prime importance for oral squamous cell carcinoma (OSCC) in the present scenario. Molecular changes in OSCC are well documented with the occurrence of a wide range of genetic damage. Identification of the genetic damage in OSCC using various diagnostic aids is mandatory, and one of the important advances in this field is cytogenetics using fluorescence in-situ hybridization (FISH). The aim of the present study is to analyze the genetic alteration in OSCC using FISH as a diagnostic aid.

Materials and Methods:

Peripheral blood was analyzed in 20 clinically and histopathologically proven OSCC cases and 10 healthy controls for chromosomal alteration under standardized conditions.

Results:

Of the 20 OSCC cases, 7 (35%) cases showed chromosomal alterations. No cases from the control group showed any chromosomal changes. Of the positive cases in OSCC, 30% cases showed increased copy number of cyclin D1 gene and 1 (5%) case showed positivity indicating extra copy of chromosome 11p11.11-q11 region.

Interpretation and Conclusion:

Increased genetic damage in OSCC which is a prominent feature can be identified by the use of FISH as seen from the present study. The findings suggest that FISH can be used as a diagnostic aid in the detection of genetic changes occurring in OSCC. The present study also suggests the importance of peripheral blood as a medium for assessing cytogenetic damage in OSCC.

Molecular logic underlying chromosomal translocations, random or non-random?

Chromosomal translocations serve as essential diagnostic markers and therapeutic targets for leukemia, lymphoma, and many types of solid tumors. Understanding the mechanisms of chromosomal translocation generation has remained a central biological question for decades. Rather than representing a random event, recent studies indicate that chromosomal translocation is a non-random event in a spatially regulated, site-specific, and signal-driven manner, reflecting actions involved in transcriptional activation, epigenetic regulation, three-dimensional nuclear architecture, and DNA damage-repair. In this review, we will focus on the progression toward understanding the molecular logic underlying chromosomal translocation events and implications of new strategies for preventing chromosomal translocations.

Cytogenetics of jaw cysts - a pilot study

The pathogenesis of cysts that arise in the jaws is still not certain, and the underlying mechanisms of epithelial proliferation are not fully understood. Cysts of the jaw may involve a reactive, inflammatory, or neoplastic process. Cytogenetics, the study of the number and structure of chromosomes, has provided valuable information about the diagnosis, prognosis, and targeted treatment in many cancers, including oral squamous cell carcinoma. Cytogenetics can also provide information about the possible aetiology or neoplastic potential of a lesion, though to our knowledge no studies of this technique have been used for cysts in the jaws. In this pilot study we used cytogenetics in a series of 10 cysts (3 radicular, 4 dentigerous, 2 of the nasopalatine duct, and 1 dermoid). In all cases we found normal karyotypes. Further work and larger numbers are needed for a definitive study, but we can hypothesise from this pilot study that these cysts do not have cytogenetic aberrations and so have no neoplastic potential.

Cytogenetics of neurofibromas: two case reports and literature review

Only a few karyotypes of neurofibromas have been documented in the literature. In this report, we describe two new cases in which conventional cytogenetics demonstrated the presence of abnormal clones. Combining karyotypes of the nine previously reported cases, we found that the most frequent structural rearrangements involved chromosome 9p. Including the two cases reported here, 5/11 cases involved 9p, and four of these involved the 9p21 approximately p22 region.

Recurrent genomic gains in preinvasive lesions as a biomarker of risk for lung cancer

Lung carcinoma development is accompanied by field changes that may have diagnostic significance. We have previously shown the importance of chromosomal aneusomy in lung cancer progression. Here, we tested whether genomic gains in six specific loci, TP63 on 3q28, EGFR on 7p12, MYC on 8q24, 5p15.2, and centromeric regions for chromosomes 3 (CEP3) and 6 (CEP6), may provide further value in the prediction of lung cancer. Bronchial biopsy specimens were obtained by LIFE bronchoscopy from 70 subjects (27 with prevalent lung cancers and 43 individuals without lung cancer). Twenty six biopsies were read as moderate dysplasia, 21 as severe dysplasia and 23 as carcinoma in situ (CIS). Four-micron paraffin sections were submitted to a 4-target FISH assay (LAVysion, Abbott Molecular) and reprobed for TP63 and CEP 3 sequences. Spot counts were obtained in 30-50 nuclei per specimen for each probe. Increased gene copy number in 4 of the 6 probes was associated with increased risk of being diagnosed with lung cancer both in unadjusted analyses (odds ratio = 11, p<0.05) and adjusted for histology grade (odds ratio = 17, p<0.05). The most informative 4 probes were TP63, MYC, CEP3 and CEP6. The combination of these 4 probes offered a sensitivity of 82% for lung cancer and a specificity of 58%. These results indicate that specific cytogenetic alterations present in preinvasive lung lesions are closely associated with the diagnosis of lung cancer and may therefore have value in assessing lung cancer risk.

Alterations in genes of the EGFR signaling pathway and their relationship to EGFR tyrosine kinase inhibitor sensitivity in lung cancer cell lines

Background

Deregulation of EGFR signaling is common in non-small cell lung cancers (NSCLC) and this finding led to the development of tyrosine kinase inhibitors (TKIs) that are highly effective in a subset of NSCLC. Mutations of EGFR (mEGFR) and copy number gains (CNGs) of EGFR (gEGFR) and HER2 (gHER2) have been reported to predict for TKI response. Mutations in KRAS (mKRAS) are associated with primary resistance to TKIs.

Methodology/Principal Findings

We investigated the relationship between mutations, CNGs and response to TKIs in a large panel of NSCLC cell lines. Genes studied were EGFR, HER2, HER3 HER4, KRAS, BRAF and PIK3CA. Mutations were detected by sequencing, while CNGs were determined by quantitative PCR (qPCR), fluorescence in situ hybridization (FISH) and array comparative genomic hybridization (aCGH). IC50 values for the TKIs gefitinib (Iressa) and erlotinib (Tarceva) were determined by MTS assay. For any of the seven genes tested, mutations (39/77, 50.6%), copy number gains (50/77, 64.9%) or either (65/77, 84.4%) were frequent in NSCLC lines. Mutations of EGFR (13%) and KRAS (24.7%) were frequent, while they were less frequent for the other genes. The three techniques for determining CNG were well correlated, and qPCR data were used for further analyses. CNGs were relatively frequent for EGFR and KRAS in adenocarcinomas. While mutations were largely mutually exclusive, CNGs were not. EGFR and KRAS mutant lines frequently demonstrated mutant allele specific imbalance i.e. the mutant form was usually in great excess compared to the wild type form. On a molar basis, sensitivity to gefitinib and erlotinib were highly correlated. Multivariate analyses led to the following results:

 1. mEGFR and gEGFR and gHER2 were independent factors related to gefitinib sensitivity, in descending order of importance.

 2. mKRAS was associated with increased in vitro resistance to gefitinib.

Conclusions/Significance

Our in vitro studies confirm and extend clinical observations and demonstrate the relative importance of both EGFR mutations and CNGs and HER2 CNGs in the sensitivity to TKIs.

Role of chromosome structure variation in carcinogenesis and progression of gastric cancer

The carcinogenesis of gastric cancer is a multifactor process with many steps, of which, both the losing activity of tumor suppressor genes resulting from the abnormal structure of the chromosomes, and the activation of the oncogenes play important roles in these process. Therefore, identification of the tumor suppressor gene and oncogene through researching on the structural chromosomal abnormality has become an important means for the research of gastric cancer and oncology. This paper reviews the researches on current progresses on structural chromosomal abnormality in gastric cancer, especially on the aspect of methodology, and explained the application of various molecular genetics and molecular biology means used in structural chromosomal abnormality research. This paper aimed at providing references for the choice of researching methods for the readers.

Chromosomal instability is a risk factor for poor prognosis of adenocarcinoma of the lung: Fluorescence in situ hybridization analysis of paraffin-embedded tissue from Korean patients

BACKGROUND

In this study, we sought to evaluate the prognostic importance of chromosomal instability (CIN) in adenocarcinoma (AC) of the lung. The relationship between CIN detected by fluorescence in situ hybridization (FISH) and survival in AC patients was examined.

METHODS

Sixty-three surgical specimens of lung AC were analyzed. To identify tumors with CIN, p16 and multi-target DNA FISH assays for c-myc, chromosome 6, EGFR, and chromosome 5 (LAVysion, Vysis) were performed on nuclei extracted from paraffin-embedded tumor tissues. Survival rates were compared in terms of sex, age, histology, T factor, N factor, CIN, and smoking status. A sample was classified as CIN-positive if at least three of the five chromosomes were positive.

RESULTS

Out of the 63 specimens, 32 (39.7%) were CIN-positive. The 5-year overall disease-free survival rate was 58.7% as a whole, 46.9% for CIN-positive patients and 71.0% for the CIN-negative patients [hazard ratio (HR), 2.34; 95% confidence interval (CI), 1.04-5.26; p = 0.04]. The 5-year overall survival rate was 81.0%, 68.7% for CIN-positive patients and 93.5% for the CIN-negative patients (HR, 5.64; 95% CI, 1.23-25.70; p = 0.026). In multivariate analysis after adjusting for pathologic nodal staging, tumor staging, sex, age, and smoking history, compared with the CIN-negative patients, the CIN-positive status remained significantly associated with decreased overall survival (HR, 8.48; 95% CI, 1.66-43.42; p = 0.010).

CONCLUSIONS

CIN can be effectively detected in primary AC of lung using FISH analysis. CIN is associated with poor prognosis for AC, and may thus be utilized as an independent prognostic factor for the disease.

Comparative genomic hybridization analysis of abnormalities in chromosome 21 in childhood osteosarcoma

Osteosarcomas (OS) are aggressive tumors of the bone and often have a poor prognosis. The tumors exhibit karyotypes with a high degree of complexity, which has made it difficult to determine whether any recurrent chromosomal aberrations characterize OS. To address inherent difficulties associated with classical cytogenetic analysis, comparative genomic hybridization (CGH) was applied to OS tissue. Forty-one pediatric OS specimens were analyzed by a CGH technique: 24 female and 17 male patients, with a median age of 12 years and 4 months. Chromosomal abnormalities were highly diverse and variable, including gains of chromosome 1p, 2p, 3q, 5q, 5p, and 6p and losses of 14q (50% in 14q11.2), 15q, and 16p. A high level of losses of chromosome 21 was present (26/41 cases; P = 0.008), most often loss of the 21q11.2 approximately 21 region. These novel findings in chromosome 21 of pediatric OS tumors suggest that specific sequences mapping to these chromosomal regions are likely to play a role in the development of OS.

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Cytogenetic alterations in nonmelanoma skin cancer: a review

Since the advent of cytogenetic analysis, knowledge about fundamental aspects of cancer biology has increased, allowing the processes of cancer development and progression to be more fully understood and appreciated. Classical cytogenetic analysis of solid tumors had been considered difficult, but new advances in culturing techniques and the addition of new cytogenetic technologies have enabled a more comprehensive analysis of chromosomal aberrations associated with solid tumors. Our purpose in this review is to discuss the cytogenetic findings on a number of nonmelanoma skin cancers, including squamous- and basal cell carcinomas, keratoacanthoma, squamous cell carcinoma in situ (Bowen's disease), and solar keratosis. Through classical cytogenetic techniques, as well as fluorescence-based techniques such as fluorescence in situ hybridization and comparative genomic hybridization, numerous chromosomal alterations have been identified. These aberrations may aid in further defining the stages and classifications of nonmelanoma skin cancer and also may implicate chromosomal regions involved in progression and metastatic potential. This information, along with the development of newer technologies (including laser capture microdissection and comparative genomic hybridization arrays) that allow for more refined analysis, will continue to increase our knowledge about the role of chromosomal events at all stages of cancer development and progression and, more specifically, about how they are associated with nonmelanoma skin cancer.

Clinical implications of advanced molecular cytogenetics in cancer

The field of cytogenetics has already entered the molecular era and a rapid expansion of its contribution is seen in genomic disease management. Among the evolving advanced molecular techniques, with an impeccable balance of high specificity, sensitivity and assay rapidity, fluorescence in situ hybridization has made its home in routine clinical laboratory. Today, its clinical application is vivid in every phase of disease management of a number of malignancies. The rapid growth in the knowledge of specific associations between distinct chromosomal abnormalities and different types of cancers will necessitate simultaneous detection of multiple abnormalities using multicolor/multiplex fluorescence in situ hybridization tests more often in the near future. Also, as the human genome sequence is ascertained, genome-wide screening with microarray technology will gain eminence in the clinical scenario, yield better solutions and bring the concept of personalized medicine in cancer closer to reality than ever before.

Multi-target interphase fluorescence in situ hybridization assay increases sensitivity of sputum cytology as a predictor of lung cancer

Survival rates for lung cancer are low because patients have disseminated disease at diagnosis; therefore tests for early diagnosis are highly desirable. This pilot study investigated occurrence of chromosomal aneusomy in sputum from a 33 case-control cohort matched on age, gender, and date of sample collection. Subjects had chronic obstructive pulmonary disease and > or = 30 pack-years of tobacco use, and aneusomy was tested using a multi-target DNA FISH assay (LAVysion, Abbott/Vysis). In specimens collected within 12 months of lung cancer diagnosis, abnormality was more frequent among the 18 cases (41%) than the 17 controls (6%; P = 0.04). Aneusomy had no significant association with cytologic atypia, which might indicate that molecular and morphological changes could be independent markers of tumorigenesis. Combining both tests, abnormality was found in 83% of the cases and 20% of the controls (P = 0.0004) suggesting that FISH may improve the sensitivity of cytologic atypia as a predictor of lung cancer.