TPX2 Amplification-Driven Aberrant Mitosis in Culture Adapted Human Embryonic Stem Cells With Gain of 20q11.21

Despite highly effective machinery for the maintenance of genome integrity in human embryonic stem cells (hESCs), the frequency of genetic aberrations during in-vitro culture has been a serious issue for future clinical applications. By passaging hESCs over a broad range of timepoints, we found that mitotic aberrations, such as the delay of mitosis, multipolar centrosomes, and chromosome mis-segregation, were increased in parallel with polyploidy compared to early-passaged hESCs (EP-hESCs) with normal copy number. Through high-resolution genome-wide approaches and transcriptome analysis, we found that culture adapted-hESCs with a minimal amplicon in chromosome 20q11.21 highly expressed TPX2, a key protein for governing spindle assembly and cancer malignancy. Consistent with these findings, the inducible expression of TPX2 in EP-hESCs reproduced aberrant mitotic events, such as the delay of mitotic progression, spindle stabilization, misaligned chromosomes, and polyploidy, suggesting that the increased transcription of TPX2 in culture adapted hESCs could contribute to an increase in aberrant mitosis due to altered spindle dynamics.

P–561 Male and female blastocyst: any difference other than the sex?

Study question Is there any imbalance in the sex ratio (SR) and in the aneuploidy rate of male and female human blastocysts from a PGT-A programme? Summary answer Although SR in human blastocysts is significantly male-biased, more aneuploidies are observed among male blastocysts, resulting in comparable euploid male and female embryos available. What is known already More boys than girls are born worldwide, meaning that the SR at birth is biased towards males. Differences in the SR of children born after ART have been also reported. Factors such as the insemination technique or the day of embryo transfer have been shown to be related to the SR at birth, but whether the SR is shifted during the preimplantation and/or postimplantation development remains unknown. Study design, size, duration: Embryos from patients undergoing 921 PGT-A cycles from September 2017 to February 2020 were included in the study. Data from the chromosomal constitution of 2637 biopsied blastocysts was retrospectively analysed. Participants/materials, setting, methods Embryos were cultured in time-lapse incubators with low oxygen tension (5%) (Embryoscope®; Geri®) using single-step medium (Global®, LifeGlobal®; GTL™, Vitrolife). Blastocyst biopsy was performed between D5-D7 followed by immediate vitrification (Cryotop®, Kitazato). Trophectoderm samples were analysed by NGS. Embryos were categorized as euploid, aneuploid or mosaic. Embryos were called as mosaic when the deviation from the normal copy number was ≥30% and <70%. Main results and the role of chance Overall biopsies from 2637 blastocysts were analysed, 1320 on day 5 (50.1%), 1169 on day 6 (44.3%) and 148 on day 7 (5.6%). Sex distribution among the embryos analysed was skewed in favor of male sex with 1401 diagnosed as male (53.1%) and 1236 were female (46.9%), [OR (95%CI):1.13(1.05–1.22)]. As a consequence of this biased SR, more male embryos reached the blastocyst stage and were biopsied both on day 5/6 (708/1320, 53.6% on day 5 and 619/1169, 53% on day 6). Embryos biopsied on day 7 were balanced between sexes with 50% being male and 50% being female. Following biopsy and PGT-A, 1086 (41.2%) of the embryos were classified as euploid, 1349 (51.16%) as aneuploid, and 202 (7.7%) as mosaic embryos. More chromosomal anomalies were observed among male blastocysts when compared to the female ones, 738 (52.7%) vs 611 (49.4%). Similarly, mosaicism was more frequents in male as compared with female blastocysts, 123 (8.8%) vs 79 (6.4%). (P = 0.000). As more aneuploidies are observed among male blastocysts, the final number of available euploid blastocysts for embryo transfer was comparable between sexes (540 male/546 female), [OR (95%CI): 0.99 (0.87–1.11)]. Limitations, reasons for caution This is a retrospective study. Only embryos at the blastocyst stage have been analyzed. Potential confounding factors such as sperm quality or the female age have not been analyzed. No data regarding the SR at birth have been analyzed in these study. Wider implications of the findings: In our study, more male embryos develop to the blastocyst when compared to female ones. It can be hypothesized that female embryos can be more affected by an early arrest at cleavage stages. SR at birth would be expected to be similar as more aneuploidy is observed in male embryos. Trial registration number Not applicable

46,XY,r(8)/45,XY,−8 Mosaicism as a Possible Mechanism of the Imprinted Birk-Barel Syndrome: A Case Study

Ring chromosome 8 (r(8)) is one of the least frequent ring chromosomes. Usually, maternal chromosome 8 forms a ring, which can be lost from cells due to mitotic instability. The 8q24 region contains the imprinted KCNK9 gene, which is expressed from the maternal allele. Heterozygous KCNK9 mutations are associated with the imprinting disorder Birk-Barel syndrome. Here, we report a 2.5-year-old boy with developmental delay, microcephaly, dysmorphic features, diffuse muscle hypotonia, feeding problems, motor alalia and noncoarse neurogenic type of disturbance of muscle electrogenesis, partially overlapping with Birk-Barel syndrome phenotype. Cytogenetic analysis of lymphocytes revealed his karyotype to be 46,XY,r(8)(p23q24.3)[27]/45,XY,−8[3]. A de novo 7.9 Mb terminal 8p23.3p23.1 deletion, a 27.1 Mb 8p23.1p11.22 duplication, and a 4.4 Mb intact segment with a normal copy number located between them, as well as a 154-kb maternal LINGO2 gene deletion (9p21.2) with unknown clinical significance were identified by aCGH + SNP array. These aberrations were confirmed by real-time PCR. According to FISH analysis, the 8p23.1-p11.22 duplication was inverted. The ring chromosome originated from maternal chromosome 8. Targeted massive parallel sequencing did not reveal the KCNK9 mutations associated with Birk-Barel syndrome. Our data allow to assume that autosomal monosomy with inactive allele of imprinted gene arising from the loss of a ring chromosome in some somatic cells may be an etiological mechanism of mosaic imprinting disorders, presumably with less severe phenotype.

Association Analysis to Copy Number Variation (CNV) of Opn4 Gene with Growth Traits of Goats

Extensive research has been carried out regarding the correlation between the growth traits of livestock and genetic polymorphisms, including single nucleotide polymorphisms and copy number variations (CNV). The purpose of this study was to analyze the CNV and its genetic effects of the Opn4 gene in 284 Guizhou goats (Guizhou black goat: n = 186, Guizhou white goat: n = 98). We used qPCR to detect the CNV of the Opn4 gene in Guizhou goats, and the classification results were correlated with the corresponding individual growth traits by SPSS software. The results showed that the Opn4 gene had a superior effect on growth traits with multiple copy variants in Guizhou black goats, and there was a significant correlation between copy number variation sites and body length traits. Contrary to the former conclusion, in Guizhou white goats, individuals with the Normal copy number type showed superior growth traits and copy number variant sites were significantly associated with body weight traits. Therefore, the CNV of the Opn4 gene can be used as a candidate molecular genetic marker to improve goat growth traits, speeding up the breeding process of goat elite varieties.

Two Patients with Complex Rearrangements Suggestive of Germline Chromoanagenesis

Chromoanagenesis, a phenomenon characterized by complex chromosomal rearrangement and reorganization events localized to a limited number of genomic regions, includes the subcategories chromothripsis, chromoanasynthesis, and chromoplexy. Although definitions of these terms are evolving, constitutional chromoanagenesis events have been reported in a limited number of patients with variable phenotypes. We report on 2 cases with complex genomic events characterized by multiple copy number gains and losses confined to a single chromosome region, which are suggestive of constitutional chromoanagenesis. Case 1 is a 43-year-old male with intellectual disability and recently developed generalized tonic-clonic seizures. Chromosomal microarray analysis identified a complex rearrangement involving chromosome region 14q31.1q32.2, consisting of 16 breakpoints ranging in size from 0.2 to 6.2 Mb, with 5 segments of normal copy number present between these alterations. Interestingly, this case represents the oldest known patient with a complex rearrangement indicative of constitutional chromoanagenesis. Case 2 is a 2-year-old female with developmental delay, speech delay, low muscle tone, and seizures. Chromosomal microarray analysis identified a complex rearrangement consisting of 28 breakpoints localized to 18q21.32q23. The size of the copy number alterations ranged from 0.042 to 5.1 Mb, flanked by 12 small segments of normal copy number. These cases add to a growing body of literature demonstrating complex chromosomal rearrangements as a disease mechanism for congenital anomalies.

Nucleotide Transition 390C-T in the Wilms' Tumor 1 Gene: A Risk Factor of Hypospadias?

Introduction: The gene Wilms' tumor 1 (WT1) encodes a unique transcription factor. Its defects are known to cause a wide range of complex genitourinary malformations and may contribute to non-syndromic forms of hypospadias. Materials and Methods: We performed WT1 mutation analysis and copy number analysis of WT1-interacting protein in 13 Hungarian patients diagnosed with isolated hypospadias. Results: Sequencing of WT1 revealed a high frequency of heterozygosity for transition 390C-T (5 heterozygotes out of 13 patients, including 2 brothers). WT1-interacting protein had a normal copy number in all patients. Conclusion: Nucleotide substitution 390C-T may play a role in the pathogenesis of non-syndromic hypospadias. The genotype-phenotype correlation should be confirmed by a larger-scale analysis.

Topoisomerase IIα Amplification Does Not Predict Benefit From Dose-Intense Cyclophosphamide, Doxorubicin, and Fluorouracil Therapy in HER2-Amplified Early Breast Cancer: Results of CALGB 8541/150013

Purpose We have demonstrated that patients with HER2-amplified tumors derive more benefit from higher doses of doxorubicin-containing chemotherapy (cyclophosphamide, doxorubicin, and fluorouracil [CAF]). Because topoisomerase IIα (Topo-IIα) is a target for doxorubicin and is coamplified in 20% to 50% of HER2-amplified tumors, we postulated that Topo-IIα copy number might account for the benefit from CAF dose escalation in HER2-positive tumors. To address this hypothesis, we examined Topo-IIα and HER2 copy number, CAF dose, and clinical outcomes in Cancer and Leukemia Group B (CALGB) 8541. Patients and Methods Topo-IIα and HER2 copy number were measured by fluorescent in situ hybridization (FISH) using a triple-probe system, which includes Topo-IIα, HER2, and chromosome 17 (CEP17). Topo-IIα and/or HER2 were classified as amplified (≥ two copies/CEP17, deleted (≤ 0.67 copies/CEP17) and normal copy number (> .67 to < 2.0 copies/CEP17). Results Topo-IIα/HER2/CEP17 measurement was successful in 624 of 687 cases. HER2 was amplified in 117 cases (19%). Topo-IIα was amplified in 41 cases (7%) and deleted in 69 cases (11%). Topo-IIα amplification was highly correlated with HER2 amplification (39 of 41; P < .0001), HER2 by immunohistochemistry, and by dual-probe FISH. Topo-IIα was deleted in both the HER2-amplified (30 of 69; 43%), normal (22 of 69; 32%) and HER2-deleted tumors (17 of 69; 25%). Although Topo-IIα–amplified tumors were nearly always HER2 amplified, these tumors did not receive benefit from increasing the dose of CAF (P = .15). Conclusion The correlative companion study CALGB 8541-150013 does not support the hypothesis that Topo-IIα amplification is the mechanism behind benefit from increased dose of anthracyclines in HER2-positive breast cancer.

Hidden abnormalities and novel classification of t(15;17) acute promyelocytic leukemia (APL) based on genomic alterations

Acute promyelocytic leukemia (APL) is a hematopoietic malignant disease characterized by the chromosomal translocation t(15;17), resulting in the formation of the PML-RARA gene. Here, 47 t(15;17) APL samples were analyzed with high-density single-nucleotide polymorphism microarray (50-K and 250-K SNP-chips) using the new algorithm AsCNAR (allele-specific copy-number analysis using anonymous references). Copy-number-neutral loss of heterozygosity (CNN-LOH) was identified at chromosomes 10q (3 cases), 11p (3 cases), and 19q (1 case). Twenty-eight samples (60%) did not have an obvious alteration (normal-copy-number [NC] group). Nineteen samples (40%) showed either one or more genomic abnormalities: 8 samples (17%) had trisomy 8 either with or without an additional duplication, deletion, or CNN-LOH (+8 group); and 11 samples (23%) had genomic abnormalities without trisomy 8 (other abnormalities group). These chromosomal abnormalities were acquired somatic mutations. Interestingly, FLT3-ITD mutations (11/47 cases) occurred only in the group with no genomic alteration (NC group). Taken together, these results suggest that the pathway of development of APL differs in each group: FLT3-ITD, trisomy 8, and other genomic changes. Here, we showed for the first time hidden abnormalities and novel disease-related genomic changes in t(15;17) APL.