Somatic Chromosomal Alterations Research Articles

Abstract B004: PISCA-box: A user-friendly interface for Phylogenetic Inference using Somatic Chromosomal Alterations (PISCA)

Abstract PISCA, originally introduced by Martinez et al. in 2018, represents a pivotal Bayesian phylogenetics tool for the modeling of tumor evolution using multi-region somatic chromosomal alteration (SCA) data. PISCA takes allele-specific copy number data, typically obtained from deep genome sequencing or SNP arrays, or absolute copy number data from low-pass genome sequencing methodologies. It extends the classic BEAST1 framework and inherits a rich repertoire of evolutionary models. Importantly, PISCA leverages longitudinal sampling to estimate SCA mutational clock rates, either employing strict clock models, where mutation rates remain constant throughout the evolutionary tree, or relaxed clocks, which allow each branch or subtree to possess its distinct mutation rate. This nuanced approach empowers PISCA to account for the heterogeneous rates of mutations, a pivotal consideration in understanding tumor evolution dynamics. However, PISCA has historically posed a formidable entry barrier for wider community adoption due to platform and Java dependencies for installation, as well as the need for manual or custom-scripted XML file generation. Here we showcase PISCA-box, a user-friendly interface designed to streamline the generation and testing of XML files. Our PISCA-box Docker image works on any desktop machine to create a locally hosted webpage, where users can input SCA data, sampling dates, select clock and demographic models, and set priors for key parameters - similar to the BEAST XML generator, BEAUTi. The Docker or Singularity installation can then be used for longer analyses using high-performance computing resources. To demonstrate its practical utility, we present novel colorectal cancer data. First, we examine data from a patient with a long-standing history of inflammatory bowel disorder (IBD), a known high-risk factor for colorectal cancer. This patient had undergone surveillance colonoscopies for many years, which provided 38 samples, and subsequently an additional 118 samples were collected from a total colectomy. All were analyzed with low-coverage whole genome sequencing. We find some samples from surveillance and colectomy form lineages with overlapping copy number events, that we used to construct a phylogeny, finding a cancer-adjacent clade that appears to evolve rapidly. A second dataset of multi-region samples from a cohort of exceptional survivors of oligometastatic colorectal cancer who lived >60 months from metastatic diagnosis with biopsies/resections across 3-10 time points is examined and temporal models are used to estimate the ages of metastatic clades. PISCA therefore harnesses the power of longitudinal SCA data to enable a comprehensive study of SCA dynamics. We are currently expanding this framework to include fluctuating methylation clocks which PISCA-box will soon include. By providing this accessible tool, we enable researchers to readily apply Bayesian phylogenetics to real-world clinical datasets to better understand tumor evolution. Citation Format: Heather E. Grant, Rachel Alcraft, Pablo Bousquets-Muñoz, Calum Gabbutt, Alison Berner, Mehmet Yalchin, Carlo C. Maley, Trevor A. Graham, Diego Mallo. PISCA-box: A user-friendly interface for Phylogenetic Inference using Somatic Chromosomal Alterations (PISCA) [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Translating Cancer Evolution and Data Science: The Next Frontier; 2023 Dec 3-6; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_2):Abstract nr B004.

Detection of Copy-Number Variation in Circulating Cell-Free DNA in Patients With Uveal Melanoma.

Somatic chromosomal alterations, particularly monosomy 3 and 8q gains, have been associated with metastatic risk in uveal melanoma (UM). Whole genome-scale evaluation of detectable alterations in cell-free DNA (cfDNA) in UM could provide valuable prognostic information. Our pilot study evaluates the correlation between genomic information using ultra-low-pass whole-genome sequencing (ULP-WGS) of cfDNA in UM and associated clinical outcomes. ULP-WGS of cfDNA was performed on 29 plasma samples from 16 patients, 14 metastatic UM (mUM) and two non-metastatic, including pre- and post-treatment mUM samples from 10 patients treated with immunotherapy and one with liver-directed therapy. We estimated tumor fraction (TFx) and detected copy-number alterations (CNAs) using ichorCNA. Presence of 8q amplification was further analyzed using the likelihood ratio test (LRT). Eleven patients with mUM (17 samples) of 14 had detectable circulating tumor DNA (ctDNA). 8q gain was detected in all 17, whereas monosomy 3 was detectable in 10 of 17 samples. TFx generally correlated with disease status, showing an increase at the time of disease progression (PD). 8q gain detection sensitivity appeared greater with the LRT than with ichorCNA at lower TFxs. The only patient with mUM with partial response on treatment had a high pretreatment TFx and undetectable on-treatment ctDNA, correlating with her profound response and durable survival. ctDNA can be detected in mUM using ULP-WGS, and the TFx correlates with DS. 8q gain was consistently detectable in mUM, in line with previous studies indicating 8q gains early in primary UM and higher amplification with PD. Our work suggests that detection of CNAs by ULP-WGS, particularly focusing on 8q gain, could be a valuable blood biomarker to monitor PD in UM.

The association of three DNA repair genes polymorphisms on the frequency of chromosomal alterations detected by fluorescence in situ hybridization

PurposeGas station workers (GSWs) are exposed to carcinogenic agents. The aim was to study the association of high somatic chromosome alterations (CAs) rates in the blood of GSWs and the polymorphisms of three genes playing a role in DNA double-strand break repair.MethodsThis is a cross-sectional study with 114 GSWs and 115 age-matched controls. Cytogenetic analyses, blood exams, medical interviews and genotypes for RAD51/G135C (rs1801320), ATM/P1054R (rs1800057) and CHEK2/T470C (rs17879961) genes were performed.ResultsThe CA rate in GSWs was 9.8 CAs/1000 metaphases, and 19.1% of the workers had > 10 CAs per 1000 metaphases (group two). GSWs had decreased levels of monocytes (P = 0.024) in their blood exams. The number of variant alleles of the RAD51/G135C polymorphism was higher in GSWs (P = 0.011) compared to the controls, and were associated with enhanced number of CAs per worker (P = 0.008). No allele variant was found for CHEK2/T470C in this study.ConclusionThe RAD51/G135C polymorphism appears to be related to genome instability in gas station workers. Increasing the knowledge of DNA repair gene variations involved in maintaining genomic stability in GSWs may be crucial for future cancer prevention.

Abstract 1588: Germline variation in DNA repair genes and risk of Barrett's esophagus and esophageal adenocarcinoma

Abstract Incidence of esophageal adenocarcinoma (EA) has risen substantially in Western countries over recent decades. Established risk factors for EA and its precursor lesion, Barrett’s esophagus (BE), include reflux, obesity, and tobacco smoking. Inherited genetic variation also influences disease risk, although only a limited number of susceptibility loci have been identified. Genomic analyses of EA tumors have revealed a distinctive mutational signature, high mutational burden, and extensive somatic chromosome alterations, features also observed in high-risk BE tissue. To explore whether germline variation in DNA repair-related genes may be associated with altered disease susceptibility, we analyzed data from a recent meta-analysis of genome-wide association studies (GWAS) encompassing 4,112 EA cases, 6,167 BE cases, and 17,159 controls, representing the largest sample size assembled for these conditions. Using a gene-based testing approach (VEGAS2), we assessed 263 DNA repair-related genes and found that variation in NEIL2, a mediator of base excision repair (BER), was significantly associated with risk of BE (P=1.4×10-5, q<0.05). No other gene-level associations with BE or EA survived correction for multiple comparisons. SNP-level analysis of 239 polymorphisms at the NEIL2 locus revealed six variants strongly associated with altered risk of BE (P<5×10-5, q<0.01), with the index SNP classified as an intronic eQTL for NEIL2 in esophageal tissue. Four of these SNPs were also associated with risk of EA (P<0.05), with odds ratios in the same direction and of similar magnitude. Our results provide evidence that germline genetic variation in a DNA glycosylase enzyme (NEIL2) may influence risk of BE/EA, and suggest a potential novel biological role for altered BER in BE/EA pathogenesis. Citation Format: Matthew F. Buas, Li Yan, Xuan Peng, Qianya Qi, Jianhong Chen, Aaron Thrift, Qianchuan He, Lynn Onstad, Puya Gharahkhani, Stuart MacGregor, Thomas L. Vaughan, Margaret M. Madeleine. Germline variation in DNA repair genes and risk of Barrett's esophagus and esophageal adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1588.

Assessing inter-component heterogeneity of biphasic uterine carcinosarcomas

ObjectiveUterine carcinosarcoma (UCS) is a rare and aggressive form of uterine cancer. It is bi-phasic, exhibiting histological features of both malignant epithelial (carcinoma) and mesenchymal (sarcoma) elements, reflected in ambiguity in accepted treatment guidelines. We sought to study the genomic and transcriptomic profiles of these elements individually to gain further insights into the development of these tumors. MethodsWe macro-dissected carcinomatous, sarcomatous, and normal tissues from formalin fixed paraffin embedded uterine samples of 10 UCS patients. Single nucleotide polymorphism microarrays, targeted DNA sequencing and whole-transcriptome RNA-sequencing were performed. Somatic chromosomal alterations (SCAs), point mutation and gene expression profiles were compared between carcinomatous and sarcomatous components. ResultsIn addition to TP53, other recurrently mutated genes harboring putative driver or loss-of-function mutations included PTEN, FBXW7, FGFR2, KRAS, PIK3CA and CTNNB1, genes known to be involved in UCS. Intra-patient somatic mutation and SCA profiles were highly similar between paired carcinoma and sarcoma samples. An epithelial-mesenchymal transition (EMT) signature tended to differentiate components, with EMT-like status more common in advanced-stage patients exhibiting higher inter-component SCA heterogeneity. ConclusionsFrom DNA analysis, our results indicate a monoclonal disease origin for this cohort. Yet expression-derived EMT statuses of the carcinomatous and sarcomatous components were often discrepant, and advanced cases displayed greater genomic heterogeneity. Therefore, separately-profiled components of UCS tumors may better inform disease progression or potential.

Assessment of Esophageal Adenocarcinoma Risk Using Somatic Chromosome Alterations in Longitudinal Samples in Barrett's Esophagus.

Cancers detected at a late stage are often refractory to treatments and ultimately lethal. Early detection can significantly increase survival probability, but attempts to reduce mortality by early detection have frequently increased overdiagnosis of indolent conditions that do not progress over a lifetime. Study designs that incorporate biomarker trajectories in time and space are needed to distinguish patients who progress to an early cancer from those who follow an indolent course. Esophageal adenocarcinoma is characterized by evolution of punctuated and catastrophic somatic chromosomal alterations and high levels of overall mutations but few recurrently mutated genes aside from TP53. Endoscopic surveillance of Barrett's esophagus for early cancer detection provides an opportunity for assessment of alterations for cancer risk in patients who progress to esophageal adenocarcinoma compared with nonprogressors. We investigated 1,272 longitudinally collected esophageal biopsies in a 248 Barrett's patient case-cohort study with 20,425 person-months of follow-up, including 79 who progressed to early-stage esophageal adenocarcinoma. Cancer progression risk was assessed for total chromosomal alterations, diversity, and chromosomal region-specific alterations measured with single-nucleotide polymorphism arrays in biopsies obtained over esophageal space and time. A model using 29 chromosomal features was developed for cancer risk prediction (area under receiver operator curve, 0.94). The model prediction performance was robust in two independent esophageal adenocarcinoma sets and outperformed TP53 mutation, flow cytometric DNA content, and histopathologic diagnosis of dysplasia. This study offers a strategy to reduce overdiagnosis in Barrett's esophagus and improve early detection of esophageal adenocarcinoma and potentially other cancers characterized by punctuated and catastrophic chromosomal evolution.

Implications of Genome Alterations in Chironomus bernensis Klȍtzli (Diptera) for Assessment of Trace Metal Pollution in Two Bulgarian Rivers

AbstractThis study assesses the effect of sediment contaminants as indicated by the measurement of trace metal levels in two large Bulgarian rivers (river Maritsa and a tributary and the river Chaya) on the genome of the abundant chironomid species Chironomus bernensis Klȍtzli. Six trace metals: Cd, Cr, Cu, Mn, Pb and Zn were analysed in the sediments plus the overlying water. The polytene chromosomes of C. bernensis were very sensitive to the pollutants on the basis of numerous somatic chromosome alterations. Two biomarkers based on the degree of somatic structural chromosome alterations—the somatic and cytogenetic indices were applied. Both indices are a sensitive and reproducible approach for assessing the genotoxic effect of contaminants in the sediments. The somatic index from the differentially contaminated sites varied from 1.93 to 2.61, indicating the sensitivity of the C. bernensis genome to anthropogenic stress. The cytogenetic index revealed a high level of pollution in the rivers with a score between 0.27 and 0.37 (<0.5 indicates ‘highly polluted’). The genome of C. bernensis responded to the trace metal pollution by the appearance of a ‘B’ chromosome in between 4.4% and 7.1% of the individuals and detected for the first time in this species. Pollution also induced a heterozygous state in one of the Nucleolar Organizers in up to 3% of the sampled populations.The sensitivity of the C. bernensis genome shows that this species is a good candidate for detecting the presence of genotoxic compounds in freshwater and assessing their genotoxic effects. Copyright © 2015 John Wiley & Sons, Ltd.

1p36 deletion is a marker for tumour dissemination in microsatellite stable stage II-III colon cancer.

BackgroundThe clinical behaviour of colon cancer is heterogeneous. Five-year overall survival is 50-65% with all stages included. Recurring somatic chromosomal alterations have been identified and some have shown potential as markers for dissemination of the tumour, which is responsible for most colon cancer deaths. We investigated 115 selected stage II-IV primary colon cancers for associations between chromosomal alterations and tumour dissemination.MethodsFollow-up was at least 5 years for stage II-III patients without distant recurrence. Affymetrix SNP 6.0 microarrays and allele-specific copy number analysis were used to identify chromosomal alterations. Fisher’s exact test was used to associate alterations with tumour dissemination, detected at diagnosis (stage IV) or later as recurrent disease (stage II-III).ResultsLoss of 1p36.11-21 was associated with tumour dissemination in microsatellite stable tumours of stage II-IV (odds ratio = 5.5). It was enriched to a similar extent in tumours with distant recurrence within stage II and stage III subgroups, and may therefore be used as a prognostic marker at diagnosis. Loss of 1p36.11-21 relative to average copy number of the genome showed similar prognostic value compared to absolute loss of copies. Therefore, the use of relative loss as a prognostic marker would benefit more patients by applying also to hyperploid cancer genomes. The association with tumour dissemination was supported by independent data from the The Cancer Genome Atlas.ConclusionDeletions on 1p36 may be used to guide adjuvant treatment decisions in microsatellite stable colon cancer of stages II and III.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2407-14-872) contains supplementary material, which is available to authorized users.

FHACT: the FISH-based HPV-associated cancer test that detects nonrandom gain at four genomic loci as biomarkers of disease progression

Despite implementation of screening programs for human papillomavirus (HPV)-associated cancers, in particular cervical, scientific studies continue to uncover viral and host biomarkers that could serve to further optimize the detection of individuals with underlying or at risk for developing precancer or cancer. Nonrandom host somatic chromosomal alterations are frequently shared across HPV-associated cancers, but with varying frequencies, potentially with functional roles. At least for 3q26 gain, there is firm preliminary evidence to support that this genomic alteration can serve as a biomarker of disease progression of cervical cancer. In the current review, the FISH-based HPV-associated cancer test is described that enables detection of genomic imbalance at four loci (3q26, 5p15, 20q13, centromere 7) in a single hybridization on a cell-by-cell basis in cytology specimens. When implemented as a secondary screening assay, the FISH-based HPV-associated cancer test could assist in the detection of clinically relevant HPV-associated disease and help guide patient management decisions.

Application of SNP Microarrays to the Genome-Wide Analysis of Chromosomal Instability in Premalignant Airway Lesions

Chromosomal instability is central to the process of carcinogenesis. The genome-wide detection of somatic chromosomal alterations (SCA) in small premalignant lesions remains challenging because sample heterogeneity dilutes the aberrant cell information. To overcome this hurdle, we focused on the B allele frequency data from single-nucleotide polymorphism microarrays (SNP arrays). The difference of allelic fractions between paired tumor and normal samples from the same patient (delta-θ) provides a simple but sensitive detection of SCA in the affected tissue. We applied the delta-θ approach to small, heterogeneous clinical specimens, including endobronchial biopsies and brushings. Regions identified by delta-θ were validated by FISH and quantitative PCR in heterogeneous samples. Distinctive genomic variations were successfully detected across the whole genome in all invasive cancer cases (6 of 6), carcinoma in situ (3 of 3), and high-grade dysplasia (severe or moderate; 3 of 11). Not only well-described SCAs in lung squamous cell carcinoma, but also several novel chromosomal alterations were frequently found across the preinvasive dysplastic cases. Within these novel regions, losses of putative tumor suppressors (RNF20 and SSBP2) and an amplification of RASGRP3 gene with oncogenic activity were observed. Widespread sampling of the airway during bronchoscopy demonstrated that field cancerization reflected by SCAs at multiple sites was detectable. SNP arrays combined with delta-θ analysis can detect SCAs in heterogeneous clinical sample and expand our ability to assess genomic instability in the airway epithelium as a biomarker of lung cancer risk.

Temporal and Spatial Evolution of Somatic Chromosomal Alterations: A Case-Cohort Study of Barrett's Esophagus

All cancers are believed to arise by dynamic, stochastic somatic genomic evolution with genome instability, generation of diversity, and selection of genomic alterations that underlie multistage progression to cancer. Advanced esophageal adenocarcinomas have high levels of somatic copy number alterations. Barrett's esophagus is a risk factor for developing esophageal adenocarcinoma, and somatic chromosomal alterations (SCA) are known to occur in Barrett's esophagus. The vast majority (∼95%) of individuals with Barrett's esophagus do not progress to esophageal adenocarcinoma during their lifetimes, but a small subset develop esophageal adenocarcinoma, many of which arise rapidly even in carefully monitored patients without visible endoscopic abnormalities at the index endoscopy. Using a well-designed, longitudinal case-cohort study, we characterized SCA as assessed by single-nucleotide polymorphism arrays over space and time in 79 "progressors" with Barrett's esophagus as they approach the diagnosis of cancer and 169 "nonprogressors" with Barrett's esophagus who did not progress to esophageal adenocarcinoma over more than 20,425 person-months of follow-up. The genomes of nonprogressors typically had small localized deletions involving fragile sites and 9p loss/copy neutral LOH that generate little genetic diversity and remained relatively stable over prolonged follow-up. As progressors approach the diagnosis of cancer, their genomes developed chromosome instability with initial gains and losses, genomic diversity, and selection of SCAs followed by catastrophic genome doublings. Our results support a model of differential disease dynamics in which nonprogressor genomes largely remain stable over prolonged periods, whereas progressor genomes evolve significantly increased SCA and diversity within four years of esophageal adenocarcinoma diagnosis, suggesting a window of opportunity for early detection.

The effect of long-term contamination by heavy metals on community and genome alterations of Chironomidae (Diptera) in a stream with mine drainage water (southern Poland)

Abstract This paper reports on studies of the effect of heavy metals on the Chironomidae that inhabit the Matylda stream, which has been contaminated for about 100 years by discharge water from a zinc and lead ore mine. Stream sediment was strongly polluted by Cd, Pb, Cu and Zn. These metals did not affect the Chironomidae community but strongly changed the genome system of the Chironomidae species that inhabited the sediment. The salivary gland chromosomes of six species belonging to the two genera Chironomus and Prodiamesa are analyzed. In all species the somatic index is calculated on the basis of somatic chromosome alterations. Chironomus riparius has the highest numbers of somatic alterations and the highest somatic index — 9.67. The smallest chromosome G carries the key structures known as “Balbiani rings”, which play an important role in species development. This chromosome is very sensitive in the genome of the most studied species. The high sensitivity of the C. riparius genome is discussed in light of its DNA organization. The results show a high response of the salivary gland chromosomes to heavy metal pollution, and this makes them a valuable indicator in the assessment of water quality and detection of mutagenic agents in the aquatic environment.

Molecular cytogenetics as a clinical test for prognostic and predictive biomarkers in newly diagnosed ovarian cancer

BackgroundThere is a clinical need for routinely available genomic biomarker testing in newly diagnosed ovarian cancer. In the current study we performed molecular cytogenetics using a validated array based comparative genomic hybridization (array CGH) assay to screen for the presence of predictive and prognostic biomarkers in archival diagnostic tissue from ovarian cancer patients. We hypothesized that biomarkers of high-risk disease would be detectable in tumor samples from patients with treatment refractory, advanced disease, and would be detected less frequently in tumor samples from patients with more favorable outcomes. In addition, we predicted that the use of a genome-wide copy number analysis (CNA) testing platform would enable us to identify novel potentially targetable chromosomal alterations of therapeutic significance in a percentage of cases.MethodsFormalin-fixed paraffin-embedded tissue (FFPE) tumor bank specimens were retrieved from the initial surgical resection for 18 ovarian cancer patients. Molecular cytogenetics was performed by array CGH for the detection of somatic chromosomal alterations associated with high-risk disease including amplifications of the CCNE1 and HER2 genes. Genomic risk stratification results were correlated with available clinical data. CGH data from each patient’s tumor genome was also surveyed for the presence of potentially targetable aberrations. Relevant therapeutic agents and open studies for investigational drugs were reported for each patient.ResultsHigh-risk genomic alterations were identified in 12/18 (67%) of cases and all patients with high-risk markers had advanced, treatment refractory disease. Three tumors with minimal genomic changes had no high-risk markers and were from patients with Stage I/II disease that had been completely resected and under surveillance for recurrence. Eleven patients (61%) had at least one potentially targetable genomic alteration including CCNE1, HER2, KRAS gene amplifications, and somatic BRCA1 and/or BRCA2 gene deletions. Bi-allelic PTEN gene deletion was detected in one patient’s tumor.ConclusionsClinical genomic profiling of ovarian tumors by array CGH augments pathologic grade and stage to help stratify newly diagnosed ovarian cancer into high and low-risk disease. This personalized genomic information can also help guide treatment planning and disease monitoring by identifying novel potentially targetable genomic alterations that can be used by clinicians to choose rational directed therapies for patients with chemo-resistant disease.

Genome-Wide Somatic Copy Number Alterations in Low-Grade PanINs and IPMNs from Individuals with a Family History of Pancreatic Cancer

Characterizing the earliest chromosomal alterations of pancreatic precursor neoplasms from individuals with a familial aggregation of pancreatic cancer may provide clues as to the loci of pancreatic cancer susceptibility genes. We used Illumina 370/660K SNP arrays to conduct genome-wide copy number analysis in 60 benign neoplasms [58 mostly low-grade pancreatic intraepithelial neoplasias (PanIN) and intraductal papillary mucinous neoplasms (IPMN) and two pancreatic neuroendocrine tumors (PNET)] and matched normal tissues from 16 individuals with a family history of pancreatic cancer. PanINs and IPMNs were analyzed for KRAS codon 12/13 mutations. Of 40 benign neoplasms with adequate SNP calls and allele ratios, somatic chromosomal copy number changes were identifiable in only nine lesions, including eight of the 38 PanIN/IPMNs (two of which had identical alterations) and one of the two PNETs. Only two precursor lesions had more than one somatic copy number alteration. In contrast, the overwhelming majority (∼95%) of PanINs harbored KRAS mutations. The chromosomal alterations identified included nine chromosomal arms affected by chromosomal loss and two by chromosomal gain. Copy number loss spanning 9p21.3 was identified in three precursor lesions; two precursors had chromosomal losses affecting 6q and 17p. Low- and intermediate-grade PanINs and IPMNs from patients with a family history of pancreatic cancer harbor few if any somatic chromosomal alterations. The absence of a locus of recurrent chromosomal loss in most low-grade pancreatic cancer precursor lesions supports the hypothesis that there is no one tumor suppressor gene locus consistently involved in initiating familial pancreatic neoplasia.

Genome instability ofChironomus ripariusMg. andChironomus pigerStrenzke (Diptera, Chironomidae)

Intra and interspecific variation was evaluated in two Bulgarian populations (Pancharevo and Koka- lijane) of the two sibling and homosequential species Chironomus riparius Mg. and Chironomus piger Strenzke, by analyzing structural and functional alterations in salivary gland polytene chromosomes. In both species genome in- stability was demonstrated, which was expressed by structural and functional somatic chromosomal alterations. In the C. riparius population from Pancharevo, living in sediments containing high concentrations of Cu, Pb and Zn, salivary gland cells containing somatic rearrangements appeared at a significantly higher frequency (51.92%) than in the Kokalijane C. piger population, living in heavy metal-unpolluted sediments (21.3%). In the C. riparius popu- lation, somatic aberrations were distributed at different points along the chromosomes while in the C. piger popula- tion, somatic rearrangements were concentrated in the pericentromeric regions of chromosomes CD, EF and in proximal part of arms D and F. At the cytological level using FISH analysis, both species can be identified also by the different location of tandem-repetitive minisatellite DNA clusters of Alu and Hinf families, and insertion sites of the LINE retrotransposon NLRCTh1. While location of the former is fixed, NLRCth1 appeared to have both fixed and inter-individually variable positions in both species. On average, 19.0 ± 9.5 insertions of NLRCth1 per individ- ual were observed in C. riparius and 5.57 ± 2.09 in C. piger. In both species locations of minisatellite DNA clusters, NLRCth1 retrotransposons and aberration breakpoints concentrated in proximal regions of chromosomes, and the majority of the breakpoints were located in sections containing blocks of repetitive DNA clusters.

Chromosomal Organization and Transcriptional Regulation of Human GEM and Localization of the Human and Mouse GEM Loci Encoding an Inducible Ras-Like Protein

The mitogen-induced gene, GEM, encodes a GTP-binding protein that belongs to a new family within the Ras superfamily. The regulated expression pattern of Gem suggests a role for this protein in cellular responses to growth stimulation. To facilitate the assessment of the possible role of GEM in heritable and spontaneous disease processes, the genomic organization of human GEM and the chromosomal localization of human and murine GEM have been determined. GEM has been localized to the long arm of human chromosome 8 (8q13-q21) between the D8S85 and CA2 loci by genetic linkage analysis using an MspI restriction fragment length polymorphism within GEM . No consistent somatic chromosomal alterations or heritable diseases are associated with this region. Mouse Gem maps to the proximal region of chromosome 4 between Mos and Cga. To gain insight into the transcriptional regulation of GEM, we have established the transcription initiation site of GEM in human T cells and defined a 5′ upstream region sufficient for mitogen-responsive, inducible transcription.