Chromosomal Aberrations In Patients Research Articles

The study of the impact of additional chromosomal aberrations and c-MYC and BCR::ABL1 genes amplification on CML patient’s characteristics: relation to haematological parameters and patient outcome

BackgroundChronic myeloid leukaemia is characterised by genetic instability which results in additional cytogenetic aberrations that have been linked to progression to advanced phase. Genomic study linked amplified genes in the form of c-MYC and/or the rare BCR::ABL1 genes amplification to chronic myeloid leukaemia. The effect of these genes’ amplification on patients’ characteristics and disease progression still needs further study.This cross-sectional study aimed to investigate the frequency of additional chromosomal aberrations in addition to c-MYC and BCR::ABL1 genes amplification in chronic myeloid leukaemia patients and their impact on patient’s characteristics, disease progression, and level of remission. The study included cytogenetic analysis of 49 Philadelphia positive chronic myeloid leukaemia patients and investigation of c-MYC and BCR::ABL1 genes amplification by fluorescence in situ hybridization.ResultsPatients with additional chromosomal aberrations represented 36.7% and had significantly lower platelet count (P = 0.003) and higher blast count (P = 0.008). The acquisition of additional chromosomal aberrations was significantly higher in chronic myeloid leukaemia patients with advanced stages (P = 0.014). Follow-up of the patients for 6 months revealed significant higher frequency of additional chromosomal aberrations in patients with failure of remission (P < 0.0001). A highly significant association between cases with failure of molecular remission (P = 0.001) and co-existing additional chromosomal aberrations.Amplification of the c-MYC gene was detected in 6 cases. The cases with c-MYC amplification showed significantly higher peripheral blood and bone marrow blasts (P = 0.029 and P = 0.008, respectively) and significantly lower platelet count (P = 0.044). Amplification of c-MYC was significantly associated with additional chromosomal aberrations (P = 0.011). Molecular remission was not achieved in any of the instances with c-MYC amplification. A highly significant association between c-MYC amplification and poor patient outcome was detected (P = 0.002). BCR::ABL1 amplification was detected in three cases, and ABL amplification was detected in four cases. Patients with BCR::ABL1 amplification showed significantly higher blast count. BCR::ABL1 amplification was significantly associated with disease progression and failure of molecular remission (P = 0.002).ConclusionAdditional chromosomal aberrations, c-MYC amplification, and BCR:ABL1 amplification in chronic myeloid leukaemia stratify patients with disease progression, which may lead to better interventions and improved outcome in the future chronic myeloid leukaemia patients.

The Landscape of Cytogenetic Aberrations in Light-Chain Amyloidosis with or without Coexistent Multiple Myeloma

Interphase fluorescence in situ hybridization (iFISH) has been well established in the preliminary prognostic evaluation of multiple myeloma (MM). However, the chromosomal aberrations in patients with systemic light-chain amyloidosis, notably in patients with coexistent MM, have been rarely investigated. This study aimed to evaluate the effect of iFISH aberrations on the prognosis of systemic light-chain amyloidosis (AL) with and without concurrent MM. The iFISH results and clinical characteristics of 142 patients with systemic light-chain amyloidosis were analyzed, and survival analysis was conducted. Among the 142 patients, 80 patients had AL amyloidosis alone, and the other 62 patients had concurrent MM. The incidence rate of 13q deletion, t(4;14), was higher in AL amyloidosis patients with concurrent MM than that of primary AL amyloidosis patients (27.4% vs. 12.5%, and 12.9% vs. 5.0%, respectively), and the incidence rate of t(11;14) in primary AL amyloidosis patients was higher than that in AL amyloidosis patients with concurrent MM (15.0% vs. 9.7%). Moreover, the two groups had the similar incidence rates of 1q21 gain (53.8% and 56.5%, respectively). The result of the survival analysis suggested that patients with t(11;14) and 1q21 gain had a shorter median overall survival (OS) and progression-free survival (PFS), irrespective of the presence or absence of MM, and patients with AL amyloidosis and concurrent MM carrying t(11;14) had the poorest prognosis, with a median OS time of 8.1 months.

Citogenetička analiza odabranih genetski uvjetovanih bolesti u istočnoj Slovačkoj

This work presents the results of cytogenetic analysis performed during the period 1990-2021. The work focuses on cytogenetic analysis of selected diseases that represent a serious medical and social problem in the Prešov region of eastern Slovakia. The analysis also included the determination of cytogenetic and molecular-genetic marker frequency related to selected clinical genetic diseases in a specified population of Roma ethnicity. Chromosome analysis confirmed a wide spectrum of chromosomal aberrations in patients with Down’s syndrome and Turner syndrome, revealing a spectrum of aberrations from monosomy X, isochromosome Xq, and deletions Xp to marker chromosomes. Chromosomal aberrations cause 5.5% of fertility disorders in couples, with numerical and structural chromosomal aberrations found in 2.1 and 3.4% respectively, revealing a risk finding for offspring of carriers of balanced translocations. Microdeletions, combined microdeletions (AZFb,c) and complete deletion of the AZF region of the Y chromosome were found in men diagnosed with azoospermia. In addition, pathological karyotypes were detected in men and women (13 and 10%). Another set of analyses in patients with onco-haematological diseases revealed presence of Philadelphia chromosome (Ph1) in 94.4% of patients with chronic myeloid leukaemia, complex translocation of chromosomes 8, 9, 22; mosaic karyotype of Ph1. Chromosomal aberrations in patients with myelodysplastic syndrome also included also atypical and as yet unpublished cytogenetic markers. Myeloproliferative diseases were detected in 28.3% of patients with heterogenous chromosomal aberrations. Revelations from cytogenetic analysis enable improvement in the efficiency of health care, diagnostics, therapeutic significance and prognosis of affected people in the majority population and Roma minority in this region of Slovakia.

Chromosomal Aberrations and Oxidative Stress in Psoriatic Patients with and without Metabolic Syndrome.

Psoriasis and metabolic syndrome (MetS), a common comorbidity of psoriasis, are associated with mild chronic systemic inflammation that increases oxidative stress and causes cell and tissue damage. At the cellular level, chromosomal and DNA damage has been documented, thus confirming their genotoxic effect. The main objective of our study was to show the genotoxic potential of chronic inflammation and determine whether the presence of both pathologies increases chromosomal damage compared to psoriasis alone and to evaluate whether there are correlations between selected parameters and chromosomal aberrations in patients with psoriasis and MetS psoriasis. Clinical examination (PASI score and MetS diagnostics according to National Cholesterol Education Expert Panel on Detection, Evaluation, and Treatment of High Blood Cholesterol in Adults; NCE/ATPIII criteria), biochemical analysis of blood samples (fasting glucose, total cholesterol, low density and high density lipoproteins; LDL, HDL, non-HDL, and triglycerides;TAG), DNA/RNA oxidative damage, and chromosomal aberration test were performed in 41 participants (20 patients with psoriasis without MetS and 21 with MetS and psoriasis). Our results showed that patients with psoriasis without metabolic syndrome (nonMetS) and psoriasis and MetS had a higher rate of chromosomal aberrations than the healthy population for which the limit of spontaneous, natural aberration was <2%. No significant differences in the aberration rate were found between the groups. However, a higher aberration rate (higher than 10%) and four numerical aberrations were documented only in the MetS group. We found no correlations between the number of chromosomal aberrations and the parameters tested except for the correlation between aberrations and HDL levels in nonMetS patients (rho 0.44; p < 0.02). Interestingly, in the MetS group, a higher number of chromosomal aberrations was documented in non-smokers compared to smokers. Data from our current study revealed an increased number of chromosomal aberrations in patients with psoriasis and MetS compared to the healthy population, especially in psoriasis with MetS, which could increase the genotoxic effect of inflammation and the risk of genomic instability, thus increasing the risk of carcinogenesis.

Dynamic observation of bone marrow suppression and chromosomal aberrations in patients with acute colchicine poisoning.

Dynamic observation of bone marrow suppression and chromosomal aberrations in patients with acute colchicine poisoning.

Spontaneous and induced chromosomal aberrations in peripheral blood of women with endometriosis: evidence of genomic instability.

Endometriosis is a prevalent gynecological disease which can lead to certain types of cancers. We investigated the spontaneous and induced chromosomal aberrations in peripheral blood lymphocytes (PBL) of endometriosis patients. We performed a pilot study utilizing mitomycin C (MMC) to assess chromosomal instability in the peripheral blood of participants. The patient group consisted of 20 infertile endometriosis patients and the controls of 20 healthy fertile women. Blood samples were collected, and two distinct lymphocyte cultures were prepared to evaluate the baseline and the MMC induced chromosomal aberrations. The results showed a significant difference before and after MMC treatment in both groups (P<0.001) and also revealed that endometriosis patients are far more sensitive to MMC than controls (P<0.001). The significantly higher frequency of induced and spontaneous chromosomal aberrations in patients can be consider as a sign of genomic instability and the defect in DNA repair mechanisms, which can be both assumed as a driver of cancer development in endometriosis patients.

Meiotic susceptibility for induction of sperm with chromosomal aberrations in patients receiving combination chemotherapy for Hodgkin lymphoma

Improvements in survival rates with gonad-sparing protocols for childhood and adolescence cancer have increased the optimism of survivors to become parents after treatment. Findings in rodents indicate that chromosomal aberrations can be induced in male germ cells by genotoxic exposures and transmitted to offspring and future generations with effects on development, fertility and health. Thus, there is a need for effective technologies to identify human sperm carrying chromosomal aberrations to assess the germ-line risks, especially for cancer survivors who have received genotoxic therapies. The time-dependent changes in the burden of sperm carrying structural chromosomal aberrations were assessed for the first time in a cancer setting, using the AM8 sperm FISH protocol which simultaneously detects abnormalities in chromosomal structure and number in sperm. Nine Hodgkin lymphoma (HL) patients provided 20 semen samples before, during, and after NOVP therapy (Novantrone, Oncovin, Velban and Prednisone) and radiation therapy that produced scattered gonadal doses from <0.05 to 0.6 Gy. Late meiosis was found to be the most sensitive to NOVP treatment for the production of sperm with chromosomal abnormalities, both in structure and number. Earlier stages of spermatogenesis were less sensitive and there was no evidence that therapy-exposed stem cells resulted in increased frequencies of sperm with abnormalities in chromosomal structure or number. This indicates that NOVP therapy may increase the risks for paternal transmission of chromosomal structural aberrations for sperm produced 32 to 45 days after a treatment with these drugs and implies that there are no excess risks for pregnancies conceived more than 6 months after this therapy. This clinical evaluation of the AM8 sperm FISH protocol indicates that it is a promising tool for assessing an individual’s burden of sperm carrying chromosomal structural aberrations as well as aneuploidies after cancer therapy, with broad applications in other clinical and environmental situations that may pose aneugenic or clastogenic risks to human spermatogenesis.

Clinical Significance of Segmental Chromosomal Aberrations in Patients with Neuroblastoma: First Report in Korean Population.

BackgroundThis study aimed to investigate the incidence and clinical significance of segmental chromosomal aberrations (SCAs) in Korean patients with neuroblastoma.MethodsPatients diagnosed with neuroblastoma from 2012 to 2018 were included for retrospective review. Fluorescence in situ hybridization (FISH) was used to analyze four SCAs (MYCN amplification, 1p deletion, 11q deletion, and 17q gain). Clinical characteristics at diagnosis, early tumor response (reduction in primary tumor volume and neuron-specific enolase level after the first three cycles of chemotherapy), and survival rates were compared according to SCAs.ResultsAmong 173 patients with FISH results, 92 (53.2%) had at least one of the four SCAs, while 25 (14.5%) had two co-aberrations, and eight (4.6%) had three co-aberrations. SCAs detected in our study were MYCN amplification (n = 17, 9.8%), 1p deletion (n = 26, 15.2%), 11q deletion (n = 44, 25.6%), and 17q gain (n = 46, 27.1%). Patients with MYCN amplification showed a better early response but a worse survival than those without (5-year overall survival: 46.2% ± 13.1% vs. 88.6% ± 3.4%). Furthermore, 1p deletion was associated with a better early response but a worse survival; however, it was not an independent factor for survival. We could not find any prognostic significance associated with 11q deletion or 17q gain.ConclusionThis is the first study investigating SCAs in Korean neuroblastoma patients. Prognostic significance of SCAs other than MYCN amplification was different from those reported in western countries. Further study with a larger cohort and longer follow-up is needed to confirm our findings.

Molecular Detection of Fusion Oncogenes in Zambian Patients with Acute Lymphoblastic Leukemia.

Introduction:Chromosomal aberrations play a significant role in the pathogenesis of acute lymphoblastic leukemia (ALL) with prognostic and therapeutic implications. Despite the availability of molecular tools, low-resource settings struggle to diagnose the disease due to limited diagnostic capacity. The objective of this study was to detect common chromosomal aberrations in patients with ALL attending the University Teaching Hospital (UTH) in Lusaka, Zambia.Materials and Methods:In this prospective study, 19 blood samples from patients with ALL were screened for the presence of BCR-ABL, E2A-PBX1, MLL-AF4, and ETV6-RUNX1 fusion oncogenes using reverse transcriptase-polymerase chain reaction assay. Blood counts and clinical characteristics of patients were also assessed.Results:The age of patients ranged from 1½ to 72 years and comprised 57.9% of males and 42.1% of females. The majority of these patients were children (68%), and adults only comprised 32%. Only BCR-ABL and E2A-PBX1 oncogenes were detected in 3/19 of cases. The BCR-ABL gene was detected in a 4-year-old female child and a 15-year-old child. Both cases were associated with hepatomegaly and anemia coupled with low hemoglobin, white blood cell, and platelet counts. E2A-PBX1 was detected in a 12-year-old child with lymphadenopathy and splenomegaly, coupled with low hemoglobin, white blood cell, and platelet counts. All the three patients who harbored these fusion oncogenes died.Conclusion:This is the first study from Zambia to investigate the presence of fusion oncogenes in leukemia patients, which were found only among the older children population. Based on these findings, we recommend that molecular diagnosis be made a priority for the younger leukemia patient population at UTH.

De Novo and Therapy-Related Acute Myeloid Leukemia and Myelodysplastic Syndrome: Similarities and Differences in SNP-Array Detected Chromosomal Aberrations in Pre-Transplant Blood Samples

De Novo and Therapy-Related Acute Myeloid Leukemia and Myelodysplastic Syndrome: Similarities and Differences in SNP-Array Detected Chromosomal Aberrations in Pre-Transplant Blood Samples

The Implication of Cytogenetic Alterations in Pancreatic Ductal Adenocarcinoma and Intraductal Papillary Mucinous Neoplasm Identified by Fluorescence In Situ Hybridization and Their Potential Diagnostic Utility

Background/AimsWe investigated chromosomal aberrations in patients with pancreatic ductal adenocarcinoma (PDAC) and intraductal papillary mucinous neoplasm (IPMN) by fluorescence in situ hybridization (FISH) to identify cytogenetic changes and molecular markers that may be useful for preoperative diagnosis.MethodsTissue samples from 48 PDAC and 17 IPMN patients were investigated by FISH analysis using probes targeting chromosomes 7q, 17p, 18q, 20q, and 21q and the pericentromeric region of chromosome 18 (CEP18).ResultsThe PDAC samples harbored 17p deletion (95.8%), 18q deletion (83.3%), CEP18 deletion (81.2%), 20q gain (81.2%), 21q deletion (77.1%), and 7q gain (70.8%). The IPMN samples had 17p deletion (94.1%), CEP18 deletion (94.1%), 21q deletion (70.6%), 18q deletion (58.8%), 20q gain (58.8%), and 7q gain (58.8%). A significant difference in CEP18 gain was identified between the PDAC and IPMN groups (p=0.029). Detection of 17p or 18q deletion had the highest diagnostic accuracy (80.0%) for PDAC.ConclusionsChromosomal alterations were frequently identified in both PDAC and IPMN with similar patterns. CEP18 gain and 17p and 18q deletions might be involved in the later stages of PDAC tumorigenesis. Chromosome 17p and 18q deletions might be excellent diagnostic markers.

Features of the chromosomal apparatus in patients with juvenile idiopathic arthritis with concomitant multifactorial pathology

Aim. To determine the level of chromosomal disorders in peripheral blood lymphocytes of children and adolescents with juvenile idiopathic arthritis with concomitant multifactorial pathology in vitrо. Methods. Cytogenetic analysis was carried out in patients with juvenile idiopathic arthritis with concomitant multifactorial pathology in vitro, using a common methodology. Statistical analysis of the results of research was carried out using Excel software package and SPSS Statistics 17.0. Results. Chromosomal aberrations in peripheral blood lymphocytes were revealed in 100 % of patients. The general level of chromosomal abnormalities in the patients with concomitant pathology was 5.57 per 100 cells, and in the comparison group – 4.10 per 100 cells. In both groups aberrations of chromatid type prevailed. Conclusions. In patients with juvenile idiopathic arthritis, accompanied by different multifactorial disorders, spontaneous level of chromosomal abnormalities in blood lymphocytes in vitro was 1.4 times higher compared to the level of chromosomal aberrations in patients without concomitant pathology. The frequency of chromatid type aberrations was higher than the chromosome type aberrations rate in 1.6 times in the main group and in 2.2 times in the comparison group.&#x0D; Keywords: juvenile idiopathic arthritis, children, adolescents, chromosomes, aberrations, concomitant multifactorial pathology.

Complex cytogenetic research of cryptic chromosomal aberrations in patients with multiple myeloma

Background . Multiple myeloma (MM) is a malignant lymphoproliferative B-cell disease characterization by clonal proliferation of plasma cells in the bone marrow and beyond its borders. Currently, a wide range of cytogenetic anomalies and molecular-biological parameters are studied as prognostic factors.Objective: a comparative study of the frequency, features and clinical significance of chromosomal abnormalities in MM by conventional cytogenetic and fluorescent in situ hybridization (FISH) methods.Materials and methods . 77 patients with MM, which admitted in N.N. Blokhin National Medical Research Center of Oncology, were included in the study from 2016 to 2017.Results . Chromosomal alterations were detected only in one case (1/77) by conventional cytogenetic method G-banding. However cytogenetic aberrations were revealed in 26 % of cases (20/77) using FISH. Deletions of different regions of chromosomes, indicating the possible presence of a hypodiploid clone or loss of some regions, were found in one patient in the second FISH analysis after 6 months. In the cohort of patients with chromosomal abnormalities (n = 20) a partial trisomy 11q, a deletion of the region q32 of the chromosome 14, a translocation t(4;14)(p16;q32) and IGHV gene rearrangement were determined in 30 % (6/20) as sole anomalies. Two or more cytogenetic aberrations were identified in the remaining 14 patients. Our study confirms that chromosomal abnormalities are more likely detected at later stages of MM (IA и IIA – 0 %, IIIA и IIIВ – 27 and 47 % respectively).Conclusion . FISH allows to detect chromosomal changes in tumor plasma cells regardless of the mitosis phase. In MM, it becomes particularly important in connection with low proliferative activity of plasma cells. Additionally, in the fourth of MM patients in the study submicroscopic chromosomal aberrations were discovered using FISH. The improvement of the probe panel and the widespread use of locus specific FISH don’t replace G-banding that allows to see damages of all chromosomes at once.

Copy number neutral loss of heterozygosity at 17p and homozygous mutations of TP53 are associated with complex chromosomal aberrations in patients newly diagnosed with myelodysplastic syndromes

Complex karyotypes are seen in approximately 20% of patients with myelodysplastic syndromes (MDS) and are associated with a high risk of transformation to acute myeloid leukemia and poor outcomes in patients. Copy number neutral loss of heterozygosity (CN-LOH, i.e., both copies of a chromosomal pair or their parts originate from one parent) might contribute to increased genomic instability in the bone-marrow cells of patients with MDS. The pathological potential of CN-LOH, which arises as a clonal aberration in a proportion of somatic cells, consists of tumor suppressor gene and oncogene homozygous mutations. The aim of our study was to evaluate the frequency of CN-LOH at 17p in bone-marrow cells of newly diagnosed MDS patients with complex chromosomal aberrations and to assess its correlation with mutations in the TP53 gene (17p13.1). CN-LOH was detected in 40 chromosomal regions in 21 (29%) of 72 patients analyzed. The changes in 27 of the 40 regions identified were sporadic. The most common finding was CN-LOH of the short arm of chromosome 17, which was detected in 13 (18%) of 72 patients. A mutational analysis confirmed the homozygous mutation of TP53 in all CN-LOH 17p patients, among which two frameshift mutations are not registered in the International Agency for Research on Cancer TP53 Database. CN-LOH 17p correlated with aggressive disease (median overall survival 4 months) and was strongly associated with a complex karyotype in the cohort studied, which might cause rapid disease progression in high-risk MDS. No other CN-LOH region previously recorded in MDS or AML patients (1p, 4q, 7q, 11q, 13q, 19q, 21q) was detected in our cohort of patients with complex karyotype examined at the diagnosis of MDS. The LOH region appeared to be balanced (i.e., with no DNA copy number change) when examined with conventional and molecular cytogenetic methods. Therefore, a microarray that detects single-nucleotide polymorphisms is an ideal method with which to identify and further characterize CN-LOH. Our data should specify the prognosis and should lead to the identification of potential targets for therapeutic interventions.

Genetic study in 50 cases of carcinoma breast: a prospective study

Background: Carcinoma breast is the leading cancer among urban Indian women. The main aim of our study was to focus on the chromosomal aberrations in patients of carcinoma breast. Methods: Fifty case of carcinoma breast admitted in our institute between June 2009 to December 2011 were studied. Results: In our study premature centromere division was seen in 50% patients while chromatid break was seen in 60% patients. 20% patients had an acenteric fragment. Break in the same locus in both the chromatids of a single chromosome i.e. chromosomal break was seen in 1 patient in 1p, 1q, 2q, 12q chromosome. Terminal deletion was seen 31 times in different chromosomes with most common being in 2q, 3q, 2p, 1q. Chromatid gap was seen in 24 chromosomes most common being in 1q, 2q, 3q, 6p while dicentric chromosomes was seen in 33.33% of patients. Conclusions: Most common chromosome involved in chromosomal aberrations were 1q (CHTB, CHRB, CHTG); 2q ( CHRB, TER del, CHTG); 1p, 12q (CHRB); 3q (TER del).

Direct cytogenetic study of chorionic samples of the arrested pregnancy tissues according to the Regional Reproductive Center materials

Aim. Detection of chromosomal aberrations in patients during spontaneous abortion. Methods and results. Cytogenetic study of chorionic samples of the abortions on first trimester of pregnancy. According to the study, the karyotype anomalies were the cause of cardiac embryonic development in 59% of cases. Conclusion. Due to numerous cytogenetic researches of abortion material, anomalies of karyotype are the leading reason of embryonic destruction. The present paper summarizes results of cytogenetic study of the chorionic samples of 26 arrested pregnancies. Frequency and spectrum of karyotype pathology and its correlation with maternal age and term of gestation, sex ratio and type of aberration have been analyzed. The results are compared and discussed with other studies. Most anomalies of karyotype have been conditioned by sporadic genome mutations arising up at ripening of gametes, at an impregnation or in the period of crushing.

Xq28 Duplications and Epilepsy: Influence of the Combinatory Duplication of MECP2 and GDI1

Xq28 duplications including the MECP2 (Methyl-CpG-binding protein 2) cause an X-linked recessive neurodegenerative disorder that presents symptoms such as early developmental delay, progressive deterioration, and intractable epilepsy. Submicroscopic interstitial duplication in the MECP2 region is one of the most frequently observed submicroscopic chromosomal aberrations in patients with intellectual disability. This high prevalence is derived from the genomic instability characteristic of this region due to segmental duplications that are densely located in this region, which are prone to cause nonallelic homologous recombination during meiosis. Patients with MECP2 duplications generally begin to show epilepsy after 6 years of age. Therefore, incidence of epilepsy is high in adolescents. Although many types of seizures have been reported in patients, the most frequently observed seizure types were absence seizure and generalized tonic–clonic seizures. Because drop attacks are frequently seen, such epileptic attacks are sometimes life-threatening. We encountered a patient who showed epileptic spasms during infancy with a relatively larger duplication that encompasses MECP2 and GDI1 (GDP dissociation inhibitor-1). This led us to speculate that the combinatory duplication that includes MECP2 and GDI1 may cause severe epileptic features; however, most of the previously reported patients with combined duplications of MECP2 and GDI1 did not showed early occurrence of epilepsy. Therefore, further information would be required to confirm if the combinatory duplication of MECP2 and GDI1 exerts any influence on the severity of epilepsy.

ILF2 Is a Regulator of RNA Splicing and DNA Damage Response in 1q21-Amplified Multiple Myeloma

In the last decade, significant effort has been directed toward the stratification of multiple myeloma (MM) patients for targeted therapy, and many studies have shown that some genetic alterations, especially t(4;14) translocation, loss of the short arm of chromosome 17, and amplification of chromosome 1q21, are associated with a poor outcome. The 1q21 amplicon spans a region of 10-15 Mb and contains a large number of possible candidate genes; it is among the most frequent chromosomal aberrations in patients with MM and is associated with poor prognosis, disease progression, and drug resistance. Therefore, the identification of critical 1q21 genes may yield potential therapeutic targets for this high-risk MM subgroup and provide a rationale for patient stratification.In an effort to accomplish this goal, we first identified a high-priority list of 78 copy number-driven 1q21 MM-relevant genes by integrating high-resolution array comparative genomic hybridization (aCGH) and matched expression profiling of the 254 MM samples deposited in the Multiple Myeloma Research Consortium (MMRC) database. Then, we performed a high-throughput systematic shRNA screen in vitroto identify 1q21 genes whose loss of function resulted in the selective death and/or growth inhibition of MM cells carrying the 1q21 amplification. We used shRNA targeting (excluding shRNAs that displayed cytotoxic activity regardless of 1q21 amplification) and a GFP competitive growth assay to identify 1q21-resident targets whose downregulation significantly decreased the percentage of GFP-positive MM cells with 1q21 amplification over a time of 7 days. These assays identified UBAPL2, INTS3, LASS2, KRTCAP2, and ILF2 as key targets for further analysis.Secondary validation experiments in the MM cell lines JJN3 and H929 confirmed that the downregulation of all of our top five candidate genes induced significant levels of apoptosis, inhibition of proliferation, and cell cycle arrest. Integration of copy number analysis, expression profiling, and clinical outcome indicated that only UBAPL2 and ILF2 were highly significant prognostic genes, and target validation in NOD-SCID mice showed that ILF2, but not UBAPL2, downregulation had a significant impact on in vivo survival. Therefore, we sought to further characterize ILF2’s role in 1q21-amplified MM.ILF2 encodes NF45, the regulatory subunit of NF90/NF110 complexes, which are involved in mitotic control, DNA break repair, and RNA splicing regulation. Downregulation of ILF2 in MM cells with 1q21 amplification resulted in multinucleated phenotypes and abnormal nuclear morphologies (nucleoplasmic bridges and buds and micronuclei) that were associated with a significant accumulation of phospho-H2AX foci and DNA damage response activation, increased sensitivity to the DNA damaging agent melphalan, and impaired activation of DNA repair pathways. Experiments of immunoprecipitation combined with mass spectometry showed that ILF2 interacts with numerous RNA binding proteins directly implicated in DNA repair or regulation of DNA damage response by modulating alternative splicing and stability of specific pre-mRNAs. Accordingly, RNA-seq analysis of ILF2-depleted MM cells, when compared to cells carrying scrambled shRNAs, identified specific changes in RNA splicing patterns both before and after treatment with melphalan.In conclusion, our studies have revealed an unanticipated link between 1q21 amplification, DNA damage response, and RNA splicing. We identified ILF2 as a key driver of this interaction, and our findings support the development of strategies designed to modulate ILF2 expression in patients with high-risk MM carrying 1q21 amplification. DisclosuresNo relevant conflicts of interest to declare.

Deciphering the pathogenic consequences of chromosomal aberrations in human genetic disease.

Chromosomal aberrations include translocations, deletions, duplications, inversions, aneuploidies and complex rearrangements. They underlie genetic disease in roughly 15% of patients with multiple congenital abnormalities and/or mental retardation (MCA/MR). In genetic diagnostics, the pathogenicity of chromosomal aberrations in these patients is typically assessed based on criteria such as phenotypic similarity to other patients with the same or overlapping aberration, absence in healthy individuals, de novo occurrence, and protein coding gene content. However, a thorough understanding of the molecular mechanisms that lead to MCA/MR as a result of chromosome aberrations is often lacking. Chromosome aberrations can affect one or more genes in a complex manner, such as by changing the regulation of gene expression, by disrupting exons, and by creating fusion genes. The precise delineation of breakpoints by whole-genome sequencing enables the construction of local genomic architecture and facilitates the prediction of the molecular determinants of the patient’s phenotype. Here, we review current methods for breakpoint identification and their impact on the interpretation of chromosome aberrations in patients with MCA/MR. In addition, we discuss opportunities to dissect disease mechanisms based on large-scale genomic technologies and studies in model organisms.Electronic supplementary materialThe online version of this article (doi:10.1186/s13039-014-0100-9) contains supplementary material, which is available to authorized users.

Application of array comparative genomic hybridization (array- CGH) for detection of chromosomal imbalances in children with developmental delay/congenital malformations in Saudi Arabia

Background Microarray–based Comparative Genomic Hybridization (a-CGH) has enabled wide investigation of the genome at high resolution and has been implemented in different centers as a clinical diagnostic tool. Chromosomal imbalances are implicated in the etiology of Developmental Delay (DD)/Intellectual Disability (ID)/Congenital Malformations. However, most of these cases may not be diagnosed by conventional cytogenetic techniques. We aimed to establish a-CGH technique and assess its potential as a diagnostic tool for chromosomal imbalances and to detect known and novel chromosomal aberrations in patients with DD/ congenital malformations.