Specific Aneuploidies Research Articles

P-518 Differentially gene expression identified by RNA seq in aneuploid human blastocysts is more influenced by the phenomenon of aneuploidy than the involved chromosome

Abstract Study question What insights do RNA-Seq profiles provide about gene expression in aneuploid blastocysts with small and large chromosomes compared to euploid blastocysts? Summary answer The difference in gene expression is affected by aneuploidy and is more related to the presence of aneuploidy than the size of the aneuploid chromosomes. What is known already Embryonic aneuploidy is one of the main common causes of implantation failure and miscarriage. RNA-Seq investigations of the embryo in the early stages of preimplantation indicate that with the gradual replacement of the embryonic profile and the reduction of the oocyte residues, the gene expression profile in the blastocyst is more dependent on the embryo’s genome. A recent study by comparing the gene expression profile of euploid blastocysts and specific aneuploidies such as trisomy 21, trisomy 18, XXY and XO syndromes using RNA-Seq, showed how the type of aneuploidy might affect gene expression. Study design, size, duration This study was conducted on surplus embryos of the patients with history of recurrent implantation failure or recurrent miscarriage following PGT by Day-5 trophectoderm biopsy. Inclusion criteria involved maternal age ≤37, normal parental karyotypes, and ovulation by long stimulation protocol. As advanced maternal age and ovarian stimulation method can affect the aneuploidy rate and expression profile, embryos belonging to mothers > 37 years and included only patients with the long stimulation protocol were excluded. Participants/materials, setting, methods The normal embryos and those with single aneuploidy were selected for comparison of gene expression profiles using RNA sequencing. The single aneuploid embryos were classified in two groups: with defined aneuploidy(DA) of small chromosomes (including chromosomes 16, 20, 21, 22), and with undefined aneuploidy(UA) as single aneuploids for other chromosomes. To neutralize the effect of genomic content on gene expression profile in DA group, embryos were pooled reciprocally (trisomy and monosomy for the same chromosome). Main results and the role of chance Principal Component Analysis (PCA) validated embryos classification considering their differentially expressed genes (DEG) clustering into three distinct groups. To minimize the role of chance, only genes with significant adjusted P-values in both STAR and Hisat data analyses were included in consequent interpretations. In addition to comparison between and among the DA, UA and normal groups, the entire set of aneuploid groups was compared with the normal group. The DEG in both aneuploid groups compared to the normal group represented eminent upregulation rather than downregulation. Gene Ontology analyses indicated an upregulation of transcription, ubiquitination, autophagy, mitochondrial, chromosome segregation and DNA repair pathways in both DA and UA compared to normal group. Overexpression of the DNA repair pathway and other validated genes of interest in aneuploid embryos was in agreement with qPCR findings. Translation and protein synthesis pathways also showed overexpression as part of the functional response to aneuploidy. Upregulation of apoptotic process pathway was evident in the UA group. While comparison of gene expression between DA and UA showed overexpression of 143 genes, but cellular lipid synthesis was the only pathway with a significant difference. The distribution of DEG on chromosomes in the DA group was not associated with selected aneuploidies. Limitations, reasons for caution The number of biological replicates in each category was limited in order to provide more confident data by minimizing the time interval between providing the samples and RNA sequencing. Larger studies might change some affected pathways due to differences in identified DEG. Wider implications of the findings This study shed light on the black box of human preimplantation aneuploidy. Considering that the transcriptome is affected by the genomic status and some debates on genomic based current PGT approaches, this study is a step for selection of healthy and viable embryos by revealing the molecular mechanisms. Trial registration number not applicable

O-030 The impact of aneuploidy on human peri-implantation development: findings from the extended in vitro culture of 191 human embryos

Abstract Study question How does aneuploidy affect lineage specification and the developmental potential of human embryos cultured up to 12 days post fertilization (D12)? Summary answer While distinct types of aberrations carry their own risk of embryonic arrest, prevailing aneuploidies appear to compromise lineage specification beyond the blastocyst stage of development. What is known already Chromosomal instability is a hallmark of human preimplantation development, with up to 50% of embryos diagnosed as aneuploid following preimplantation genetic testing (PGT). Aneuploidies are a major cause of implantation failure, pregnancy loss and human congenital defects. Yet despite their clinical relevance, the impact of distinct aberrations on early human development remains poorly understood. Innovative platforms for culturing human embryos up to D12 provide an important opportunity for investigating chromosomal instability. Understanding the effects of specific aneuploidies on human peri-implantation development will be key for advancing human embryo research and improving the interpretation of findings from in vitro embryo models. Study design, size, duration A total of 191 PGT blastocysts obtained from 103 patients were included in the study. Blastocysts were selected based on their original diagnosis, including embryos with single whole-chromosome aneuploidies (single trisomies, n = 37 and single monosomies, n = 71), single segmental aberrations (n = 22), embryos with complex chromosomal constitutions (two or more abnormalities, n = 44), as well as control euploid embryos (n = 17). Participants/materials, setting, methods Vitrified blastocysts were warmed and cultured up to D12 using an optimized protocol to generate embryo outgrowths. We correlated the original PGT diagnoses to developmental outcomes, including outgrowth viability, morphology and outgrowth size. We evaluated blastocyst quality using the Gardner grading system. Following culture, we immunostained 38 viable outgrowths for lineage-specific markers, including OCT4 (epiblast), GATA6 (hypoblast) and CK-7 (trophoblast). Fisher’s exact test was used for statistical analysis (p < 0.05 was considered significant). Main results and the role of chance Following extended culture, 43.5% of embryos remained viable and attached, while 56.5% degenerated and detached. No significant correlation was found between embryo grade and attachment rate. Euploid embryos exhibited the highest attachment rate, with 88.2% (15/17) forming viable outgrowths. Euploid embryos also generated significantly larger outgrowths than trisomic and monosomic embryos (p = 0.01). Embryos diagnosed with trisomies and segmental aberrations exhibited attachment rates comparable to euploid embryos, at 70.3% (p = 0.18) and 68.2% (p = 0.25), respectively. However, embryos with monosomies and complex chromosomal constitutions arrested more readily (28.2% and 15.9% viable, <0.00001, respectively). All euploid embryos (6/6) retained a discernible OCT4+ epiblast-like structure. This was similar to embryos with segmental aberrations and trisomies, with 75% (3/4) and 53.8% (7/13) of outgrowths containing OCT4+ cells, respectively. Nonetheless, distinct trisomies exerted varying effects on peri-implantation development in vitro. For instance, viable trisomies (13, 18, 21) developed similarly to euploid embryos, while outgrowths carrying a trisomy 22 had fewer OCT4+ cells (p = 0.02) and a higher number of GATA6+ cells (p < 0.01), suggesting a potential lineage proliferation defect. Monosomies had the most profound effects on development. Compared to euploid embryos, monosomic embryos formed significantly fewer OCT4+ outgrowths (28.6%, p = 0.02) and contained fewer epiblast (p < 0.0001) and hypoblast-like (p = 0.003) cells. Limitations, reasons for caution The limited number of embryos in certain groups warrants careful interpretation. The central drawback of the models is that embryo outgrowths are predominately flattened, which confounds identification of three-dimensional structures formed during normal embryogenesis. Future studies should encompass additional lineage specification markers and potential culture refinements to enhance our interpretation. Wider implications of the findings Our findings underscore the critical importance of reporting the chromosomal composition of human embryos utilized for research. This practice will enable a more nuanced interpretation of results from in vitro embryo models and ultimately advance our capabilities in human embryo research. Trial registration number not applicable

Abstract PR016: Investigating vulnerabilities associated with chromosome arm aneuploidy in cancer

Abstract Aneuploidy – loss or gain of whole chromosomes or chromosome arms, is rare and poorly tolerated in normal cells but occurs in ∼90% of solid tumors; however, the mechanisms through which specific aneuploidies affect cancer development are unclear. Additionally, generating mammalian models of specific chromosome arm alterations is technically difficult, limiting further study. Cancers have tumor, cell, and tissue type-specific patterns of chromosome arm copy-number alterations that influence tumor evolution and sensitivity to anti-cancer therapies. Squamous cell carcinomas (SCCs) affecting lung, head and neck, esophageal, and cervical tissues have been shown to feature conserved early losses and gains of arms 3p and 3q, respectively, and are associated with relatively few oncogenic drivers and treatment options. These aneuploidies are particularly well established in lung SCC and have been shown to promote tumorigenesis, metastasis, and poor prognosis. To study cancer vulnerabilities associated with chromosome 3 arm aneuploidies, we used CRISPR-Cas9 to delete a 3p copy in human immortalized lung epithelial cell lines—the lung SCC cell-of-origin. A subset of clones duplicated a wild type chromosome 3 copy, transitioning to 3q gain and providing us with independent models for chromosome 3 wild type, 3p loss, and 3q gain. Next, we performed a CRISPRi screen and found that 3q gain cells are more sensitive to knockdown of sterol regulatory element-binding factor 1 (SREBF1)—a master regulator of cholesterol and fatty acid biosynthesis, its co-factor SREBP cleavage activating protein (SCAP), and downstream target HMG-CoA reductase (HMGCR)—the rate-limiting enzyme for cholesterol synthesis. 3q gain cells also showed up-regulated fatty acid metabolites, ceramides, triglycerides, and phosphatidylinositols. After performing a chemical screen, 3q gain cells showed reduced proliferation, increased apoptosis, and DNA damage in response to statins (HMGCR inhibitors). Statins have previously been shown to induce tumor-specific apoptosis and reduced cancer risk, although these studies have associated with variable efficacy and underlying mechanisms. We hypothesize that 3q gain is a biomarker of statin response and sensitivity in squamous cancers. We aim to study the mechanism through which aneuploidy alters lipid metabolism and contributes to cancer. Investigating aneuploidy-induced vulnerabilities will help us understand how cancers exploit aneuploidies to promote tumorigenesis and to elucidate novel and specific therapeutic targets for cancers with shared copy-number profiles. Citation Format: Nadja Zhakula-Kostadinova, Sejal Jain, Laura Byron, Matthew L. Meyerson, Alison M. Taylor. Investigating vulnerabilities associated with chromosome arm aneuploidy in cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Expanding and Translating Cancer Synthetic Vulnerabilities; 2024 Jun 10-13; Montreal, Quebec, Canada. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(6 Suppl):Abstract nr PR016.

Aneuploidy Can Be an Evolutionary Diversion on the Path to Adaptation.

Aneuploidy is common in eukaryotes, often leading to decreased fitness. However, evidence from fungi and human tumur cells suggests that specific aneuploidies can be beneficial under stressful conditions and facilitate adaptation. In a previous evolutionary experiment with yeast, populations evolving under heat stress became aneuploid, only to later revert to euploidy after beneficial mutations accumulated. It was therefore suggested that aneuploidy is a "stepping stone" on the path to adaptation. Here, we test this hypothesis. We use Bayesian inference to fit an evolutionary model with both aneuploidy and mutation to the experimental results. We then predict the genotype frequency dynamics during the experiment, demonstrating that most of the evolved euploid population likely did not descend from aneuploid cells, but rather from the euploid wild-type population. Our model shows how the beneficial mutation supply-the product of population size and beneficial mutation rate-determines the evolutionary dynamics: with low supply, much of the evolved population descends from aneuploid cells; but with high supply, beneficial mutations are generated fast enough to outcompete aneuploidy due to its inherent fitness cost. Our results suggest that despite its potential fitness benefits under stress, aneuploidy can be an evolutionary "diversion" rather than a "stepping stone": it can delay, rather than facilitate, the adaptation of the population, and cells that become aneuploid may leave less descendants compared to cells that remain diploid.

Human Tumor Cells Display an Oncogene-like Addiction to Aneuploidy.

Tumor cells exhibit oncogene-like dependencies on specific aneuploidy events that span cancer types.

Oncogene-like addiction to aneuploidy in human cancers.

Most cancers exhibit aneuploidy, but its functional significance in tumor development is controversial. Here, we describe ReDACT (Restoring Disomy in Aneuploid cells using CRISPR Targeting), a set of chromosome engineering tools that allow us to eliminate specific aneuploidies from cancer genomes. Using ReDACT, we created a panel of isogenic cells that have or lack common aneuploidies, and we demonstrate that trisomy of chromosome 1q is required for malignant growth in cancers harboring this alteration. Mechanistically, gaining chromosome 1q increases the expression of MDM4 and suppresses p53 signaling, and we show that TP53 mutations are mutually exclusive with 1q aneuploidy in human cancers. Thus, tumor cells can be dependent on specific aneuploidies, raising the possibility that these "aneuploidy addictions" could be targeted as a therapeutic strategy.

Targeted assembly of ectopic kinetochores to induce chromosome‐specific segmental aneuploidies

Cancer cells display persistent underlying chromosomal instability, with individual tumour types intriguingly exhibiting characteristic subsets of whole, and subchromosomal aneuploidies. Few methods to induce specific aneuploidies will exist, hampering investigation of functional consequences of recurrent aneuploidies, as well as the acute consequences of specific chromosome mis‐segregation. We therefore investigated the possibility of sabotaging the mitotic segregation of specific chromosomes using nuclease‐dead CRISPR‐Cas9 (dCas9) as a cargo carrier to specific genomic loci. We recruited the kinetochore‐nucleating domain of centromere protein CENP‐T to assemble ectopic kinetochores either near the centromere of chromosome 9, or the telomere of chromosome 1. Ectopic kinetochore assembly led to increased chromosome instability and partial aneuploidy of the target chromosomes, providing the potential to induce specific chromosome mis‐segregation events in a range of cell types. We also provide an analysis of putative endogenous repeats that could support ectopic kinetochore formation. Overall, our findings provide new insights into ectopic kinetochore biology and represent an important step towards investigating the role of specific aneuploidy and chromosome mis‐segregation events in diseases associated with aneuploidy.

A kinesin‐based approach for inducing chromosome‐specific mis‐segregation in human cells

Various cancer types exhibit characteristic and recurrent aneuploidy patterns. The origins of these cancer type‐specific karyotypes are still unknown, partly because introducing or eliminating specific chromosomes in human cells still poses a challenge. Here, we describe a novel strategy to induce mis‐segregation of specific chromosomes in different human cell types. We employed Tet repressor or nuclease‐dead Cas9 to link a microtubule minus‐end‐directed kinesin (Kinesin14VIb) from Physcomitrella patens to integrated Tet operon repeats and chromosome‐specific endogenous repeats, respectively. By live‐ and fixed‐cell imaging, we observed poleward movement of the targeted loci during (pro)metaphase. Kinesin14VIb‐mediated pulling forces on the targeted chromosome were counteracted by forces from kinetochore‐attached microtubules. This tug‐of‐war resulted in chromosome‐specific segregation errors during anaphase and revealed that spindle forces can heavily stretch chromosomal arms. By single‐cell whole‐genome sequencing, we established that kinesin‐induced targeted mis‐segregations predominantly result in chromosomal arm aneuploidies after a single cell division. Our kinesin‐based strategy opens the possibility to investigate the immediate cellular responses to specific aneuploidies in different cell types; an important step toward understanding how tissue‐specific aneuploidy patterns evolve.

Adaptation to spindle assembly checkpoint inhibition through the selection of specific aneuploidies.

Both the presence of an abnormal complement of chromosomes (aneuploidy) and an increased frequency of chromosome missegregation (chromosomal instability) are hallmarks of cancer. Analyses of cancer genome data have identified certain aneuploidy patterns in tumors; however, the bases behind their selection are largely unexplored. By establishing time-resolved long-term adaptation protocols, we found that human cells adapt to persistent spindle assembly checkpoint (SAC) inhibition by acquiring specific chromosome arm gains and losses. Independently adapted populations converge on complex karyotypes, which over time are refined to contain ever smaller chromosomal changes. Of note, the frequencies of chromosome arm gains in adapted cells correlate with those detected in cancers, suggesting that our cellular adaptation approach recapitulates selective traits that dictate the selection of aneuploidies frequently observed across many cancer types. We further engineered specific aneuploidies to determine the genetic basis behind the observed karyotype patterns. These experiments demonstrated that the adapted and engineered aneuploid cell lines limit CIN by extending mitotic duration. Heterozygous deletions of key SAC and APC/C genes recapitulated the rescue phenotypes of the monosomic chromosomes. We conclude that aneuploidy-induced gene dosage imbalances of individual mitotic regulators are sufficient for altering mitotic timing to reduce CIN.

Preprint Highlight: A motor-based approach to induce chromosome-specific mis-segregations in human cells.

Aneuploidy, a key hallmark of cancer cells, is caused by chromosome missegregation. Correct chromosome alignment in the mitotic spindle depends on the action of microtubule plus-end directed motors. However tools to induce missegregation of specific chromosomes of interest in human cells are limited. The authors demonstrate targeting of a microtubule minus-end directed motor to specific chromosomes to move them away from the metaphase plate. This inducible chromosome misalignment leads to lagging chromosomes during telophase and missegregation of chromosomes into daughter cells, resulting in copy number alterations after a single cell division. This new method will enable researchers to link specific aneuploidies to subsequent changes in cellular physiology and study how these chromosomal instabilities contribute to the development of diseases like cancer.

Nuclear chromosome locations dictate segregation error frequencies

Chromosome segregation errors during cell divisions generate aneuploidies and micronuclei, which can undergo extensive chromosomal rearrangements such as chromothripsis1–5. Selective pressures then shape distinct aneuploidy and rearrangement patterns—for example, in cancer6,7—but it is unknown whether initial biases in segregation errors and micronucleation exist for particular chromosomes. Using single-cell DNA sequencing8 after an error-prone mitosis in untransformed, diploid cell lines and organoids, we show that chromosomes have different segregation error frequencies that result in non-random aneuploidy landscapes. Isolation and sequencing of single micronuclei from these cells showed that mis-segregating chromosomes frequently also preferentially become entrapped in micronuclei. A similar bias was found in naturally occurring micronuclei of two cancer cell lines. We find that segregation error frequencies of individual chromosomes correlate with their location in the interphase nucleus, and show that this is highest for peripheral chromosomes behind spindle poles. Randomization of chromosome positions, Cas9-mediated live tracking and forced repositioning of individual chromosomes showed that a greater distance from the nuclear centre directly increases the propensity to mis-segregate. Accordingly, chromothripsis in cancer genomes9 and aneuploidies in early development10 occur more frequently for larger chromosomes, which are preferentially located near the nuclear periphery. Our findings reveal a direct link between nuclear chromosome positions, segregation error frequencies and micronucleus content, with implications for our understanding of tumour genome evolution and the origins of specific aneuploidies during development.

EP446: High rates of ‘atypical’ panorama noninvasive prenatal screening results among consanguineous Arab American women

Panorama is one of the most accurate and commonly used methods of cell free DNA noninvasive prenatal screening (NIPS). The results are reported as either high risk for a specific aneuploidy, high risk due to fetal fraction, insufficient fetal DNA, atypical, high risk, or no results. It is the only form of NIPS that uses a single nucleotide polymorphism (SNP) method, representing genetic changes that are present in over 1% of the general population, to screen for common fetal aneuploidies and microdeletion syndromes.

O-085 In-depth analysis of embryo development: Differences among monosomic, trisomic and chromosomally chaotic embryos compared to euploid embryos

Abstract Study question Is there any visible variation in the development of aneuploid embryos depending on the type of chromosome abnormality? Summary answer There were significant visible differences in the development of euploid, monosomic, trisomic and, especially, chaotic embryos. What is known already Aneuploidy rates are remarkably high in in vitro fertilized human embryos, with up to 50% of embryos diagnosed as aneuploid based on preimplantation genetic testing for aneuploidies (PGT-A). However, very little is known about the impact of specific aneuploidies during the early human embryo development. A recent publication showed that embryos with single chromosomal gain or loss reached the blastocyst stage later or earlier depending on the chromosome affected (Shahbazi et al., 2020). In our study, we wanted to detect observable differences in embryo behavior between embryos with different chromosomal abnormalities during the entire in vitro development. Study design, size, duration This was a retrospective study including 2,500 blastocysts with PGT-A results. Embryos were cultured in EmbryoScope systems until the fifth/sixth day of development (up to the time of trophectoderm biopsy). Automatic-annotations for division times and quality gradings were supervised routinely by senior embryologists using Guided Annotations Tool. Out of the total, 1,000 were euploid embryos used for reference and 1,500 were aneuploid embryos with one or more defects, including monosomic, trisomic and chromosomally chaotic embryos. Participants/materials, setting, methods Chromosome analysis was performed using next-generation sequence technology. Then, an in-depth analysis of time-lapse videos and supervised-automatic annotations was performed. We calculated the proportion of embryos, in each aneuploid category, that reached one specific event later than the expected value for euploid embryos plus one standard deviation. Later, we calculated the “relative risk” of an embryo of reaching the milestone late. We did the same for the time between milestones and for pairs of milestones. Main results and the role of chance Every aneuploid category was more likely to reach each specific embryo developmental event later than euploid embryos and the time gaps between developmental milestones were also statistically longer in aneuploid embryos (p < 0.0001). The following results were the most interesting relative risks (RR) when we compared the proportion of embryos (in each aneuploid category) to the proportion of euploid embryos (RR for euploid = 1). For reaching the division time to two cells (t2): 1.31 in monosomic embryos, 1.50 in trisomic embryos and 2.43 in chaotic embryos. For the division time to four cells (t4): 1.42 in monosomic embryos, 1.54 in trisomic embryos and 3.07 in chaotic embryos. For the division time to eight cells (t8) and the time of starting blastulation: 1.45 in monosomic embryos, 1.22 in trisomic embryos and 2.74 in chaotic embryos. Combined milestones were stronger indicators than each milestone by itself, the RR were: 1.63 in monosomic embryos, 1.81 in trisomic embryos and 3.35 in chaotic embryos for t2 and t4; 1.50 in monosomic embryos, 1.80 in trisomic embryos and 2.84 in chaotic embryos for t2 and t8; 1.46 in monosomic embryos, 1.90 in trisomic embryos and 3.43 in chaotic embryos for t4 and t8. Limitations, reasons for caution At this stage, we did not go down to specific chromosome abnormality as there were very few cases in each fully detailed category. Also, not all the embryos reached every developmental milestone. Wider implications of the findings Aneuploid embryos were significantly different from euploid embryos in the first five days of development. A large proportion of aneuploid embryos could be rejected because their developmental milestones falling outside the normal range. This could form part of an automated system for determining euploidy/aneuploidy from observation of embryos in vitro. Trial registration number 1902-VLC-018-MM

Abstract 2135: Functional models of chromosome arm aneuploidies in lung squamous cell carcinoma

Abstract Aneuploidy, which we define as whole chromosome or chromosome arm copy number imbalance, is a near-universal characteristic of human cancers. Cancer subtypes are often characterized by tumor specific patterns of chromosome arm copy number alterations; for example, squamous cell carcinomas (SCCs) from different tissues of origin (including lung, head and neck, esophagus, and bladder) have a pattern of chromosome 3p loss and chromosome 3q gain. Although these alterations are frequent, they are not well understood due to difficulty in modeling specific aneuploidy alterations in the matching cell type. However, recent advances in genome engineering allow generation of large chromosomal alterations. We used the CRISPR-Cas9 system to delete one copy of chromosome 3p in human immortalized lung epithelial cells most similar to upper airway basal cells. Deletion of chromosome 3p was validated by whole genome sequencing and karyotyping. Consistent with patient data, expression of 3p genes was decreased upon deletion, as well as increased expression of interferon response genes. Phenotypic characterization revealed that cells with chromosome 3p deletion initially proliferated more slowly than their siblings. These chromosome 3p deleted cells had increased G1 arrest but did not undergo increased apoptosis or cell death. Interestingly, after several passages in culture, the proliferation defect was rescued in chromosome 3p deleted cells. Genome sequencing and karyotype analyses found that evidence of chromosome 3 duplication, transitioning the cell to a state of chromosome 3q gain. We isolated sibling cells with chromosome 3p deletion or chromosome 3q gain and demonstrated that duplication of chromosome 3 could indeed rescue proliferation rates. With our cellular model of chromosome arm-level aneuploidy, we uncovered a selection mechanism that allowed aneuploidy tolerance in vitro, and a possible explanation for joint alteration of both arms of chromosome 3. In conclusion, our genome engineering approach to model chromosome arm-level deletions provides a robust model that will address a gap in our understanding of aneuploidy in cancer. Citation Format: Alison Marie Taylor, Sejal Jain, Juliann Shih, Andrew D. Cherniack, Rameen Beroukhim, Matthew Meyerson. Functional models of chromosome arm aneuploidies in lung squamous cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2135.

Developmental potential of aneuploid human embryos cultured beyond implantation

Aneuploidy, the presence of an abnormal number of chromosomes, is a major cause of early pregnancy loss in humans. Yet, the developmental consequences of specific aneuploidies remain unexplored. Here, we determine the extent of post-implantation development of human embryos bearing common aneuploidies using a recently established culture platform. We show that while trisomy 15 and trisomy 21 embryos develop similarly to euploid embryos, monosomy 21 embryos exhibit high rates of developmental arrest, and trisomy 16 embryos display a hypo-proliferation of the trophoblast, the tissue that forms the placenta. Using human trophoblast stem cells, we show that this phenotype can be mechanistically ascribed to increased levels of the cell adhesion protein E-CADHERIN, which lead to premature differentiation and cell cycle arrest. We identify three cases of mosaicism in embryos diagnosed as full aneuploid by pre-implantation genetic testing. Our results present the first detailed analysis of post-implantation development of aneuploid human embryos.

Aneuploid embryo transfer: clinical policies and provider opinions at United States fertility clinics

To describe institutional clinical policies and individual provider opinions regarding aneuploid embryo transfer (aET). A survey about clinical policies was electronically sent to Society for Assisted Reproductive Technology (SART) member laboratory directors, and a separate survey about personal opinions was electronically sent to all SART members. Not applicable. Patients pursuing preimplantation genetic testing for aneuploidy (PGT-A). Not applicable. Current clinical policies about aET were described. Individual provider opinions about aET in the context of specific aneuploidies and mosaicism were also described. A total of 48 laboratory directors and 212 individual providers responded to their respective surveys. Twelve (25%) clinics report that they do not have a policy regarding aET, but clinics performing PGT-A in >100 cycles per year were more likely to have a policy. Half of the individual providers agree that an embryo with trisomy 21 should be available for aET, but most disagreed with aET of embryos with other aneuploidies and most were either unsure about or unwilling to transfer embryos with mosaicism. Those who worked in primarily patient-facing roles held more agreeable opinions regarding aET. There is no consensus regarding ideal clinical policies for aET. The wide range of current clinical practices and individual provider opinions regarding under what circumstances, if any, aET should be available to patients indicates that this is a divisive issue among ART providers, and there is a clear need for specific professional guidelines to address this issue.

Single-Chromosomal Gains Can Function as Metastasis Suppressors and Promoters in Colon Cancer.

High levels of cancer aneuploidy are frequently associated with poor prognosis. To examine the relationship between aneuploidy and cancer progression, we analyzed a series of congenic cell lines that harbor single extra chromosomes. We found that across 13 different trisomic cell lines, 12 trisomies suppressed invasiveness or were largely neutral, while a single trisomy increased metastatic behavior by triggering a partial epithelial-mesenchymal transition. In contrast, we discovered that chromosomal instability activates cGAS/STING signaling but strongly suppresses invasiveness. By analyzing patient copy-number data, we demonstrate that specific aneuploidies are associated with distinct outcomes, and the acquisition of certain aneuploidies is in fact linked with a favorable prognosis. Thus, aneuploidy is not a uniform driver of malignancy, and different aneuploidies can uniquely influence tumor progression. At the same time, the gain of a single chromosome is capable of inducing a profound cell state transition, thereby linking genomic plasticity, phenotypic plasticity, and metastasis.

A natural histone H2A variant lacking the Bub1 phosphorylation site and regulated depletion of centromeric histone CENP-A foster evolvability in Candida albicans.

Eukaryotes have evolved elaborate mechanisms to ensure that chromosomes segregate with high fidelity during mitosis and meiosis, and yet specific aneuploidies can be adaptive during environmental stress. Here, we identify a chromatin-based system required for inducible aneuploidy in a human pathogen. Candida albicans utilizes chromosome missegregation to acquire tolerance to antifungal drugs and for nonmeiotic ploidy reduction after mating. We discovered that the ancestor of C. albicans and 2 related pathogens evolved a variant of histone 2A (H2A) that lacks the conserved phosphorylation site for kinetochore-associated Bub1 kinase, a key regulator of chromosome segregation. Using engineered strains, we show that the relative gene dosage of this variant versus canonical H2A controls the fidelity of chromosome segregation and the rate of acquisition of tolerance to antifungal drugs via aneuploidy. Furthermore, whole-genome chromatin precipitation analysis reveals that Centromere Protein A/ Centromeric Histone H3-like Protein (CENP-A/Cse4), a centromeric histone H3 variant that forms the platform of the eukaryotic kinetochore, is depleted from tetraploid-mating products relative to diploid parents and is virtually eliminated from cells exposed to aneuploidy-promoting cues. We conclude that genetically programmed and environmentally induced changes in chromatin can confer the capacity for enhanced evolvability via chromosome missegregation.

PAX5 biallelic genomic alterations define a novel subgroup of B-cell precursor acute lymphoblastic leukemia.

Chromosomal rearrangements and specific aneuploidy patterns are initiating events and define subgroups in B-cell precursor acute lymphoblastic leukemia (BCP-ALL). Here we analyzed 250 BCP-ALL cases and identified a novel subgroup ('PAX5-plus', n = 19) by distinct DNA methylation and gene expression profiles. All patients in this subgroup harbored mutations in the B-lineage transcription factor PAX5, with p.P80R as hotspot. Mutations either affected two independent codons, consistent with compound heterozygosity, or suffered LOH predominantly through chromosome 9p aberrations. These biallelic events resulted in disruption of PAX5 transcriptional programs regulating B-cell differentiation and tumor suppressor functions. Homozygous CDKN2A/B deletions and RAS-activating hotspot mutations were highly enriched as cooperating events in the genomic profile of PAX5-plus ALL. Together, this defined a specific pattern of triple alterations, exclusive to the novel subgroup. PAX5-plus ALL was observed in pediatric and adult patients. Although restricted by the limited sample size, a tendency for more favorable clinical outcome was observed, with 10 of 12 adult PAX5-plus patients achieving long-term survival. PAX5-plus represents the first BCP-ALL subgroup defined by sequence alterations in contrast to gross chromosomal events and exemplifies how deregulated differentiation (PAX5), impaired cell cycle control (CDKN2A/B) and sustained proliferative signaling (RAS) cooperatively drive leukemogenesis.

Whole Transcriptome RNA Sequencing As a Comprehensive Diagnostic Tool for Acute Myeloid Leukemia

IntroductionAcute myeloid leukemia (AML) is characterized by uncontrolled proliferation of malignant myeloid progenitor cells in the bone marrow that are arrested in differentiation. In AML, genetic aberrations often involve the same genes and play an important role in risk assessment and treatment of AML. In the WHO classification 2016 (Arber et al., Blood 2016), nine AML subtypes of clinical and prognostic importance are distinguished by distinct and practically mutually exclusive mutations, covering 50-60% of AML cases. By analysing an extended panel of genes, Papaemmanuil et al. (NEJM 2016) developed a purely genomic classification of AML. In this system, 11 groups are defined including 6 entities characterized by chromosomal translocations. Similar as in WHO 2016, these 6 entities each account for less than 5% of AML and are identified by metaphase cytogenetics. Of these 6 entities, 5 groups are defined by fusion genes and one group by inv(3)/t(3;3) leading to overexpression of EVI1. The 5 remaining classes include 4 entities with cytogenetically normal AML defined by mutations in NPM1 (27%), bi-allelic CEBPA (4%), genes regulating RNA splicing, chromatin or transcription (18%) and IDH2 R172 mutations (1%) and one entity characterized by mutations in TP53, a complex karyotype or specific aneuploidies (13%). Although the majority of patients can be classified by this new system, 15% of patients still lack class-defining lesions and expression levels of structurally normal genes, which can also have a decisive prognostic impact, are not considered. We propose that whole transcriptome messenger RNA sequencing provides a single and flexible platform to identify the diversity of genetic aberrations relevant for classification of AML.MethodsA panel of hundred AML were analysed and HAMLET (Human AMLExpedited Transcriptomics) was developed as bioinformatics pipeline to detect fusion genes, small variants in thirteen genes, long tandem duplications in FLT3 and KMT2A and overexpression of EVI1. In HAMLET, a new algorithm based on soft clipped reads was developed to detect long tandem repeats in FLT3 and KMT2A. All genetic aberrations called by HAMLET were validated by diagnostic data and targeted re-sequencing.ResultsThe data showed that HAMLET correctly called all genetic aberrations relevant for current classification of AML with high sensitivity and specificity. Moreover, the new soft clipped approach that has been integrated in HAMLET proved to be useful not only to detect long tandem duplications in FLT3 and KMT2A, but also to determine the allelic ratio of mutant-to-wild type FLT3, which is predictive for overall survival. By filtering small variants for predicted importance according to large AML sequencing data sets (Jaiswal et al., NEJM 2017), we classified the 100 AML according to genomic classification and showed that 87 cases were classified in single entities, 4 cases in two subgroups and 9 cases had no class-defining lesions. Of the 9 cases without class-defining lesions, 8 cases had detectable driver mutations and one case had no detectable driver mutation. These numbers perfectly match percentages reported by Papaemmanuil et al. (NEJM 2016). Apart from genetic aberrations that are relevant for current classification of AML, HAMLET also identified additional abnormalities. Of particular interest is NUP98-NSD1 (Hollink et al., Blood 2011), a cryptic fusion gene that is missed by metaphase cytogenetics in three AML with no class-defining lesions, and EVI1 overexpression in 5 cases without inv(3)/t(3;3) including three KMT2A-rearranged AML with extremely poor prognosis (Groschel et al., JCO 2013).ConclusionsHAMLET correctly called all genetic aberrations relevant for current classification of AML and provides a wealth of additional information with potential consequences for patient management. In conclusion, HAMLET is a comprehensive and reliable pipeline for RNA sequence analysis that may contribute to better risk assessment and personalized treatment of AML. DisclosuresBorras:GenomeScan B.V.: Employment. Janssen:GenomeScan B.V.: Employment.