Regulation of protein complex partners as a compensatory mechanism in aneuploid tumors

Aneuploidy, a state of chromosome imbalance, is a hallmark of human tumors, but its role in cancer still remains to be fully elucidated. To understand the consequences of whole chromosome-level aneuploidies on the proteome, we integrated aneuploidy, transcriptomic and proteomic data from hundreds of TCGA/CPTAC tumor samples. We found a surprisingly large number of expression changes happened on other, non-aneuploid chromosomes. Moreover, we identified an association between those changes and co-complex members of proteins from aneuploid chromosomes. This co-abundance association is tightly regulated for aggregation-prone aneuploid proteins and those involved in a smaller number of complexes. On the other hand, we observe that complexes of the cellular core machinery are under functional selection to maintain their stoichiometric balance in aneuploid tumors. Ultimately, we provide evidence that those compensatory and functional maintenance mechanisms are established through post-transcriptional control and that the degree of success of a tumor to deal with aneuploidy-induced stoichiometric imbalance impacts the activation of cellular protein degradation programs and patient survival.

Copy number variations of chromosome 17p11.2 region in children with development delay and in fetuses with abnormal imaging findings

Background Deletion and duplication of the 3.7 Mb region in 17p11.2 result in two syndromes, Smith-Magenis syndrome and Potocki-Lupski syndrome, which are well-known development disorders. The purpose of this study was to determine the prevalence, genetic characteristics and clinical phenotypes of 17p11.2 deletion/duplication in Chinese children with development delay and in fetuses with potential congenital defects. Methods 7077 children with development delay and/or intellectual disability were screened by multiplex ligation-dependent probe amplification P245 assay. 7319 fetuses with potential congenital defects were tested using next generation sequencing technique. Results 417 of 7077 pediatric patients were determined to carry chromosome imbalance. 28 (28/7077, 0.4%) cases had imbalance at chromosome 17p11.2. Among them, 12 cases (42.9%) had heterozygous deletions and 16 cases (57.1%) had heterozygous duplications. The clinical phenotypes were variable, including neurobehavioral disorders, craniofacial/skeletal anomalies, immunologic defects, ocular problems and organ malformations. 263 of 7319 fetuses were recognized to have genomic copy number variations. Only 2 of them were found to harbor 17p11.2 imbalance. The fetus with deletion presented with ventricular septal defect and the fetus with duplication had cerebral ventricle dilation. Conclusion Our study highlights the phenotypic variability associated with 17p11.2 variations in China. The results further expand the phenotypic spectrum of SMS/PTLS and increase awareness of these disruptive mutations among clinicians.

Copy number variations of chromosome 17p11.2 region in children with development delay and in fetuses with abnormal imaging findings

Background: Deletion and duplication of the -3.7 Mb region in 17p11.2 result in two reciprocal syndromes, Smith-Magenis syndrome and Potocki-Lupski syndrome, which are well-known development disorders. The purpose of this study is to identify the prevalence, genetic characteristics and clinical phenotype of 17p11.2 deletion/duplication in Chinese children with development delay and in fetuses with potential congenital defects.Methods: 7077 children with development delay and/or intellectual disability were screened by multiplex ligation-dependent probe amplification (MLPA) P245 assay. 7319 fetuses with potential congenital defects were detected using next generation sequencing (NGS) technique.Results: 417 of 7077 children patients were identified to carry chromosome imbalance. Among them, 28 (28/7077, 0.4 %) cases had imbalance at chromosome 17p11.2, of which 12 cases (42.9 %) had heterozygous deletions and 16 (57.1 %) had heterogeneous duplications. The phenotypes of these 28 children were variable, including neurobehavioral disorders, craniofacial/skeletal anomalies, immunologic defects, ocular problems, and organ malformations. 263 of 7319 fetuses were recognized to have genomic copy number variations (CNV). Only 2 of them were found to harbor 17p11.2 imbalance. The fetus with deletion presented with ventricular septal defect and the fetus with reciprocal duplication had cerebral ventricle dilation.Conclusion: Our study highlights the phenotypic variability associated with 17p11.2 variations in China. The results further expand the phenotypic spectrum of SMS/PTLS and increase awareness of these disruptive mutations among clinicians.

Permanence of de novo segmental aneuploidy in sequential embryo biopsies

STUDY QUESTION Is de novo segmental aneuploidy (SA) a biological event or an artifact that is erroneously interpreted as partial chromosome imbalance? SUMMARY ANSWER The detection of de novo SA in sequential biopsies of preimplantation embryos supports the biological nature of SA. WHAT IS KNOWN ALREADY Although some SAs are detected in oocytes and in blastocysts, the highest incidence is observed in cleavage-stage embryos. Based on these findings, we can postulate that the majority of cells affected by SAs are eliminated by apoptosis or that affected embryos mainly undergo developmental arrest. STUDY DESIGN, SIZE, DURATION This retrospective study includes 342 preimplantation genetic testing for aneuploidy (PGT-A) cycles performed between January 2014 and December 2018. Chromosome analysis was performed on 331 oocytes, 886 cleavage-stage embryos and 570 blastocysts (n = 1787). From 268 expanded blastocysts, the blastocoelic fluid (BF) was also analyzed (resulting in 2025 samples in total). In cases of SAs involving loss or gain in excess of 15 Mb, embryos were not considered for transfer and sequential biopsies were performed at following stages. This resulted in 66 sets where the initial diagnosis of SAs (4 made in polar bodies, 25 in blastomeres and 37 in trophectoderm (TE) cells) was followed up. PARTICIPANTS/MATERIALS, SETTING, METHODS A total of 2082 samples (2025 + 27 whole embryos) were processed by whole genome amplification followed by array comparative genomic hybridization. MAIN RESULTS AND THE ROLE OF CHANCE The incidence of SAs was 6.3% in oocytes, increased to 16.6% in cleavage-stage embryos (P < 0.001) and decreased to 11.2% in blastocysts (P < 0.025 versus oocytes; P < 0.01 versus cleavage-stage embryos). The highest incidence of SAs was found in BFs (26.1%, P < 0.001). The analysis of 66 sets of sequential biopsies revealed that the initial finding was confirmed in all following samples from 39 sets (59.1% full concordance). In 12 additional sets, SAs were detected in some samples while in others the interested chromosome had full aneuploidy (18.2%). In three more sets, there was a partial concordance with the initial diagnosis in some samples, but in all TE samples the interested chromosome was clearly euploid (4.5%). In the remaining 12 sets, the initial SA was not confirmed at any stage and the corresponding chromosomes were euploid (18.2% no concordance). The pattern of concordance was not affected by the number of SAs in the original biopsy (single, double or complex) or by the absence or presence of concomitant aneuploidies for full chromosomes. LIMITATIONS, REASONS FOR CAUTION Chromosome analyses were performed on biopsies that might not be representative of the true constitution of the embryo itself due to the occurrence of mosaicism. WIDER IMPLICATIONS OF THE FINDINGS The permanence of SAs throughout the following stages of embryo development in more than half of the analyzed sets suggests for this dataset a very early origin of this type of chromosome imbalance, either at meiosis or at the first mitotic divisions. Since SAs remained in full concordance with the initial diagnosis until the blastocyst stage, a corrective mechanism seems not to be in place. In the remaining cases, it is likely that, as for full chromosome aneuploidy, mosaicism derived from mitotic errors could have occurred. In following cell divisions, euploid cell lines could prevail preserving the embryo chances of implantation. Due to the scarcity of data available, the transfer of embryos with SAs should be strictly followed up to establish possible clinical consequences related to this condition. STUDY FUNDING/COMPETING INTEREST(S) No specific funding was obtained. There are no conflicts of interest.

The study of chromosomal abnormalities in fetuses with ultrasound markers and malformations

Микроделеционные и микродупликационные синдромы выявляются примерно у 8% плодов с врожденными пороками развития (ВПР), однако диагностика патогенных CNVs в пренатальном периоде в данный момент не регламентирована и зачастую основана на технических возможностях лаборатории. Представлены результаты исследования плодов, которые имели ВПР и/или маркеры хромосомной патологии, установленные по УЗИ, методом хромосомного микроматричного анализа (ХМА). В выборке (N=1048) у 10,3% плодов были обнаружены числовые аномалии хромосом и у 7,4% плодов были выявлены патогенные хромосомные аномалии, которые невозможно выявить при стандартном кариотипировани из-за их малого размера. Результаты нашего анализа согласуются с данными литературы, демонстрирующей большую эффективность SNP-микроматриц по сравнению с классическими цитогенетическими методами. Microdeletion and microduplication syndromes are detected in approximately 8% of fetuses with congenital malformations, however, the diagnosis of pathogenic CNVs in the prenatal period, at the moment, is unregulated and often based on the technical capabilities of the laboratory. The thesis presents the result of a study of fetuses that had congenital malformations and / or markers of chromosomal abnormalities, determined by ultrasound, by the method of chromosomal microarray analysis. Using chromosomal microarray analysis in our sample (N = 1048), numerical chromosome abnormalities were detected in 10.3% of the fetuses and pathogenic chromosome imbalance was revealed in 7.4% of the fetuses, which cannot be detected by standard karyotyping. The results of our analysis are consistent with the data of the scientific literature, which demonstrates the greater efficiency of using SNP microarrays in comparison with classical cytogenetic methods.

Autosomal reciprocal translocations: prenatal selection, segregation and assessment of empirical risks for reciprocal translocation carriers of having a liveborn child with chromosome imbalance

Аутосомные реципрокные транслокации (АРТ), являются наиболее частой структурной хромосомной перестройкой. Носители АРТ имеют повышенный риск рождения детей с хромосомным дисбалансом, который может варьировать от низкого до высокого в зависимости от характеристик транслокации и типа патологической мейотической сегрегации. Целью исследования являлся анализ пренатальной селекции, мейотической сегрегации и оценка эмпирического риска рождения жизнеспособного ребенка с хромосомным дисбалансом у 49 носителей АРТ. Оценка пахитенной диаграммы проводилась для каждой транслокации на основании количественных характеристик мейотического квадривалента. Наблюдаемый и ожидаемый хромосомный дисбаланс при всех типах патологической сегрегации оценивался в процентах от гаплоидной длины аутосом. Оценка жизнеспособности плодов и потенциальных зигот с хромосомным дисбалансом проводилась с использованием модели, основанной на измерении хромосомных сегментов дистальнее точек разрывов и определении относительного размера хромосомного дисбаланса. Установлена тенденция к преимущественной пренатальной селекции зигот вследствие альтернативного типа сегрегации АРТ. Показано, что анализ количественных характеристик квадривалента и пахитенной диаграммы позволяет оценить тип патологической мейотической сегрегации, приводящей к наименьшему хромосомному дисбалансу, и риск формирования несбалансированных гамет. Определено, что оценка жизнеспособности зигот, основанная на сопоставлении относительного размера несбалансированных хромосомных сегментов, может быть дополнительным этапом при установлении повторного риска рождения ребенка с хромосомной патологией у носителей АРТ. В 80% случаев транслокаций риск рождения жизнеспособного ребенка с хромосомным дисбалансом расценивается как низкий. Мейотическая сегрегация хромосом у носителей АРТ происходит с преимущественным формированием и последующей пренатальной селекцией зигот вследствие альтернативного, непатологического типа сегрегации. Для каждой транслокации необходимо проводить оценку наиболее вероятного типа патологической сегрегации и жизнеспособности плодов или новорожденных. Эмпирический риск не может быть использован как единственный и решающий фактор при оценке повторного риска рождения жизнеспособного ребенка с хромосомным дисбалансом. Autosomal reciprocal translocations are among the most frequent chromosomal rearrangements in man. Though phenotypically normal, the carrier of reciprocal translocation may be at increased risk of having a chid with multiple malformations and mental retardation due to malsegregation at meiosis resulting in gametes with chromosome imbalance. An accurate estimate of the probability of this event is understandably desirable. Aim. The aim of this investigation was an analysis of prenatal selection, meiotic segregation and assessment of empirical risks for reciprocal translocation carriers of having a liveborn child with unbalanced karyotype on 49 reciprocal translocation carriers. Materials and Methods. The pachytene diagrams were analyzed for each translocation taking in account the exact lengths of the chromosomes involved. The observed and most probable unbalanced segments were evaluated using the Chromosome Imbalance Size-Viability Model and Surface of Viable Unbalances consisting of the measurement of chromosomal segments distal to the breakpoints expressed in percentage of haploid autosomal length - %HAL. Results. The tendency to preferential prenatal selection of zygotes is established due to the 2:2 alternate segregation. It is shown that the analysis of quantitative characteristics of quadrivalent and pachytene diagram allows to estimate the type of malsegregation producing the smallest imbalance and the risk of formation of unbalanced gametes. Evaluation of viability of zygotes may be an additional step in establishing of the recurrence risks. In 80% of cases the risk of a viable child with a chromosomal imbalance is regarded as low. Conclusions. Meiotic segregation of chromosomes in carriers of autosomal reciprocal translocations occurs with preferential formation and subsequent prenatal selection of zygotes due to alternate segregation. It is necessary to assess segregation giving the smallest imbalance and viability of the imbalance. Empirical risk was not found to be useful as a discriminating risk predictor in individual genetic counselling.

A new direction for prenatal chromosome microarray testing: software-targeting for detection of clinically significant chromosome imbalance without equivocal findings

Purpose. To design and validate a prenatal chromosome microarray testing strategy that moves away from size-based detection thresholds, towards a more clinically relevant analysis, providing higher resolution than G-banded chromosomes but avoiding the detection of imbalances of unclear prognosis that cause parental anxiety. Methods. All prenatal samples fulfilling our criteria for karyotype analysis (n=342) were tested by chromosome microarray and only copy number variants of established deletion/duplication syndrome regions and any other imbalance >3Mb were detected and reported. A retrospective full-resolution analysis of 249 of these samples was carried out to ascertain the performance of this testing strategy. Results. Using our prenatal analysis, 23/342 (6.7%) samples were found to be abnormal. Of the remaining samples, 249 were anonymized and reanalyzed at full-resolution; a further 46 regions of imbalance were detected in 44 of these traces (17.7%). None of these additional imbalances were of clear clinical significance. Conclusion. This prenatal chromosome microarray strategy detected all CNVs of clear prognostic value and did not miss any imbalances of clear clinical significance. This strategy avoided both the problems associated with interpreting imbalances of uncertain prognosis and the parental anxiety that are a result of such findings.