Numerical Chromosomal Alterations Research Articles

Chromosomal Damage, Chromosome Instability, and Polymorphisms in GSTP1 and XRCC1 as Biomarkers of Effect and Susceptibility in Farmers Exposed to Pesticides.

In the department of Boyacá, Colombia, agriculture stands as one of the primary economic activities. However, the escalating utilization of pesticides within this sector has sparked concern regarding its potential correlation with elevated risks of genotoxicity, chromosomal alterations, and carcinogenesis. Furthermore, pesticides have been associated with a broad spectrum of genetic polymorphisms that impact pivotal genes involved in pesticide metabolism and DNA repair, among other processes. Nonetheless, our understanding of the genotoxic effects of pesticides on the chromosomes (as biomarkers of effect) in exposed farmers and the impact of genetic polymorphisms (as susceptibility biomarkers) on the increased risk of chromosomal damage is still limited. The aim of our study was to evaluate chromosomal alterations, chromosomal instability, and clonal heterogeneity, as well as the presence of polymorphic variants in the GSTP1 and XRCC1 genes, in peripheral blood samples of farmers occupationally exposed to pesticides in Aquitania, Colombia, and in an unexposed control group. Our results showed statistically significant differences in the frequency of numerical chromosomal alterations, chromosomal instability, and clonal heterogeneity levels between the exposed and unexposed groups. In addition, we also found a higher frequency of chromosomal instability and clonal heterogeneity in exposed individuals carrying the heterozygous GSTP1 AG and XRCC1 (exon 10) GA genotypes. The evaluation of chromosomal alterations and chromosomal instability resulting from pesticide exposure, combined with the identification of polymorphic variants in the GSTP1 and XRCC1 genes, and further research involving a larger group of individuals exposed to pesticides could enable the identification of effect and susceptibility biomarkers. Such markers could prove valuable for monitoring individuals occupationally exposed to pesticides.

Behavioral Assessment of Central Auditory Processing in Turner Syndrome.

Introduction Turner syndrome (TS) affects ∼ 1 in 2,500 live births. The presence of hearing alterations is one of the comorbidities found in this syndrome. Objective The present study aimed to evaluate the central auditory abilities in TS and to associate the alterations found with the cytogenetic pattern of the syndrome. Methods We included children and adults aged 9 to 39 years old, diagnosed with TS, with numerical or structural alterations of sex chromosomes in their karyotype. A battery of behavioral tests of central auditory processing (CAP) was performed, including a test within the modalities: monoaural low-redundancy, dichotic listening, binaural interaction, and temporal processing (resolution and ordering). We studied auditory skills in the total sample and in the sample stratified by age, divided into groups: G1 (9 to 13 years old), G2 (14 to 19 years old), and G3 (20 to 31 years old). For the association of the cytogenetic pattern, the division was T1 (chromosome monosomy X), and T2 (other TS cytogenetic patterns). Statistical analysis presented data expressed as median and interquartile range for numerical data and as frequency and percentage for categorical data. Results We found alterations in four auditory skills in the three age groups, but there was a statistically significant difference between the age groups only in the Gaps in Noise Test (GIN) ( p -value = 0.009). Regarding karyotype, a greater number of alterations in the T1 cytogenetic pattern (chromosome monosomy X) was observed in four auditory skills, but without a statistically significant difference. Conclusion The alterations found point to an impairment in CAP in TS.

VHL-deficiency leads to reductive stress in renal cells

Heritable renal cancer syndromes (RCS) are associated with numerous chromosomal alterations including inactivating mutations in von Hippel-Lindau (VHL) gene. Here we identify a novel aspect of the phenotype in VHL-deficient human renal cells. We call it reductive stress as it is characterised by increased NADH/NAD+ ratio that is associated with impaired cellular respiration, impaired CAC activity, upregulation of reductive carboxylation of glutamine and accumulation of lipid droplets in VHL-deficient cells. Reductive stress was mitigated by glucose depletion and supplementation with pyruvate or resazurin, a redox-reactive agent. This study demonstrates for the first time that reductive stress is a part of the phenotype associated with VHL-deficiency in renal cells and indicates that the reversal of reductive stress can augment respiratory activity and CAC activity, suggesting a strategy for altering the metabolic profile of VHL-deficient tumours.

CINmetrics: an R package for analyzing copy number aberrations as a measure of chromosomal instability.

Genomic instability is an important hallmark of cancer and more recently has been identified in others like neurodegenrative diseases. Chromosomal instability, as a measure of genomic instability, has been used to characterize clinical and biological phenotypes associated with these diseases by measuring structural and numerical chromosomal alterations. There have been multiple chromosomal instability scores developed across many studies in the literature; however, these scores have not been compared because of the lack of a single tool available to calculate and facilitate these various metrics. Here, we provide an R package CINmetrics, that calculates six different chromosomal instability scores and allows direct comparison between them. We also demonstrate how these scores differ by applying CINmetrics to breast cancer data from The Cancer Genome Atlas (TCGA). The package is available on CRAN at https://cran.rproject.org/package=CINmetrics and on GitHub at https://github.com/lasseignelab/CINmetrics.

Apoptosis as a Barrier against CIN and Aneuploidy.

Aneuploidy is the gain or loss of entire chromosomes, chromosome arms or fragments. Over 100 years ago, aneuploidy was described to be a feature of cancer and is now known to be present in 68-90% of malignancies. Aneuploidy promotes cancer growth, reduces therapy response and frequently worsens prognosis. Chromosomal instability (CIN) is recognized as the main cause of aneuploidy. CIN itself is a dynamic but stochastic process consisting of different DNA content-altering events. These can include impaired replication fidelity and insufficient clearance of DNA damage as well as chromosomal mis-segregation, micronuclei formation, chromothripsis or cytokinesis failure. All these events can disembogue in segmental, structural and numerical chromosome alterations. While low levels of CIN can foster malignant disease, high levels frequently trigger cell death, which supports the "aneuploidy paradox" that refers to the intrinsically negative impact of a highly aberrant karyotype on cellular fitness. Here, we review how the cellular response to CIN and aneuploidy can drive the clearance of karyotypically unstable cells through the induction of apoptosis. Furthermore, we discuss the different modes of p53 activation triggered in response to mitotic perturbations that can potentially trigger CIN and/or aneuploidy.

Deciphering the Somatic and Germline Structural Variation Landscape in Pediatric B-Cell Precursor Acute Lymphoblastic Leukemia By Whole Genome Optical Mapping

Background: B-cell precursor acute lymphoblastic leukemia (BCP-ALL) is the most frequent pediatric cancer. The most common numerical and structural chromosomal alterations are high hyperdiploidy (HHD, 51-67 chromosomes) and t(12;21)(p13;q22) leading to ETV6::RUNX1 fusion. However, for a full-blown leukemia, secondary alterations are required. Furthermore, it is increasingly recognized that germline variants may enhance ALL susceptibility in ~4% of the patients (Bloom et al. 2019, Klco & Mullighan 2020). In large-scale genomic studies, the mutational landscape of somatic and germline single nucleotide variants and small indels has been well described in BCP-ALL. However, a comprehensive analysis of somatic and germline structural variants (SVs) in ETV6::RUNX1 and HHD tumors is still lacking. Recent feasibility studies showed that whole genome optical mapping (WGOM) is a novel method for reliable SV detection which could abrogate conventional cytogenetics and array based methods in the future (Neveling et al. 2021, Mantere et al. 2021). The aim of the study was to analyze the structural variation landscape in pediatric BCP-ALL patients by employing WGOM to gain significant insights on leukemia predisposition and development. Methods: We studied 60 pediatric patients diagnosed with ETV6::RUNX1 (n=30) or HHD (n=30) BCP-ALL with a median age at diagnosis of 3.9 (range 1.7-17) and a male to female ratio of 1.14:1. We collected tumor material at initial diagnosis and included fibroblast or remission material as matched non-tumor control of each patient. Ultra-high molecular weight DNA was extracted from 120 samples and labeled by a sequence specific enzyme. Fluorescently labeled DNA was analyzed using a Saphyr instrument (Bionano Genomics). We integrated comprehensive datasets of 60 matched tumor/non-tumor genomes to identify somatically acquired SVs >500bp. Corresponding data of standard methods as cyto- (karyotype, fluorescence in situ hybridization) and molecular genetics (SNP-array) of the leukemia samples were compared to WGOM data. In addition, the prevalence of rare germline SVs (<1% of 160 healthy control samples [Bionano] and minor allele frequency <0.01 in dbVar) occurring in known cancer predisposition genes was analyzed in the non-tumor samples. Results: WGOM was able to detect 94% (438/464) of previously observed events by conventional methods, including ETV6::RUNX1 and high hyperdiploid hallmark alterations in all BCP-ALL cases. Beyond that, we discovered 895 additional SVs with WGOM not detected by standard cyto- and molecular genetics. WGOM detected a median of 25 (range 0-70) somatic SVs secondary to the hallmark alterations in ETV6::RUNX1 tumors compared to 13 (range 0-28) SVs in HHD cases. We identified 60 recurrently altered regions occurring in ≥3 BCP-ALL cases including 12p13.2 (ETV6, 19/60), 9p13.2 (PAX5, 13/60), 9p21.3 (CDKN2A/B, 12/60), 11p12 (RAG2, 10/60), 20p12.2 (MKKS/SLXIP, 10/60) or 3q13.2 (CD200/BTLA, 8/60). We detected ETV6::RUNX1 subtype specific recurrent focal deletions in ATF7IP (10/30), BTG1 (10/30), NSD2 (5/30) and TBL1XR1 (4/30). Interestingly, we discovered recurrent SVs affecting putative novel genes involved in BCP-ALL leukemogenesis such as STAG2, GPN3 and UBA2 which are affected in ~10% of the BCP-ALL patients. Strikingly, WGOM revealed in total 9 novel potential in-frame fusion transcripts in both tumor subtypes, including a potential fusion of the cohesin complex members PDS5B::STAG2, arising through a t(X;13)(q25;q13.1) in an ETV6::RUNX1 patient (Figure 1). In addition, we detected 28 rare germline SVs targeting 22 known cancer predisposing genes in 35% (21/60) of the pediatric patients. 40% (9/22) of the affected genes were involved in hematopoietic or lymphoid organ development as ETV6, FANCA, IKZF1, ITCH or PTPRC. In 18% (11/60) of the children, the identified germline alteration potentially altered a coding region of a known cancer predisposing gene including a duplication of CIITA in an ETV6::RUNX1 patient. Conclusions: By applying the novel technology WGOM, we could detect a significant amount of previously hidden SVs in our BCP-ALL cohort in addition to conventional methods. We further generated a comprehensive landscape of somatic and germline SVs in childhood BCP-ALL, revealing recurrently altered regions and novel potential players in ALL leukemogenesis and predisposition. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Telomere Dysfunction Is Associated with Altered DNA Organization in Trichoplein/Tchp/Mitostatin (TpMs) Depleted Cells.

Recently, we highlighted a novel role for the protein Trichoplein/TCHP/Mitostatin (TpMs), both as mitotic checkpoint regulator and guardian of chromosomal stability. TpMs-depleted cells show numerical and structural chromosome alterations that lead to genomic instability. This condition is a major driving force in malignant transformation as it allows for the cells acquiring new functional capabilities to proliferate and disseminate. Here, the effect of TpMs depletion was investigated in different TpMs-depleted cell lines by means of 3D imaging and 3D Structured illumination Microscopy. We show that TpMs depletion causes alterations in the 3D architecture of telomeres in colon cancer HCT116 cells. These findings are consistent with chromosome alterations that lead to genomic instability. Furthermore, TpMs depletion changes the spatial arrangement of chromosomes and other nuclear components. Modified nuclear architecture and organization potentially induce variations that precede the onset of genomic instability and are considered as markers of malignant transformation. Our present observations connect the tumor suppression ability of TpMs with its novel functions in maintaining the proper chromosomal segregation as well as the proper telomere and nuclear architecture. Further investigations will investigate the connection between alterations in telomeres and nuclear architecture with the progression of human tumors with the aim of developing personalized therapeutic interventions.

Molecular cytogenetics reveals an uncommon structural and numerical chromosomal heteromorphism in Zephyranthes brachyandra (Amaryllidaceae)

Background and aims: Zephyranthes brachyandra belongs to a tribe of ornamental Amaryllidaceae native of South America, whose genera circumscription and phylogenetic relationships are still unclear. Cytologically, Z. brachyandra is a tetraploid whose chromosomes are of similar size and morphology, hindering the identification of its 2n = 24 chromosomes. The aim of this study was to investigate the stability of the many CMA+ and DAPI+ bands and the occurrence of B chromosomes by a cytomolecular approach. M&amp;M: For this investigation we conducted a cytomolecular analysis with CMA/DAPI staining and fluorescence in situ hybridization with 5S and 35S rDNA probes, and the TTTAGGG telomeric probe. Results: In the present work, a cytomolecular analysis of Z. brachyandra, revealed a large and variable number of CMA+ and DAPI+ heterochromatic bands and 5S and 35S rDNA sites, and a regular distribution of the TTTAGGG telomeric sequences. In addition, one individual was monotrisomic with 2n = 24, and another one had a B chromosome. Both numerical and structural chromosome alterations were clearly characterized by CMA/DAPI bands and rDNA sites. Conclusions: Comparing the present data with the cytological data for other species of Zephyranthes, it becomes clear that a cytomolecular approach is fundamental to the understanding of the chromosome variation and cytotaxonomy of the group.

Centromere Protein A Goes Far Beyond the Centromere in Cancers

Centromere dysfunctions leading to numerical chromosome alterations are believed to be closely related to human cancers. As a centromere-specific protein, centromere protein A (CENP-A) replaces the histone H3 in centromeres and is therefore considered a key factor of centromere identity. Researches have shown that CENP-A is overexpressed in many types of human cancers. However, the behavior and function of CENP-A in tumorigenesis have not yet been systematically summarized. In this article, we describe the pleiotropic roles of CENP-A in human cells. Moreover, we provide a comprehensive review of the current knowledge on the relationship between aberrant expression and ectopic localization of CENP-A and tumorigenesis, and the mechanism of the ectopic deposition of CENP-A in cancers. Furthermore, we note that some oncogenic viruses can modulate the expression and localization of this centromere protein along with its chaperone. At last, we also discuss the therapeutic potential of targeting CENP-A for cancer therapy.

A Case of Aldosterone Producing Adrenocortical Carcinoma

Introduction: Adrenocortical carcinomas (ACCs) are rare and aggressive cancers. Approximately 60% of ACCs are functional, presenting with Cushing syndrome and/or virilization. Aldosterone producing ACCs account for about 1-3% of hormonally active ACCs. Despite aldosterone production, their mutational landscape is not different from other functional ACCs - they do not harbor mutations of known aldosterone-producing adenoma (APA) associated genes. They present with uncontrolled hypertension and hypokalemia, as seen in this case. Case: 63 year old Asian female with previously well controlled hypertension experienced resistant hypertension and hypokalemia for over a year. Since the onset of hypokalemia, patient noticed worsening hypertension despite addition of multiple medications. CT abdomen during an episode of severe gastroenteritis revealed a 3.7 cm heterogenous multilobulated left adrenal mass. Hormonal workup showed elevated aldosterone of 35 ng/dl with suppressed plasma renin activity of 0.41 ng/ml/h and serum potassium of 3.4 while patient was on 50 mg of spironolactone. Plasma and urine metanephrine levels were unremarkable. Plasma ACTH was <5 ng/L, cortisol was 12 ug/dl and DHEA-S was 149 ng/dl. 24 hour urine free cortisol result was not available. Repeated CT abdomen revealed a 5.2 cm left adrenal mass (Non-contrast HU of 38, 50% absolute wash out), increasing in size from 3.7 cm in 6 months. The mass was FDG avid with SUV of 13.2. Patient underwent laparoscopic left adrenalectomy and surgical pathology revealed a 4.2 cm, high grade ACC with vascular invasion, Ki67 index of 35% and modified Weiss score of 6. Hypertension and hypokalemia resolved after tumor removal, no longer requiring antihypertensive medications. Plasma aldosterone level also remains normal after surgery. However, postoperative CT (6 weeks after surgery) revealed numerous pulmonary metastases. Germline genetic testing is pending. Genomic interrogation of the primary tumor identified CDKN2A and CDKN2B deletions, along with pathogenic mutations in CTNNB1 and DNMT3A. Copy number analysis revealed numerous large scale chromosomal alterations including many arm level and whole chromosome gains and losses. These somatic mutations affect p53/Rb1 signaling (CDKNs), chromatic remodeling (DNMT3A) and wnt signaling pathway (CTNNB1). Together with noisy pattern of copy number alterations, these genomic alterations likely account for the aggressive nature of this tumor. Clinical Lessons: (1) Clinicians should raise the suspicion of ACC during the workup for primary hyperaldosteronism, especially if an adrenal mass does not have the reassuring radiographic features suggestive of a benign adrenal mass. (2) Metastatic lesions may not necessarily produce aldosterone as the primary tumor does. (3) Mutational analysis of the tumor informs molecular subtypes of ACC, prognosis, and treatment decisions.

Genomic variations in patients with myelodysplastic syndrome and karyotypes without numerical or structural changes

Myelodysplastic syndrome (MDS) is an onco-hematologic disease with distinct levels of peripheral blood cytopenias, dysplasias in cell differentiation and various forms of chromosomal and cytogenomic alterations. In this study, the Chromosomal Microarray Analysis (CMA) was performed in patients with primary MDS without numerical and/or structural chromosomal alterations in karyotypes. A total of 17 patients was evaluated by GTG banding and eight patients showed no numerical and/or structural alterations. Then, the CMA was carried out and identified gains and losses CNVs and long continuous stretches of homozygosity (LCSHs). They were mapped on chromosomes 1, 2, 3, 4, 5, 6, 7, 9, 10, 12, 14, 16, 17, 18, 19, 20, 21, X, and Y. Ninety-one genes that have already been implicated in molecular pathways important for cell viability were selected and in-silico expression analyses demonstrated 28 genes differentially expressed in mesenchymal stromal cells of patients. Alterations in these genes may be related to the inactivation of suppressor genes or the activation of oncogenes contributing to the evolution and malignization of MDS. CMA provided additional information in patients without visible changes in the karyotype and our findings could contribute with additional information to improve the prognostic and personalized stratification for patients.

Typical numerical alterations in genome identified by array CGH analysis in neuroblastoma tumors

&lt;abstract&gt;&lt;sec&gt; &lt;title&gt;Introduction&lt;/title&gt; &lt;p&gt;The clinical variability in the course of neuroblastoma (NB) is closely linked to diverse genetic changes acquired by tumor cells. Rapid NB progression is associated with oncogene MYCN amplification (MNA) and segmental chromosomal aberrations (SCA). Alternatively, numerical chromosomal alterations (NCA) have positive impact on treatment. So far, no studies have been undertaken to identify NCA that may group NB patients. Therefore, the aim of the study was to identify NCA typical for NB.&lt;/p&gt; &lt;/sec&gt;&lt;sec&gt; &lt;title&gt;Materials and methods&lt;/title&gt; &lt;p&gt;Copy number alterations in NB tumor genome (fresh samples N = 94; formalin-fixed paraffin-embedded specimens N = 66) were analyzed with a pangenomic array CGH technique.&lt;/p&gt; &lt;/sec&gt;&lt;sec&gt; &lt;title&gt;Results&lt;/title&gt; &lt;p&gt;The profile with NCA was observed in 72 (45%) cases, NCA+SCA in 37 (23%), normal in 35 (22%) and MNA in 16 (10%). Samples with NCA were characterized by whole chromosome gains: 17, 7, 6 (78%, 65%, 51%, respectively) and copy loss of chromosome 14 (57%). Similarly to NCA, patients with a combined NCA and SCA profile were also characterized by gain of whole chromosome 17 and 7 (35% both) and loss of chromosome 14 (38%), but with lower frequency. In the combined NCA and SCA profiles, typical NB changes such as deletion 1p36 (27%) and gain 17q (41%) were observed, as well as deletion 11q (24%). The same alterations were detected in MNA samples (44%, 44%, 19%, respectively). A difference was found in spanning 11q deletion between MNA and NCA+SCA subgroup, which may suggest new prognostic markers in NB. In MNA subgroup specific NCA was not indicated.&lt;/p&gt; &lt;/sec&gt;&lt;sec&gt; &lt;title&gt;Conclusions&lt;/title&gt; &lt;p&gt;The hypothesis that NCA in NB tumors are more frequent in younger children with good prognosis was confirmed. To gain new insights into the pathogenesis of NB and to establish molecular targets for diagnosis and therapy, candidate genes in the altered chromosomal regions must be investigated.&lt;/p&gt; &lt;/sec&gt;&lt;/abstract&gt;

Integrating pathology, chromosomal instability and mutations for risk stratification in early-stage endometrioid endometrial carcinoma

BackgroundRisk stratifications for endometrial carcinoma (EC) depend on histopathology and molecular pathology. Histopathological risk stratification lacks reproducibility, neglects heterogeneity and contributes little to surgical procedures. Existing molecular stratification is useless in patients with specific pathological or molecular characteristics and cannot guide postoperative adjuvant radiotherapies. Chromosomal instability (CIN), the numerical and structural alterations of chromosomes resulting from ongoing errors of chromosome segregation, is an intrinsic biological mechanism for the evolution of different prognostic factors of histopathology and molecular pathology and may be applicable to the risk stratification of EC.ResultsBy analyzing CIN25 and CIN70, two reliable gene expression signatures for CIN, we found that EC with unfavorable prognostic factors of histopathology or molecular pathology had serious CIN. However, the POLE mutant, as a favorable prognostic factor, had elevated CIN signatures, and the CTNNB1 mutant, as an unfavorable prognostic factor, had decreased CIN signatures. Only if these two mutations were excluded were CIN signatures strongly prognostic for outcomes in different adjuvant radiotherapy subgroups. Integrating pathology, CIN signatures and POLE/CTNNB1 mutation stratified stageIendometrioid EC into four groups with improved risk prognostication and treatment recommendations.ConclusionsWe revealed the possibility of integrating histopathology and molecular pathology by CIN for risk stratification in early-stage EC. Our integrated risk model deserves further improvement and validation.

Cytogenetic differences in blood and cancer tissue samples of the same patient group

Breast cancer (BC) is the most prevalent malignant disease in females worldwide. Genomic instability in tumor tissue has been associated with tumor progression. These genetic changes may take a variety of forms, including numerical and structural chromosomal abnormalities (CAs), epigenetic changes, and gene expression alterations. Many tumor tissues are made up of genetically different cell populations, and the study of the causes and consequences of this heterogeneity play a central role in cancer research. In this study, CAs in blood and cancer tissues of patients with sporadic BC were examined. Our findings shows that the increase in numerical sex aneuploidy in BC tissues is significantly higher than in blood tissue. These aneuploidy increases in cancer tissues seem to be compatible with the development and increase of cancer, and can play a role in the pathogenesis of cancers. These changes are consistent with early and long-standing exposure to carcinogens, especially estrogens. These findings should clarify our understanding of breast carcinogenesis in breast tissues and promote development of improved methods for risk assessment and BC prevention in women.

Abstract B18: MEG3 and MEG8 aberrant methylation associated with worst prognosis in an infant with neuroblastoma

Abstract Background: Neuroblastoma (NB) is an extremely rare pediatric cancer accounting for about 12% of childhood cancer-related deaths, due to its dismal prognosis in patients diagnosed over 18 months of age with disseminated disease. However, neonates and infants with neuroblastoma are expected to have a better evolution despite their stage and even unfavorable molecular characteristics. Here, we report an unusual case of low-risk neuroblastoma (stage 2B, nonamplified MYCN) in a 9-month-old girl with unfavorable outcome despite favorable prognostic factors. Material and Methods: We investigated the coding genes expression (mRNA) and long noncoding RNAs (lncRNAs) in primary and relapse tumors of this patient to look for genomic and epigenetic alterations that could explain the clinical evolution. The cytogenetic profiles of the primary and relapse tumor samples were also obtained. Three primary tumors from patients with neuroblastoma, all classified as stage 1 (INSS) and low-risk (below 18 months of age at diagnosis, nonamplified-MYCN, all alive and free of disease 60 months after diagnosis) were used as controls in RNA sequencing (RNA-Seq. Illumina®) and DNA methylation arrays (Illumina Infinium HumanMethylation450 BeadChip). Somatic copy number alterations were investigated in the primary and relapsed sample using the array-CGH methodology in a 180K platform (Agilent). Results: The cytogenetic profiles of both samples were quite identical, with few copy number alterations. No numerical chromosomal alterations (aneuploidies) were detected; both tumors carry segmental copy number alterations in common, most of them probably present in a nonmosaic state. The differential gene expression analysis based on fold-change (≤ -2 and ≥ 2), p &amp;lt; 0.005, and FDR &amp;lt; 0.05 was used in RNA-seq to identified gene differential expression in primary and relapsed tumors. Interestingly, only two lncRNA, the imprinted maternally expressed genes MEG3 and MEG8, were downregulated in both primary and relapse tumors. MEG3 targets p53 by either directly interacting with p53 or indirectly suppressing the negative regulator MDM2. In the case of MEG8, their functions in cancer remain unknown. Our study then focused on MEG3 and MEG8 methylation analysis. DNA methylation status of the study groups (primary, relapse tumors, and controls) strongly suggested that DMR that covers promoters was responsible for silencing MEG3 and MEG8 genes in primary and relapse tumors, resulting in downregulation of MEG3 and MEG8. Tumor samples from the patient were also used to perform methylation-specific MLPA (MSMLPA) (SALSA® probemix, MRC-Holland). Hypermethylated probes at MEG3 were identified in primary and relapse tumors when compared with controls. Conclusion: Furthermore, we hypothesized that the methylation gain of the MEG3 and MEG8 locus may be accentuated during cancer progression and therefore, the increased degree of MEG3 and MEG8 suppression was associated with the overall aggressiveness of neuroblastoma. Citation Format: Estela M. Novak, Thamiris Magalhaes Gimenez, Nathalia Halley Neves, Carolina Sgarioni Camargo Vince, Ana Cristina Victorino Krepischi, Rainer Marco Lopez Lapa, Lilian M. Cristofani, Israel Bendit, Vicente Odone Filho. MEG3 and MEG8 aberrant methylation associated with worst prognosis in an infant with neuroblastoma [abstract]. In: Proceedings of the AACR Special Conference on the Advances in Pediatric Cancer Research; 2019 Sep 17-20; Montreal, QC, Canada. Philadelphia (PA): AACR; Cancer Res 2020;80(14 Suppl):Abstract nr B18.

Interplay of somatic alterations and immune infiltration modulates response to PD-1 blockade in advanced clear cell renal cell carcinoma.

PD-1 blockade has transformed the management of advanced clear cell renal cell carcinoma (ccRCC), but the drivers and resistors of the PD-1 response remain incompletely elucidated. Here, we analyzed 592 tumors from patients with advanced ccRCC enrolled in prospective clinical trials of treatment with PD-1 blockade by whole-exome and RNA sequencing, integrated with immunofluorescence analysis, to uncover the immunogenomic determinants of the therapeutic response. Although conventional genomic markers (such as tumor mutation burden and neoantigen load) and the degree of CD8+ T cell infiltration were not associated with clinical response, we discovered numerous chromosomal alterations associated with response or resistance to PD-1 blockade. These advanced ccRCC tumors were highly CD8+ T cell infiltrated, with only 27% having a non-infiltrated phenotype. Our analysis revealed that infiltrated tumors are depleted of favorable PBRM1 mutations and enriched for unfavorable chromosomal losses of 9p21.3, as compared with non-infiltrated tumors, demonstrating how the potential interplay of immunophenotypes with somatic alterations impacts therapeutic efficacy.

Concomitance of numerical chromosomal alterations with structural in an elderly with Alzheimer’s disease: a case report

AIMS: To report the first case the concomitance of numerical chromosomal abnormalities with structural as well as chromosomal abnormalities structural in a patient diagnosed with Alzheimer disease in Manaus/Amazonas.CASE DESCRIPTION: A male patient with 76 years of age was diagnosed with diagnosis of cognitive disorder- Alzheimer’s disease with late onset - temporal variant after laboratory, physical and imaging exams. Cytogenetic analysis was requested for this patient, revealing the presence the concomitant of numerical and structural chromosomal abnormalities with metaphase cells composed of 45 chromosomes with the loss of one of the homologues of chromosome 21 (monosomy) and a deletion of the long arm of one of the homologues of chromosome 1 [45, XY, -21, del (1) (q?)] and metaphase cells containing 46 chromosomes with a deletion of the long arm of one of the homologues of chromosome 15 [(46, XY, del (15) (q?)]. Currently, the patient is in outpatient treatment for maintenance and control of the disease.CONCLUSIONS: Our study has underlined that karyotyping is one of the fundamental investigations for patients with Alzheimer’s disease. It highlighted, in the form of a chromosomal abnormality, may have been the risk factor in Alzheimer’s disease.

Investigation of chromosomal alterations in patients with Alzheimer's disease in the state of Amazonas, Brazil.

Alzheimer's disease (AD) has as its main characteristic the deterioration of cerebral functions. Its etiology is still complex and undefined despite the progress made in understanding its neurological, infectious, biochemical, genetic and cytogenetic mechanisms. Considering this, the aim of this study was to investigate the presence of chromosomal alterations in the peripheral blood lymphocytes, and to verify if there was a high frequency of these alterations in patients diagnosed with AD at the University Hospital GetúLio Vargas Outpatient Clinic Araújo Lima in Manaus, Amazonas, Brazil. Among the nine patients in the AD group, only one patient did not have metaphases with chromosomal alterations (2n = 46,XX), while eight patients with AD showed numerical chromosomal alterations, classified as X chromosome aneupLoidy (2n = 45,X) and double aneupLoidy (2n = 44,X,-X,-10; 2n = 44,X,-X,-13 and 2n = 44,X,-X,-21). In the control group, no chromosomal changes were found in the karyotypes of these individuals. Therefore, the karyotypes of patients with AD undergo chromosomal alterations at different levels. These findings are being described for the first time in the population of Amazonas, and they highlight the importance of the inclusion of cytogenetic investigations in the routine management of patients with AD.

Identification Of Actionable Genetic Targets In Primary Cardiac Sarcomas.

BackgroundPrimary cardiac tumors are extremely rare; most are myxomas with a benign prognosis. However, primary sarcomas are highly aggressive and treatment options are limited. Radical surgery is often not feasible and conventional therapies provide only modest results. Due to the rare nature of primary cardiac tumors, there are no proper randomized studies to guide treatment. Their complexity requires alternative approaches in order to improve treatment efficacy.MethodsWe isolated DNA from 5 primary cardiac sarcomas; the quality of DNA from 3 of them was sufficient to perform high-resolution single nucleotide polymorphism (SNP) array analysis.ResultsIn the present study, molecular karyotyping revealed numerous segmental chromosomal alterations and amplifications affecting actionable genes that may be involved in disease initiation and/or progression. These include chromosomal break flanking AKT2 in undifferentiated pleomorphic rhabdomyosarcoma, chromosomal break in promoter of TERT, and gain of CDK4 and amplification of MDM2 in inflammatory myofibroblastic tumor. We detected segmental break flanking MOS in high-grade myxofibrosarcoma. In addition, the high number of chromosomal aberrations in high-grade myxofibrosarcoma may cause multiple tumor-specific epitopes, supporting the study of immunotherapy treatment in this type of aggressive tumor.ConclusionOur results provide a genetic rationale that supports an alternative, personalized therapeutic management of primary cardiac sarcomas.

Abstract P3-09-01: MYC dysregulates mitotic spindle function in triple-negative breast cancer creating a dependency on TPX2

Abstract Tumors that overexpress the MYC oncogene, including most receptor triple-negative breast cancers, frequently demonstrate aneuploidy, numerical chromosome alterations associated with highly aggressive cancers. Aneuploidy is also associated with rapid tumor evolution and poor patient outcome. We identify that MYC overexpression induces reversible defects in microtubule nucleation and mitotic spindle assembly, in TNBCs and other epithelial cells, promoting chromosome segregation defects, micronuclei and chromosomal instability (CIN). High TPX2 expression is permissive for mitotic spindle assembly and chromosome segregation in cells with MYC overexpression; whereas TPX2 depletion blocks mitotic progression, induces cell death and prevents tumor growth. Attenuating MYC expression reverses mitotic defects, even in established breast tumor cell lines, implicating an ongoing role for high MYC in the persistence of CIN in cancers. Our studies implicate the MYC oncogene as a regulator of spindle assembly and identify a new MYC-TPX2 synthetic-lethal interaction in TNBC that could represent a future therapeutic strategy in MYC-overexpressing cancers. Moreover, our studies suggest that blocking MYC activity can attenuate the emergence of CIN and tumor evolution. Citation Format: Goga A, Rohrberg J, Corella A, Taileb M, Kilinc S, Jokisch M-L, Camarda R, Zhou A, Balakrishnan S, Chang AN, Klein-Connolly H. MYC dysregulates mitotic spindle function in triple-negative breast cancer creating a dependency on TPX2 [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P3-09-01.