Structural Chromosomal Alterations Research Articles

P-249 Morphokinetic parameters comparison between balanced and unbalanced embryos from patients with structural chromosome abnormalities

Abstract Study question Are there morphokinetic differences between balanced and unbalanced embryos after PGT-SR? Summary answer The total time embryos remain at the morula stage (TiCAV- TM) could be a morphokinetic marker to consider in PGT-SR cycles. What is known already Due to the preimplantation genetic testing for structural rearrangements (PGT-SR) it is possible to identify embryos with an excess or defect of genetic material associated with a parental structural rearrangement. This technique is suitable for patients with a normal phenotype but a balanced chromosomal rearrangement. These patients have a higher risk of spontaneous abortion, as well as higher aneuploidy rates. Within structural chromosomal alterations, translocations are the most common presentation of chromosomal rearrangement. Study design, size, duration Within this multicentre retrospective study, we evaluated 133 embryos, from 39 cycles in which one of the partners had a karyotype with balanced reciprocal or Robertsonian translocations, from January 2021 to September 2023. After PGT-SR was carried out, we obtained 40 balanced embryos and 93 unbalanced embryos. Participants/materials, setting, methods We compared the conventional morphokinetic parameters and the duration of each state between two groups after PGT-SR samples were analysed. All embryos were cultured in Geri® time-lapse incubators, and underwent embryo biopsy on day 5-7. Statistical analysis was conducted using R software (v.4.3.1), including the following confounding variables: origin of karyotype alteration (maternal or paternal), type of translocation (Robertsonian or reciprocal), female and male gamete age, type of oocyte (fresh or frozen) and oocyte origin. Main results and the role of chance We observed that the mean age of the oocyte was significantly higher in the unbalanced embryos compared to the balanced ones (32.85±5.32 years vs.30.45±5.01 years). In terms of the altered karyotype, the paternal origin is more prevalent than the maternal one (60.9% vs. 39.1%). Regarding the type of translocation, reciprocal translocation is more predominant than Robertsonian translocation (83.5% vs. 16.5%) in our study population. When comparing morphokinetic parameters between both groups, we observed that unbalanced embryos tend to reach an expanded blastocyst stage later than balanced embryos (107.62±10.02h vs. 102.48±8.87h, respectively; p = 0.008, corrected p-value=0.186). We observed the same tendency with hatching initiation time (110.64±10.49h vs. 105.91±9.38h; p = 0.013, corrected p-value=0.296). We observed that unbalanced embryos have a slower development than balanced embryos (TiCAV-TFB 10.10±4.46h vs. 8.35±3.79h; p = 0.006, corrected p-value=0.437; TiH-TiCAV 13.03±5.98h vs. 11.79±5.50h; p = 0.017, corrected p-value=0.816). We did observe significant differences in total time at morula stage (TiCAV – TM) when comparing unbalanced and balanced embryos (12.60±6.94 vs. 8.88±5.65; p = 0.003, corrected p-value=0.001). Limitations, reasons for caution A higher number of embryos should be evaluated in order to enhance the statistical power of this study, as there is an important difference in sample size between balanced and unbalanced embryos in the PGT-SR cycles included in this study. Wider implications of the findings Further morphokinetic study of embryos from patients with structural chromosomal abnormalities can open up new lines of research and can help us to predict the final outcome of the cycle, accompanied by a genetic study. Trial registration number Not applicable

New Cytogenetic Data for the Neottieae Tribe (Orchidaceae) in the Mediterranean Region.

This work presents a summary of cytogenetic data, including new information, on several species within the tribe Neottieae, with an update of the karyotype for 23 species belonging to the genera Cephalanthera, Limodorum, Epipactis, and Neottia (including Listera). Each of these four genera also presents distinctive chromosomal features, such as bimodal karyotypes. Our research includes insights into the distribution of constitutive heterochromatin, measured using C-banding and, in some cases, specific fluorochromes for the detection of A-T- and G-C-rich DNA. In the Epipactis group, it is noteworthy that when using the Giemsa banding technique, certain species (e.g., E. placentina, E. meridionalis) with a chromosome number of 2n = 38 were observed to exhibit a conspicuous wide band of constitutive heterochromatin on the long arm of the third pair in a subcentromeric position, resembling what has been observed in E. helleborine. These differences also have the potential to contribute to the diversification of these species. Based on the karyological results obtained, a hypothesis regarding the origin of certain species within the E. helleborine group is proposed. Additionally, karyological analyses conducted on a specimen of E. microphylla revealed chromosome counts ranging from 36 to 40. Somatic metaphases exhibited evident structural alterations in certain chromosomes, showing rearrangements probably caused by translocation phenomena. Based on the data obtained from the species within the studied genera, it is conceivable that variations in chromosomes, both structurally and in the distribution of constitutive heterochromatin, exert a significant influence on the evolution of the karyotype. Moreover, in many entities belonging to the Neottieae tribe, these processes may also contribute to the diversification of the phenotype in some instances.

3D genomic analysis reveals novel enhancer-hijacking caused by complex structural alterations that drive oncogene overexpression.

Cancer genomes are composed of many complex structural alterations on chromosomes and extrachromosomal DNA (ecDNA), making it difficult to identify non-coding enhancer regions that are hijacked to activate oncogene expression. Here, we describe a 3D genomics-based analysis called HAPI (Highly Active Promoter Interactions) to characterize enhancer hijacking. HAPI analysis of HiChIP data from 34 cancer cell lines identified enhancer hijacking events that activate both known and potentially novel oncogenes such as MYC, CCND1 , ETV1 , CRKL , and ID4 . Furthermore, we found enhancer hijacking among multiple oncogenes from different chromosomes, often including MYC , on the same complex amplicons such as ecDNA. We characterized a MYC - ERBB2 chimeric ecDNA, in which ERBB2 heavily hijacks MYC 's enhancers. Notably, CRISPRi of the MYC promoter led to increased interaction of ERBB2 with MYC enhancers and elevated ERBB2 expression. Our HAPI analysis tool provides a robust strategy to detect enhancer hijacking and reveals novel insights into oncogene activation.

Abstract 6599: 3D genomic analysis reveals novel enhancer hijacking mechanisms caused by complex structural alterations that drive oncogene overexpression

Abstract Enhancer hijacking, caused by structural alterations on chromosomes as well as extrachromosomal DNA (ecDNA), is a common cancer driver event. The complexity and ubiquity of structural alterations in cancer genomes make it difficult to identify enhancer hijacking with genome sequencing alone. Here we describe a 3D genomics-based analysis called HAPI (Highly Active Promoter Interactions) to characterize enhancer hijacking caused by various types of structural alterations. Applying HAPI analysis to HiChIP data from 34 cancer cell lines, we identified novel enhancers hijacked through chromosomal rearrangements to activate both known and potentially novel oncogenes such as MYC, CCND1, ETV1, CRKL, and ID4, which we validated using CRISPRi assays and RNA-seq analysis. Furthermore, we found that ecDNAs often contain multiple oncogenes from different chromosomes, which cause nested enhancer hijacking among them. For instance, we found that MYC ecDNAs relocate additional oncogenes from other chromosomes such as CDX2, ERBB2, or CD44 near the MYC locus, co-opting MYC’s enhancers for their overexpression, which we validated using dual-color DNA FISH and CRISPRi assays. This multiple oncogenes-involved enhancer hijacking mechanism may suggest novel therapeutic strategies such as targeting either the co-opting oncogenes or the hijacked enhancers for ecDNAs. Our study provides a robust strategy to detect enhancer hijacking events using our publicly available HAPI analysis tool and reveals novel mechanisms underlying oncogene activation caused by chromosomal and extrachromosomal structural alterations. Citation Format: Katelyn L. Mortenson, Courtney Dawes, Emily R. Wilson, Nathan E. Patchen, Hailey Johnson, Jason Gertz, Swneke D. Bailey, Yan Liu, Katherine E. Varley, Xiaoyang Zhang. 3D genomic analysis reveals novel enhancer hijacking mechanisms caused by complex structural alterations that drive oncogene overexpression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6599.

The landscape of 8q24 cytoband in gastric cancer (Review).

Worldwide, gastric cancer (GC) is estimated to be the fifth most common type of cancer type in both sexes, ranking sixth for new cases, with >640,850 cases per year, and fourth in terms of mortality rate. Cancer presents numerical and structural alterations in chromosomes, often through gains and losses of regions. In GC, there are multiple genetic alterations, in which those located in cytoband 8q24 have been frequently described; essential genes are present in this cytoband, regulating the homeostasis of crucial biological processes, such as the MYC gene, which induces expression of selective genes to promote cell growth and proliferation. Conversely, DNA sequence variations can also occur when a single nucleotide in the genome sequence is altered, and this is termed a single nucleotide polymorphism (SNP). These alterations, which can serve as a biological marker, are present in at least 1% of the population and assist in identifying genes associated with GC. In the present review, 12 genes present in cytoband 8q24 related to GC (NSMCE2, PCAT1, CASC19, CASC8, CCAT2, PRNCR1, POU5F1B, PSCA, JRK, MYC, PVT1 and PTK2) are discussed. The PSCA gene was cited more frequently than others; it has four known SNPs associated with GC (rs2978980, rs2294008, rs2976392 and rs9297976). Thus, these SNPs should be further studied in different populations to determine their risk value in patients with GC.

Alteration of chromosome structure impacts gene expressions implicated in pancreatic ductal adenocarcinoma cells

BackgroundPancreatic ductal adenocarcinoma (PDAC) is a lethal malignancy with a five-year survival rate of approximately 10%. Genetic mutations are pivotal drivers in PDAC pathogenesis, but recent investigations also revealed the involvement of non-genetic alterations in the disease development. In this study, we undertook a multi-omics approach, encompassing ATAC-seq, RNA-seq, ChIP-seq, and Hi-C methodologies, to dissect gene expression alterations arising from changes in chromosome accessibility and chromatin three-dimensional interactions in PDAC.ResultsOur findings indicate that chromosomal structural alterations can lead to abnormal expressions on key genes during PDAC development. Notably, overexpression of oncogenes FGFR2, FOXA2, CYP2R1, and CPOX can be attributed to the augmentation of promoter accessibility, coupled with long-range interactions with distal elements. Additionally, our findings indicate that chromosomal structural alterations caused by genomic instability can lead to abnormal expressions in PDACs. As an example, by analyzing chromosomal changes, we identified a putative oncogenic gene, LPAR1, which shows upregulated expression in both PDAC cell lines and clinical samples. The overexpression is correlated with alterations in LPAR1-associated 3D genome structure and chromatin state. We further demonstrated that high LPAR1 activity is required for enhanced PDAC cell migration in vitro.ConclusionsCollectively, our findings reveal that the chromosomal conformational alterations, in addition to the well-known genetic mutations, are critical for PDAC tumorigenesis.

Genetic Basis of Relapse after GPRC5D-Targeted CAR T Cells

GPRC5D-targeted CAR T cell therapy was recently shown to be safe and active in patients with relapsed or refractory multiple myeloma with limited or no other therapeutic options, such as those with triple-refractory disease (to a proteasome inhibitor, an immunomodulatory drug, and an anti-CD38 antibody) and disease progression on a BCMA antibody-drug conjugate, bi-specific T-cell engager, and/or CAR T cell therapy (Mailankody S. et al. NEJM 2022). Among the 17 patients treated in our phase 1 study of the GPRC5D-targeted CAR T cell therapy MCARH109, 12 patients had an objective response and 6 patients relapsed after an initial response of 3-9 months. While there are currently no validated clinical assays to assess GPRC5D expression, we reported decreased or loss of protein expression using immunohistochemistry in all 6 patients who relapsed. This finding suggests that genetic alterations may be an important mechanism of antigen escape after GPRC5D-directed CAR T cell therapy. With BCMA-directed CAR T cell therapies recently approved for multiple myeloma, antigen loss due to genetic alterations is a rare mechanism of resistance. We first investigated the genetic status of GPRC5D in a patient (Patient 15) who underwent biopsies of a left posterior chest wall plasmacytoma at baseline and a recurrent plasmacytoma at the same site at relapse with nearly 100% tumor. This patient received the maximum tolerated dose of 150×10 6 GPRC5D-directed CAR T cells and achieved a best response of stringent complete response without minimal residual disease in the bone marrow. Unfortunately, 6 months after infusion, he relapsed with recurrent FDG-avid lesions in similar locations on PET, extensive bone marrow involvement (90-95%), rapidly rising lambda free light chain in the serum, and significantly decreased but still detectable circulating CAR T cells (CAR vector copies per mL: 666) ( Figure A). We performed droplet digital PCR (ddPCR) on extracted DNA from the plasmacytoma biopsies and estimated GPRC5D copy number to be two at baseline and 0.1 at relapse, consistent with bi-allelic loss in a significant majority of plasma cells. We then performed whole exome sequencing which revealed two balanced copies of GPRC5D at baseline and bi-allelic loss at relapse consisting of a broader deletion (~8756 kb) in chromosome 12p in one allele and a more focal deletion (~145 kb) encompassing the GPRC5D gene locus in the second allele ( Figure B). Beyond this patient, we identified that relapses after GPRC5D-directed CAR T cell therapy are associated with decreased or loss of GPRC5D mRNA expression. We measured GPRC5D mRNA expression by ddPCR on patient bone marrow or plasmacytoma samples at baseline prior to CAR T cell infusion and at disease progression. The results corresponded with those from immunohistochemistry, and all patients who relapsed showed reduced or absent GPRC5D mRNA and protein expression at disease progression. Given that two patients who responded and relapsed had low or no GPRC5D expression at baseline (Patients 10 and 13), further studies are warranted to characterize the heterogeneity of GPRC5D expression and how well immunohistochemistry and ddPCR capture its expression. Here we report that antigen escape after GPRC5D-directed CAR T cell therapy can be mediated by structural chromosome alterations resulting in bi-allelic loss of the GPRC5D gene locus in a patient with initial excellent response. We also note transcriptional downregulation of GPRC5D in other patients at relapse, but it remains to be determined whether this is transient or durable and whether it can be explained by similar on-target genetic alterations or non-genetic mechanisms. Our patients with heavily pretreated multiple myeloma may harbor greater tumor heterogeneity and genomic instability than previously described, which can facilitate clonal outgrowth of antigen-negative tumor cells under continuous selective pressure of GPRCRD-targeted CAR T cells. Potential strategies to mitigate antigen escape-mediated relapse in myeloma patients receiving T-cell engaging therapies including earlier use of these therapies, multi-antigen targeting, or combination approaches are being evaluated in ongoing trials.

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.

The spectrum of MAPK-ERK pathway genomic alterations in gynecologic malignancies: Opportunities for novel therapeutic approaches

ObjectiveTo investigate the incidence of MAPK/ERK pathway genomic alterations among patients with gynecologic malignancies. MethodsWe accessed the American Association of Cancer Research Genomics Evidence of Neoplasia Information Exchange publicly available dataset (v13.0). Patients with malignant tumors of the ovary, uterus, and cervix were identified. Following stratification by tumor site and histology, we examined the prevalence of MAPK/ERK pathway gene alterations (somatic mutation, and/or structural chromosome alterations). We included the following RAS-MAPK pathway genes known to be implicated in the dysregulation of the pathway; KRAS, NRAS, BRAF, HRAS, MAP2K1, RAF1, PTPN11, NF1, and ARAF. Data from the OncoKB database, as provided by cBioPortal, were utilized to determine pathogenic gene alterations. ResultsWe identified a total of 10,233 patients with gynecologic malignancies; 48.2% (n = 4937) with ovarian, 45.2% (n = 4621) with uterine and 6.6% (n = 675) with cervical cancer respectively. The overall incidence of MAPK pathway gene alterations was 21%; the most commonly altered gene was KRAS (13%), followed by NF1 (7%), NRAS (1.3%), and BRAF (1.2%). The highest incidence was observed among patients with mucinous ovarian (71%), low-grade serous ovarian (48%), endometrioid ovarian (37%), and endometrioid endometrial carcinoma (34%). ConclusionsApproximately 1 in 5 patients with a gynecologic tumor harbor a MAPK/ERK pathway genomic alteration. Novel treatment strategies capitalizing on these alterations are warranted.

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

Increased Frequency of Mosaic Chromosomal Alterations in Peripheral Blood Samples of Sub-Saharan African Children with Endemic Burkitt Lymphoma

Introduction: Burkitt lymphoma (BL) is an aggressive B-cell lymphoma with reciprocal IG∷MYC translocations and accounts for 50-75% of childhood cancers in sub-Saharan Africa. Mosaic chromosomal alterations (mCAs) are large, somatically acquired structural chromosomal alterations that are clonal and observed in detectable fractions of circulating mononuclear cells. mCAs have been linked to increased hematologic cancer risk, but their association with BL, a mononuclear B cell tumor, is unknown. We hypothesized that the frequency and distribution of mCAs in peripheral leukocytes would be elevated in children with BL, potentially serving as a biomarker of chromosomal instability relevant to BL risk. Methods: We investigated peripheral leukocyte DNA extracted from children enrolled in the Epidemiology of Burkitt Lymphoma in East African Children and Minors (EMBLEM) study (2010-2016) and the Infections and Childhood Cancer case-control study conducted in Malawi (2005-2010). We used genome-wide single nucleotide polymorphism (SNP) array data to investigate the frequency, type, and distribution of mCAs >2Mb in size detected in peripheral leukocytes of 931 pediatric BL cases with 3,645 healthy children in Uganda, Tanzania, and Kenya, and with 177 non-BL pediatric cancers in Malawi. Eagle2 and SHAPEIT4 software were used for phasing to infer haplotypes for SNP array data and WGS data. MoChA (v2014-05-14) was used to detect mCAs. Parallel analysis using similar methods was performed on whole genome sequences (WGS) from paired tumor-normal blood samples from two Ugandan BL patients from the BL Genome Sequencing Project (BLGSP) and from paired BL- and lymphoblastoid-derived cell lines. Results: Most samples (92%) were from the EMBLEM study, whereas 8% were from Malawi. The mean age of the BL cases and controls was similar (~7.4 years in both, P=0.60). Table 1 shows detected autosomal mCAs for BL cases and controls by country. Overall, a total of 250 autosomal mCAs were detected in 78 (8.4%) of the 931 BL cases. By comparison, a total of 188 autosomal mCAs were detected in 131 (3.4%) of the 3822 controls. Autosomal mCAs were detected in cell fractions ranging from 0.5% to 99.2% (Figure S1). The average number of autosomal mCAs per person (i.e., total of mCAs detected/number of individuals with mCAs detected) was higher in the BL cases compared to controls (3.21 [SD 3.24] versus 1.44 [SD 2.31], P-value=4.50×10-5. The higher frequency of mCAs in blood samples of children with BL compared to controls was independent of age, sex, P falciparum status, and country (OR=2.8, 95% CI=2.06-3.81, P-value=5.70×10-11, Table 1. mCAs on the X chromosome in girls were also associated with BL (5% versus 1.7%, OR=3.12, 95% CI=1.47-6.29, P-value=1.65×10-3). We did not observe an association for mCAs on the Y chromosome in boys. Analysis of paired tumor-normal samples confirmed the presence of the IG∷MYC translocation in tumor, but the same pipelines did not detect the translocation in the corresponding normal blood sample. In informative tumor-normal cases, some mCAs were only detected in tumor, others were detected in both tumor and normal blood, whereas others were detected mCAs in normal only suggesting some mCAs in blood could arise from pre-BL clones. mCAs only observed in BL cases were predominantly gains on chromosome 1q and 8 (Figure 1) which contain major drivers of Burkitt lymphomagenesis including PLEKHO1, MCL1, PSMB4, ILF2, HAX1, ATP8B2 and CKS1B.Conclusion: We report a high frequency of mCAs in healthy sub-Saharan African children and even higher frequency in pediatric BL cases. The mCAs in children with BL clustered on chromosomes 1q and 8 in regions that overlap with several significantly mutated BL genes, suggesting that mCAs may be potential biomarkers important in the natural history of BL. Using paired tumor-normal sample WGS data, we report both similar and unique mCAs in the paired samples suggesting pre-BL clones in blood. These methods are scalable to large cohorts with SNP array data to investigate health effects associated with mCAs in Africa. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

RF34 | PMON203 Copy Number Variant Analysis Reveals Novel Candidate Genes Associated with Primary Ovarian Insufficiency

Abstract Primary ovarian insufficiency (POI) is characterized by a heterogeneous genetic background. Moreover, the etiology of most POI cases remains unclear. Herein, our goal was to investigate the presence of rare deletions or duplications in patients presenting with POI, which could lead to identification of novel chromosomal regions and/or genes potentially associated with disease risk. Patients and Methods Sixty-six patients presenting idiopathic POI were evaluated; 44 had primary amenorrhea and 22 secondary amenorrhea. Chromosomal microarray analysis was performed to detect copy number variants (CNVs) using array-CGH or SNP-array. Identified CNVs were validated by population databases of either health individuals (Database of Genomic Variants - DGV) or patients carrying chromosomal structural alterations (DECIPHER). A set of rare CNVs was selected and annotated in regard to gene content and clinical associations using bioinformatic tools (RefSeq, OMIM, PubMed, Ovarian Kaleidoscope Database, and Mouse Genome Informatics). Results Fifteen rare CNVs were found in 13 patients, ten of them with primary amenorrhea. The identified CNVs comprised four deleted and 11 duplicated regions, in which the break points occurred intragenic in 8 of them. Most of the CNVs were mapped in the autosomes. Seven CNVs identified in 5 patients were classified as pathogenic or probably pathogenic; three were novel variants containing candidate genes associated with ovarian development [19q13.43 (NLRP5) and Xq13.2 (XIST)] or function [(2q37.3 (PER2)]. The other pathogenic CNVs were previously implicated in POI etiology; two of them [Xq27.2q28 del (14.5 Mb) and Xq22.1q27.1 dup (41.4 Mb)] were encompassed in a complex chromosome rearrangement, associated with 20p13 dup (2.7 Mb), and the last region was 15q25.2 deletion. Four VUS containing genes associated with ovarian development [2p23.1 (XDH and EHD3), 9p24.1 (KDM4C), 22q12.1 (ZNRF3)] or function [1p31.1 (PTGFR)] were identified. Conclusion CNVs analysis indicated a genetic etiology in 10% of these POI patients. New candidate genes associated with ovarian development and function were revealed. Presentation: Monday, June 13, 2022 12:30 p.m. - 2:30 p.m., Monday, June 13, 2022 12:54 p.m. - 12:59 p.m.

Variations of wheat (Triticum aestivum L.) chromosomes caused by the 5A chromosomes with complex cytological structure.

To study the effects of structural alterations of chromosomes caused by tandem repeats on the meiotic recombination, the wheat (Triticum aestivum L.) 5A chromosomes with different structure from ten wheat cultivars were used to investigate their meiotic recombination using non-denaturing fluorescence in situ hybridization (ND-FISH) technology. Fifteen cross combinations were carried out and they were divided into seven F1 categories. The structural difference between the intercalary regions of the long arms of the two 5A chromosomes (5AL) in the F1 categories III, VI, and VII was greater than that in the categories I and II, subsequently, the recombination frequencies in the distal regions of the 5AL arm in the progenies from the three categories were significantly lower than that from the categories I and II. For the two 5A chromosomes in the F1 categories VI and VII, the structural differences in the distal regions of both of the two arms were greater than that in the categories IV and V. So, the recombination frequencies in the intercalary region of the 5AL arm in the progeny from the categories IV and V were higher than that in the progeny from the categories VI and VII. The breakage of 5A chromosome together with the 5A translocations and the breakage of some other chromosomes were observed in the progeny from the F1 categories V, VI, and VII. These chromosomal variations were not observed in the progenies from the other four F1 categories. In conclusion, the smaller structural difference between the 5A chromosomes in distal regions of the two arms resulted in a higher recombination frequency in interstitial region and vice versa. The 5A chromosome with complex cytological structure can be used to induce genetic variations of wheat genome.

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.

Transgenic tools for targeted chromosome rearrangements allow construction of balancer chromosomes in non-melanogaster Drosophila species.

Perhaps the most valuable single set of resources for genetic studies of Drosophila melanogaster is the collection of multiply inverted chromosomes commonly known as balancer chromosomes. Balancers prevent the recovery of recombination exchange products within genomic regions included in inversions and allow perpetual maintenance of deleterious alleles in living stocks and the execution of complex genetic crosses. Balancer chromosomes have been generated traditionally by exposing animals to ionizing radiation and screening for altered chromosome structure or for unusual marker segregation patterns. These approaches are tedious and unpredictable, and have failed to produce the desired products in some species. Here, I describe transgenic tools that allow targeted chromosome rearrangements in Drosophila species. The key new resources are engineered reporter genes containing introns with yeast recombination sites and enhancers that drive fluorescent reporter genes in multiple body regions. These tools were used to generate a doubly inverted chromosome 3R in Drosophila simulans that serves as an effective balancer chromosome.

Utilization of CRISPR-Mediated Tools for Studying Functional Genomics in Hematological Malignancies: An Overview on the Current Perspectives, Challenges, and Clinical Implications.

Hematological malignancies (HM) are a group of neoplastic diseases that are usually heterogenous in nature due to the complex underlying genetic aberrations in which collaborating mutations enable cells to evade checkpoints that normally safeguard it against DNA damage and other disruptions of healthy cell growth. Research regarding chromosomal structural rearrangements and alterations, gene mutations, and functionality are currently being carried out to understand the genomics of these abnormalities. It is also becoming more evident that cross talk between the functional changes in transcription and proteins gives the characteristics of the disease although specific mutations may induce unique phenotypes. Functional genomics is vital in this aspect as it measures the complete genetic change in cancerous cells and seeks to integrate the dynamic changes in these networks to elucidate various cancer phenotypes. The advent of CRISPR technology has indeed provided a superfluity of benefits to mankind, as this versatile technology enables DNA editing in the genome. The CRISPR-Cas9 system is a precise genome editing tool, and it has revolutionized methodologies in the field of hematology. Currently, there are various CRISPR systems that are used to perform robust site-specific gene editing to study HM. Furthermore, experimental approaches that are based on CRISPR technology have created promising tools for developing effective hematological therapeutics. Therefore, this review will focus on diverse applications of CRISPR-based gene-editing tools in HM and its potential future trajectory. Collectively, this review will demonstrate the key roles of different CRISPR systems that are being used in HM, and the literature will be a representation of a critical step toward further understanding the biology of HM and the development of potential therapeutic approaches.

Assessment of cytotoxicity, genotoxicity, and mutagenicity of the dexchlorpheniramine reference standard and pharmaceutical formula in human peripheral blood mononuclear cells

Dexchlorpheniramine is a first-generation classical antihistamine, clinically used to treat allergies. The main objective of our study was to evaluate the effects of the dexchlorpheniramine reference standard (DCPA Ref. St) and a pharmaceutical formula on DNA in human peripheral blood mononuclear cells (PBMCs). We exposed PBMCs to five different concentrations (0.5, 2.5, 5, 10, and 50 ng/mL) of DCPA Ref. St DCPA Ref. St and pharmaceutical formula in order to evaluate their cytotoxic, genotoxic, and mutagenic potential. The results showed that both dexchlorpheniramine formulations did not affect PBMC viability and CD3+, CD4+, or CD8+ lymphocyte subpopulations. The DCPA Ref. St and pharmaceutical formula neither induced genotoxic or mutagenic effects nor numerical or structural chromosomal alterations in PBMCs after 24 hours of exposure.