Reciprocal Chromosomal Translocation Research Articles

Subgenome-aware analyses reveal the genomic consequences of ancient allopolyploid hybridizations throughout the cotton family

Malvaceae comprise some 4,225 species in 243 genera and nine subfamilies and include economically important species, such as cacao, cotton, durian, and jute, with cotton an important model system for studying the domestication of polyploids. Here, we use chromosome-level genome assemblies from representatives of five or six subfamilies (depending on the placement of Ochroma) to differentiate coexisting subgenomes and their evolution during the family's deep history. The results reveal that the allohexaploid Helicteroideae partially derive from an allotetraploid Sterculioideae and also form a component of the allodecaploid Bombacoideae and Malvoideae. The ancestral Malvaceae karyotype consists of 11 protochromosomes. Four subfamilies share a unique reciprocal chromosome translocation, and two other subfamilies share a chromosome fusion. DNA alignments of single-copy nuclear genes do not yield the same relationships as inferred from chromosome structural traits, probably because of genes originating from different ancestral subgenomes. These results illustrate how chromosome-structural data can unravel the evolutionary history of groups with ancient hybrid genomes.

Abstract 1093: Small molecule inhibitors of the PAX3::FOXO1 fusion protein in rhabdomyosarcoma

Abstract Rhabdomyosarcoma (RMS) is the most common pediatric soft tissue sarcoma. It is commonly divided into subtypes based on histopathological appearance. The oncogenic fusion proteins PAX3::FOXO1 or PAX7::FOXO1 are present in the alveolar subtype of RMS (ARMS). These chimeric proteins are formed by reciprocal chromosomal translocations and consist of an N-terminal portion of the PAX3 or PAX7 transcription factor fused to a C-terminal portion of the FOXO1 transcription factor. These fusion proteins have been shown to drive malignant transformation in ARMS, and patients with fusion-positive ARMS have a worse prognosis than patients with fusion-negative ARMS and embryonal RMS. We recently reported that piperacetazine, a phenothiazine derivative and first-generation antipsychotic, is capable of binding to and inhibiting the transcriptional activity of PAX3::FOXO1, reducing the expression of PAX3::FOXO1 target genes, and inhibiting the ability of fusion-positive RMS cells to grow in soft agar. We hypothesize that other phenothiazine derivatives may have stronger binding affinity for PAX3::FOXO1 and greater ability to reduce tumor growth in vivo. We employed a structure-activity relationship campaign to develop new phenothiazine derivatives that may be more potent inhibitors of PAX3::FOXO1 than piperacetazine. We synthesized and tested 10 new compounds, in addition to 9 existing FDA-approved phenothiazine derivatives, for their ability to bind to PAX3::FOXO1 and inhibit its transcriptional activity and target gene expression as well as inhibiting the growth of fusion-positive RMS cells in 3D culture. Seven derivatives inhibited PAX3::FOXO1 reporter activity better than piperacetazine, nine of them performed worse, and three of them showed comparable activity to piperacetazine. We demonstrated that piperacetazine does not alter PAX3::FOXO1 levels, subcellular localization, binding to a PAX3::FOXO1 target DNA sequence, or phosphorylation at Ser256 in the FOXO1 portion of the fusion protein. We therefore hypothesize that piperacetazine may be disrupting interactions between PAX3::FOXO1 and its partner proteins. We are employing a proximity-based biotinylation method to identify proteins that are competed away from PAX3::FOXO1 by piperacetazine. Our data suggest that it is possible to target PAX3::FOXO1 protein using small molecules that can directly bind to it and inhibit its activity in fusion-positive RMS cells. Citation Format: Taryn Shaw, Kay Nakazawa, Purushottam Tiwari, Eryn Nelson, Jeffrey Formen, Christian Wolf, Jeffrey Toretsky, Aykut Üren. Small molecule inhibitors of the PAX3::FOXO1 fusion protein in rhabdomyosarcoma [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 1093.

Genetic analysis and prenatal diagnosis of a pedigree with developmental retardation due to paternal 8q/18q translocation

Key Clinical MessageBalanced reciprocal chromosomal translocation carriers will have greater risk to experience recurrent miscarriages, embryonic death, and infertility. We show the pedigree carrying a paternal karyotype which was reported first. This research helps to better understand the clinical manifestations and prognosis of patients with this rare chromosomal abnormality.

Bioinformatic Analysis of Recurrent Genomic Alterations and Corresponding Pathway Alterations in Ewing Sarcoma.

Ewing Sarcoma (ES) is an aggressive, mesenchymal malignancy associated with a poor prognosis in the recurrent or metastatic setting with an estimated overall survival (OS) of <30% at 5 years. ES is characterized by a balanced, reciprocal chromosomal translocation involving the EWSR1 RNA-binding protein and ETS transcription factor gene (EWS-FLI being the most common). Interestingly, murine ES models have failed to produce tumors phenotypically representative of ES. Genomic alterations (GA) in ES are infrequent and may work synergistically with EWS-ETS translocations to promote oncogenesis. Aberrations in fibroblast growth factor receptor (FGFR4), a receptor tyrosine kinase (RTK) have been shown to contribute to carcinogenesis. Mouse embryonic fibroblasts (MEFs) derived from knock-in strain of homologous Fgfr4G385R mice display a transformed phenotype with enhanced TGF-induced mammary carcinogenesis. The association between the FGFRG388R SNV in high-grade soft tissue sarcomas has previously been demonstrated conferring a statistically significant association with poorer OS. How the FGFR4G388R SNV specifically relates to ES has not previously been delineated. To further define the genomic landscape and corresponding pathway alterations in ES, comprehensive genomic profiling (CGP) was performed on the tumors of 189 ES patients. The FGFR4G388R SNV was identified in a significant proportion of the evaluable cases (n = 97, 51%). In line with previous analyses, TP53 (n = 36, 19%), CDK2NA/B (n = 33, 17%), and STAG2 (n = 22, 11.6%) represented the most frequent alterations in our cohort. Co-occurrence of CDK2NA and STAG2 alterations was observed (n = 5, 3%). Notably, we identified a higher proportion of TP53 mutations than previously observed. The most frequent pathway alterations affected MAPK (n = 89, 24% of pathological samples), HRR (n = 75, 25%), Notch1 (n = 69, 23%), Histone/Chromatin remodeling (n = 57, 24%), and PI3K (n = 64, 20%). These findings help to further elucidate the genomic landscape of ES with a novel investigation of the FGFR4G388R SNV revealing frequent aberration.

Cause of hospitalization and its outcome in patient with chronic myeloid leukemia in Patan Hospital

Introduction: Chronic Myeloid Leukemia (CML) is a myeloproliferative neoplasm characterized by dysregulated proliferation of granulocytes because of reciprocal translocation of chromosome 9 and 22. Despite the advances in treatment of CML, it still has a significant burden in patients’ life because of cost of medication, frequent hospitalization and effect on quality of life. The aim of this study is to find out the cause of hospitalization and its outcome in patient with CML. Method: It is a retrospective cross-sectional study conducted at Patan Hospital. The study included data of hospitalization of CML patients over a period of 3 years from April 2020 to April 2023 which was obtained from the record files and discharge notes of the patients. The data included information regarding age and sex of the patients, phase of disease, name of Tyrosine kinase inhibitor (TKI) used, cause of hospitalization and outcome of the hospitalization. Result: There were total of 102 admissions of which 82 admissions were analyzed. The mean age was 49 y, 56% were male, 70.7% were in chronic phase of disease and imatinib was the commonest TKI used (51.2 %). Disease related events were the most common cause of hospital admission (61%); 70 patients (85.4%) improved and were discharged whereas 12 patients (14.6 %) died during hospitalization. Conclusion: The commonest cause of hospitalization in CML patient was disease related events i.e., disease progression, drug related adverse effects and new diagnosis. Transformation to blast crisis had worst prognosis with increased mortality.

A rare craniofacial anomaly associated with balanced reciprocal translocation between chromosome 1 and 7: a case report

The occurrence of balanced reciprocal translocation of chromosome 1 and 7 is one of the rare anomalies. The present case report focuses on a case of 07-year-old male patient with craniofacial anomaly due to balanced reciprocal translocation of chromosome 1 and 7 manifesting as microcephaly, microstomia, oligodontia and scrotal hypospadias with bilateral retractile testis. The patient had severe retrognathic and hyperdivergent mandible along with multiple carious and unerupted permanent teeth. After complete oral prophylaxis of the patient, the restorations of all carious teeth were carried out. Extraction of root stumps under conscious sedation has been planned in later phase. The patient will further be followed up for orthodontic correction of maxillary and mandibular arches in all three planes keeping in view of the growth status of the patient. The present case report intends to provide an overview of the clinical and radiographical features of this rare anomaly who need a prolonged interdisciplinary management and long term follow up. Further, this will add value to the existing prevalence in the available literature.

Does reciprocal translocation affect the meiotic segregation products of non-translocation chromosomes?

This retrospective cohort study aimed to assess the effect of chromosomal reciprocal translocation on meiotic segregation products of non-translocation chromosomes. A total of 744 reciprocal translocation carriers and 875 non-carriers were included in this study. A total of 6,832 blastocysts were biopsied and tested by next-generation sequencing. Blastocysts from the carrier group were classified into five subgroups according to the theoretical segregation pattern of quadrivalent structure. For carrier patients, normal meiotic segregation products of the non-translocation chromosome were classified after excluding the segregation modes of the quadrivalent structure. The proportion of normal non-translocation chromosome meiotic segregation products was similar between the carrier and noncarrier groups (p = 0.69). The generalized Estimation Equation revealed that there was no correlation between reciprocal translocation and meiotic segregation products of non-translocation chromosomes. Moreover, subgroup analyses showed that the segregation modes of quadrivalent structure (p = 0.00) and carrier’s gender (p = 0.00) may affect the meiotic segregation products of non-translocation chromosomes. In conclusion, reciprocal translocation does not directly reduce the proportion of normal segregation products of non-translocation chromosomes. The difference among subgroups of different quadrivalent segregation patterns implied that interchromosomal effect may exist but the high incidence of chromosomal abnormalities for reciprocal translocation carriers should not be attributed to interchromosomal effect.

B-lymphoblastic leukemia/lymphoma with MYC and BCL2 gene rearrangements shows evidence for clonal evolution and mitotic recombination

BackgroundB-lymphoblastic leukemia/lymphomas (B-ALL/LBL) are uncommon neoplasms that may be associated with a variety of cytogenetic and molecular changes. The mechanisms by which these changes arise have not been fully described.Aims/PurposeThis report describes an unusual case of B-ALL/LBL with complex clonal evolution that includes BCL2 and MYC gene rearrangements.MethodsImmunophenotyping was performed by immunohistochemistry and flow cytometry. Traditional G-band karyotyping was accompanied by fluorescence in-situ hybridization (FISH) using break-apart and dual fusion probes. Single nucleotide polymorphisms were assessed using a high-density DNA microarray.ResultsThe karyotype of the blasts showed reciprocal translocation of chromosomes 4 and 18, reciprocal translocation of chromosomes 8 and 14 with two copies of the oncogenic translocation derivative(14)t(8;14), and no normal chromosome 14. FISH studies showed complex IGH-BCL2 and IGH-MYC fusion signals.ConclusionsA clonal evolution model involving multiple chromosomal translocations and mitotic recombination is postulated to account for the karyotype, FISH, and microarray results but leaves unresolved the exact order of the evolutionary changes.

Childbirth in a patient with non-obstructive azoospermia and reciprocal chromosomal translocation (case report)

Childbirth in a patient with non-obstructive azoospermia and reciprocal chromosomal translocation (case report)

I-FISH Guided Cytogenetic Study of Non-Hodgkin Lymphomas in Children and Adolescents: Correlation with Etiology and Outcome

Introduction: Pediatric non-Hodgkin lymphomas (NHLs) comprise approximately 10% of all childhood cancers. The diagnosis requires extensive workup with multiple ancillary studies. Genetic testing using fluorescence in situ hybridization (FISH) is a cytogenetic approach that is often utilized in pediatric NHL. Patients and Methods: Our study included 146 children (113 boys-33 girls), aged 0.33-17.8 years (median 9.16 years), with NHL diagnosis based on histopathology (table 1). The histological diagnosis was based on the complete microscopic and immunohistochemical study of infiltrated tissue. Touch imprints from the diagnostic biopsy samples were further investigated with i-FISH (table 2). Results: In all BL cases MYC gene rearrangement was identified. At least one additional chromosomal aberration was also found in 47 patients. Six hyperdiploid cases were identified among 72 children (8.3%), with at least 3 chromosomes involved. Interestingly, there were no cases of refractory disease, relapse, or death among hyperdiploid patients, and their overall survival (OS) was comparable to that of MYC rearrangement subgroup, a unique finding. Among LBL patients, a high frequency of 9p21 region deficiency was found, as in Acute Lymphoblastic Leukemia (ALL). Also, the chromosomes most frequently involved in hyperdiploid B-LBL (X,17,21) were identical to chromosomes commonly overrepresented in ALL. In contrast, the absence of cases positive for ETV6/RUNX1 hybrid gene is surprising. Possibly, the incidence of the most common cytogenetic atypias is different between leukemia and lymphoma. Of note, the two patients with KMT2A rearrangement achieved complete remission after first-line therapy. Finally, we identified cases with a normal karyotype but existing cytogenetic atypia demonstrable by i-FISH exclusively in LBLs. ALK gene rearrangement was found in all ALCL patients while no MYC gene rearrangement was found. At least one additional atypia was identified in 6/12 patients. Interestingly, ALCL patients had proportionally more recurrences than any other histological category, but without a corresponding increase in mortality. Among DLBCL group we found the highest rate of hyperdiploidy (22.2%). Only two (non-hyperdiploid) patients with BCL6 gene rearrangement were found. The single patient who relapsed had an IGL gene rearrangement, suggesting activation of an oncogene in the context of reciprocal chromosomal translocation involving the 22q11 region. No MYC or BCL2 gene rearrangements were found among DLBCL cases. In hyperdiploid patients, overrepresentation of chromosome 8 was found, along with overrepresentation of chromosome 3 (and, in addition, 18 in one of the two cases). This combination of atypias apparently leads to supernumerary copies of MYC gene, simultaneously with the presence of supernumerary alleles of BCL6 (or BCL2, respectively). Regarding findings in FL, MZL and PTLD, due to the small number of patients in these subgroups, any observation is of limited value. Absence of BCL2 gene rearrangement in childhood FL was confirmed. In the study's only patient with MZL, the identification of trisomy 3 may not be accidental, since this atypia is common in the corresponding adult disease. Of particular interest is the one patient with PTLD. Although monomorphic Burkitt-type PTLD was diagnosed and B-clonality documented based on VDJ recombination of IGH gene, marrow karyotyping and thorough i-FISH screening revealed no chromosomal atypia. The phenomenon has been highlighted in the literature and indicates that PTLD's aggressive clinical course is not necessarily associated with genomic instability and damage. In our study no patient met double-hit lymphoma criteria. We might wonder whether, in our series, the hyperdiploid patients with supernumerary copies of intact MYC, BCL2 and/or BCL6 genes constitute a subgroup of the "alternative" double hit lymphomas. With a median follow-up time of 61.5 months (range 7-123 months), 20 patients succumbed, yielding: 3-year and 5-year progression free survival (PFS) in all patients 84.5% και 82.5% respectively, and 3-year and 5-year OS in all patients 86.7%. Conclusions: This extensive i-FISH investigation provides clinically meaningful information on the genetic profile of NHLs, raises new questions, and points to directions for further investigation within the field of childhood lymphoproliferation. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

In Silico Analysis of miR-223 and miR-181b and Their Target Genes in the Pathogenesis of Acute Promyelocytic Leukaemia

Acute promyelocytic leukaemia (APL) is the M3 subtype of acute myeloid leukaemia (AML). The hallmark for APL diagnosis is the reciprocal chromosomal translocation between chromosome 15 and 17 to produce the PML/RARα fusion gene [1]. The combination treatment of all-trans retinoic acid and arsenic trioxide (ATRA- ATO) is 97% effective in treating APL, however the molecular mechanism of the pathogenesis of APL is yet to be understood. The discovery of miRNAs and epigenetics as potential prognostic biomarkers and therapeutic targets in various cancers including APL must be further explored. miR-223 downregulation in APL was widely shown to be associated with worse prognosis in previous studies [2]; while miR-181b upregulation in APL was shown to be associated with worse prognosis in previous studies, although the findings varied based on the ethnic populations that were involved in the studies [3].&#x0D; &#x0D; In order to understand more about the roles of these miRNAs, this study was conducted with the objective to investigate the roles of targeted genes regulated by mir-223 and mir-181b in APL and other cancers, as well as the signaling pathways involving these miRNAs in the pathogenesis of APL and other cancers. In silico analysis was conducted using miRDB 6.0 database to identify the target genes of miR-223 and miR-181b and filter them to relevance and significant expression in APL cell lines NB4 and HL60. Only the target genes with a target score of 80 or higher, and target expression of 20 RPKM or higher, with confirmation by experimentally validated articles were included.&#x0D; &#x0D; In silico analysis of miR-223 revealed 162 target genes, while 612 target genes were regulated by miR-181b. The validated target genes were then obtained by comparing the predicted target genes to experimentally validated articles. 116 of the target genes of miR-223 were found to be relevant in cancers in experimentally validated articles, whereas 156 of the target genes of miR-181b were found to be relevant in cancers in experimentally validated articles. The 14 target genes of miR-223 relevant in APL cell lines with expression level more than 20 RPKM and supported by experimentally validated articles include NXT1, ACSL4, LRRFIP1, NOP2, DENR, AIMP1, DEK, LRRC59, YWHAQ, XRCC5, LAMP2, RAB14, ARF6, and ATP6V1B2. On the other hand, the 15 target genes of miR-181b relevant in APL cell lines with expression level more than 20 RPKM and supported by experimentally validated articles include DDX3X, TNPO1, DMXL2, ARF6, ZFP36L2, PTBP3, SCD, GIGYF1, SLC25A37, PNRC2, TCERG1, RBBP7, WDR82, PRKCD, and ACSL4.&#x0D; &#x0D; GeneCodis 4 database was used for pathway analysis, which identified 159 KEGG signaling pathways involving the target genes of miR-223 and 203 KEGG signaling pathways involving the target genes of miR-181b (Table 1 and Table 2). There were 13 KEGG signaling pathways involving the target genes of miR-223 which were most significant pertaining to APL and other cancers. Meanwhile, there were 14 KEGG signaling pathways involving the target genes of miR-181b which were most significant pertaining to APL and other cancers.&#x0D; It can be concluded from this study that miR-223 and miR-181b play important roles in the pathogenesis of APL through the regulation of gene expression and activation of signaling pathways. Nevertheless, the functional roles of miR-223 and miR-181b in APL need to be further investigated through experimental validation by in vitro study using APL cell lines to further aid in the discovery of novel prognostic biomarkers and potential therapeutic targets of APL.

Analysis of 2 men with t(8;22)(q13;q13) and t(8;14)(q13;q22) chromosomal translocation karyotypes.

Male infertility is a multifactorial condition that is closely associated with chromosomal abnormalities. Reciprocal chromosomal translocation (RCT) is a significant structural genetic abnormality. The specific mechanisms of forms of RCT affecting male infertility include the product of chromosomally unbalanced gametes, thereby disrupting the structure and function of important genes responsible for spermatogenesis. RCT breakpoints have been found to disrupt gene structure and function in many medical fields However, the relationship between RCT breakpoints and male infertility remains to be determined. The purpose of this study is to describe 2 male carriers of RCTs 46,XY,t(8;22)(q13;q13) and 46,XY,t(8;14)(q13;q22). Both patients were collected from the second hospital of Jilin University. Semen parameters were detected using the computer-aided semen analysis system. Cytogenetic analysis was performed using standard operating procedure. Related genes on chromosomal breakpoints were searched using Online Mendelian Inheritance in Man. One man had semen parameters within the normal range, but the couple was infertile after 5 years of marriage. The other man showed normal semen parameters, and his wife had experienced 2 spontaneous miscarriages. Using a literature search, the association between chromosome 22q13 breakpoint and fertility were investigated. The results suggest that physicians should focus on the clinical phenotype of the patients and the breakpoints of RCT in genetic counseling. An important gene related to human male infertility is clearly located in chromosome region 22q13, and its function is worthy of further study.

Epidemiology and outcomes of acute promyelocytic leukaemia in the era of all-trans retinoic acid (ATRA) chemotherapy and arsenic trioxide plus ATRA: a retrospective analysis

Acute promyelocytic leukaemia (APL) results from the reciprocal chromosomal translocation t(15;17)(q24;21) (PML-RARA gene fusion). We have formulated an oral, economical, and outpatient-based preparation of arsenic trioxide and shown that it is efficacious for newly diagnosed and relapsed APL. In this study, we aimed to define the epidemiological landscape of APL in Hong Kong and to assess the effect of oral arsenic trioxide therapy on patient outcomes. This retrospective analysis of patients diagnosed with APL in Hong Kong between Jan 1, 1991, and March 31, 2021 (data censored on Nov 30, 2021) had incidence of APL, early death (within 30 days of hospitalisation), and overall survival as primary outcomes, and incidence of other primary cancers as a secondary outcome. Oral all-trans retinoic acid (ATRA) plus chemotherapy or oral arsenic trioxide were used. ATRA plus chemotherapy comprised induction with ATRA (45 mg/m2 per day, divided in two doses, for 42 days) and daunorubicin (50 mg/m2 per day intravenously for 3 days); consolidation with two cycles of daunorubicin (for 2 days) and cytarabine (100 mg/m2 per day intravenously for 5 days); and 24 months of maintenance therapy with ATRA (for 15 days every 3 months), 6-mercaptopurine (90 mg/m2 per day), and methotrexate (15 mg/m2 per week). The arsenic trioxide approach comprised two dosing schedules: for patients diagnosed between Jan 1, 2013, and Dec 31, 2017, arsenic trioxide was included in induction and maintenance only; induction was with arsenic trioxide (0·15 mg/day for 42 days), ATRA, oral ascorbic acid (1000 mg/day for 42 days), and daunorubicin; consolidation was with two cycles of daunorubicin and cytarabine; and 24 months of maintenance with arsenic trioxide, ATRA, and ascorbic acid (all for 14 days every 2 months). For patients diagnosed between Jan 1, 2018, and March 31, 2022, arsenic trioxide was included in induction, consolidation, and maintenance, substantially reducing exposure to chemotherapy; induction was with arsenic trioxide (0·15 mg/kg per day for 42 days), ATRA and ascorbic acid (for 42 days), and daunorubicin (given only to patients presenting with a leucocyte count of 10 × 109 cells/L); consolidation was with two cycles of arsenic trioxide, ATRA, and ascorbic acid (all for 14 days every 28 days); and 24 months of maintenance therapy with arsenic trioxide, ATRA, and ascorbic acid. Multivariate cox regression analysis was used to find prognostic indicators for overall survival. This schedule required a 21-day hospital stay during the induction phase, and consolidation and maintenance phases were entirely done in outpatient settings. This ongoing study was approved by the University of Hong Kong's Institutional Review Board and is registered with ClinicalTrials.gov, NCT04251754. 751 patients (387 [51%] women and 364 [49%] men) were identified (median age 44 years [IQR 31-57]), for an annual incidence of 0·32 per 100 000 people. 469 (62%) patients received ATRA plus chemotherapy and 282 (38%) patients received oral arsenic trioxide. After a median follow-up of 75 months (IQR 14-161), 271 (36%) patients had died, with early death constituting 144 (53%) cases, all occurring in patients in the ATRA plus chemotherapy cohort. 5-year overall survival in the full cohort was 68% and 10-year overall survival was 63%. On multivariate analysis, being male (p=0·019), older than 50 years (p<0·0001), having a leucocyte count of >10 × 109cells/L at presentation (p<0·0001), and having ATRA plus chemotherapy regimens (p<0·0001) were all associated with worse overall survival. In the oral arsenic trioxide cohort, 5-year overall survival was 92% and 10-year overall survival was 85%. In the ATRA plus chemotherapy cohort, 5-year overall survival was 55% and 10-year overall survival was 51%. Second cancers developed in 21 patients (eight never exposed to oral arsenic trioxide; 13 with previous exposure to oral arsenic trioxide during induction, maintenance, or relapse). The incidence of second cancers in patients exposed to oral arsenic trioxide did not differ from that in patients never exposed to oral arsenic trioxide (incidence rate ratio 2·14 [95% CI 0·89-5·17], p=0·099). Oral arsenic trioxide plus ATRA was associated with fewer early deaths and better long-term survival than ATRA plus chemotherapy, with shorter hospital stays and outpatient treatment as distinct health-care advantages. Health and Medical Research Fund of the Hong Kong Special Administrative Region, China (code 08191946).

O-114 Preimplantation genetic testing for monogenic diseases without necessary familial members

Abstract Preimplantation genetic testing for monogenic diseases (PGT-M) is available for any single gene defects theoretically, as long as the disease-causing locus has been unequivocally identified. However, PGT-M has faced great challenges for couples with more than one genetic mutation, de novo mutations or without essential family members for linkage analysis. In order to overcome these challenges, we developed a comprehensive strategy which includes preimplantation genetic testing for aneuploidies (PGT-A) and chromosomal structural rearrangements (PGT-SR) study, as well as monogenic diagnosis study for couples bearing de novo mutations or without necessary familial members. The innovation of our strategy is to use the gamete (polar body or single sperm) or embryo as proband for linkage analyses (GEPLA) to detect an embryo’s carrier status. GEPLA strategy uses affected embryo as proband or gametes carrying mutant alleles as proband for SNP linkage analyses, that were suitable for all types of patients mentioned above. Using this novel developed method, nine autosomal dominant polycystic kidney disease (ADPKD) couples with either de novo mutation or without a positive family history were recruited. Moreover, other two couples with single gene disorders (SMA and NF2) which lack of essential family members for linkage analysis including de novo mutation, and also combined with reciprocal translocation were recruited too. For nine ADPKD couples, a total of 34 embryos from 13 PGT-M cycles were examined and two couples were successfully delivered healthy babies. For the other two couples, 15 embryos were screened, and two embryos were determined as free of the monogenic disease and specific chromosomal abnormalities created by reciprocal translocations. This study provides a creative approach for embryo diagnosis of patients with de novo mutations or patients lacking of essential family members for linkage analysis, and even for reciprocal chromosome translocation concurrently.

Detection of cryptic balanced chromosomal rearrangements using high-resolution optical genome mapping

BackgroundChromosomal rearrangements have profound consequences in diverse human genetic diseases. Currently, the detection of balanced chromosomal rearrangements (BCRs) mainly relies on routine cytogenetic G-banded karyotyping. However, cryptic BCRs are hard...

3. Complex and cryptic EWSR1-FLI1 gene fusions and 1q jumping translocation in pediatric Ewing sarcomas

Ewing sarcomas are the second most frequent bone tumor of childhood that can also occur in soft tissue. They are highly aggressive with a survival of 30% for those with metastatic disease. They are genetically characterized by balanced reciprocal chromosomal translocations in which a member of the FET gene family is fused with an ETS transcription factor, with the most common translocation being the t(11;22)(q24;q12). The t(11;22) reciprocal translocation fuses the N-terminal transactivation domain of the Ewing sarcoma breakpoint region 1 protein (EWSR1) with the C-terminal DNA binding domain of the Friend leukemia integration 1 transcription factor (FLI1). The EWSR1-FLI1 fusion occurs in ∼90% of Ewing sarcoma cases and is a tumor-specific chimeric transcription factor that massively revamps the transcriptome. Therefore, the detection of EWSR1-FLI1 fusions is of important diagnostic value. Here, we present two pediatric Ewing sarcomas with atypical EWSR1-FLI1 fusions. The first case had a complex t(9;11;22)(q22;q24;q12) three-way translocation and a 1q jumping translocation by chromosome analysis. EWSR1 rearrangements using a EWSR1 break-apart FISH probe set revealed 5’ EWSR1 on der(22)(q12) and 3’ EWSR1 on der(9)(q22). Metaphase FISH using dual-color dual-fusion EWSR1-FLI1 FISH probe set revealed a EWSR1-FLI1 fusion at the derivative chromosome 22 involving the three-way translocation. 1q amplification by jumping translocations were confirmed by SNP microarray. The second case had a t(4;22)(q35;q12) reciprocal translocation and tetrasomy 8 by chromosome analysis. EWSR1 rearrangements using a EWSR1 break-apart FISH probe set revealed 5’ EWSR1 on der(22)(q12) and 3’ EWSR1 on der(4)(q35). Metaphase FISH using dual-color dual-fusion EWSR1-FLI1 FISH probe set revealed a EWSR1-FLI1 fusion at the derivative chromosome 22 involving the 4;22 translocation. Both cases had EWSR1-FLI1 gene fusions detected by Nanostring gene fusion panel. Recognizing complex and cryptic EWSR1-FLI1 gene fusions using various diagnostic methods is important for diagnosis, prognosis, and treatment outcome of pediatric Ewing sarcomas.

Zooming in on Long Non-Coding RNAs in Ewing Sarcoma Pathogenesis.

Ewing sarcoma (ES) is a rare aggressive cancer of bone and soft tissue that is mainly characterized by a reciprocal chromosomal translocation. As a result, about 90% of cases express the EWS-FLI1 fusion protein that has been shown to function as an aberrant transcription factor driving sarcomagenesis. ES is the second most common malignant bone tumor in children and young adults. Current treatment modalities include dose-intensified chemo- and radiotherapy, as well as surgery. Despite these strategies, patients who present with metastasis or relapse still have dismal prognosis, warranting a better understanding of treatment resistant-disease biology in order to generate better prognostic and therapeutic tools. Since the genomes of ES tumors are relatively quiet and stable, exploring the contributions of epigenetic mechanisms in the initiation and progression of the disease becomes inevitable. The search for novel biomarkers and potential therapeutic targets of cancer metastasis and chemotherapeutic drug resistance is increasingly focusing on long non-coding RNAs (lncRNAs). Recent advances in genome analysis by high throughput sequencing have immensely expanded and advanced our knowledge of lncRNAs. They are non-protein coding RNA species with multiple biological functions that have been shown to be dysregulated in many diseases and are emerging as crucial players in cancer development. Understanding the various roles of lncRNAs in tumorigenesis and metastasis would determine eclectic avenues to establish therapeutic and diagnostic targets. In ES, some lncRNAs have been implicated in cell proliferation, migration and invasion, features that make them suitable as relevant biomarkers and therapeutic targets. In this review, we comprehensively discuss known lncRNAs implicated in ES that could serve as potential biomarkers and therapeutic targets of the disease. Though some current reviews have discussed non-coding RNAs in ES, to our knowledge, this is the first review focusing exclusively on ES-associated lncRNAs.

Dysregulated heparan sulfate proteoglycan metabolism promotes Ewing sarcoma tumor growth.

The Ewing sarcoma family of tumors is a group of malignant small round blue cell tumors (SRBCTs) that affect children, adolescents, and young adults. The tumors are characterized by reciprocal chromosomal translocations that generate chimeric fusion oncogenes, the most common of which is EWSR1-FLI1. Survival is extremely poor for patients with metastatic or relapsed disease, and no molecularly targeted therapy for this disease currently exists. The absence of a reliable genetic animal model of Ewing sarcoma has impaired investigation of tumor cell/microenvironmental interactions in vivo. We have developed a new genetic model of Ewing sarcoma based on Cre-inducible expression of human EWSR1-FLI1 in wild-type zebrafish, which causes rapid onset of SRBCTs at high penetrance. The tumors express canonical EWSR1-FLI1 target genes and stain for known Ewing sarcoma markers including CD99. Growth of tumors is associated with activation of the MAPK/ERK pathway, which we link to dysregulated extracellular matrix metabolism in general and heparan sulfate proteoglycan catabolism in particular. Targeting heparan sulfate proteoglycans with the specific heparan sulfate antagonist Surfen reduces ERK1/2 signaling and decreases tumorigenicity of Ewing sarcoma cells in vitro and in vivo. These results highlight the important role of the extracellular matrix in Ewing sarcoma tumor growth and the potential of agents targeting proteoglycan metabolism as novel therapies for this disease.

EP049: Discordant fluorescence in situ hybridization and RNASeq results in the identification of fusion partners in recurring translocations in hematological malignancies

Reciprocal chromosomal translocations are implicated in neoplastic transformation in tumors. These can be identified by chromosome analysis, by fluorescence in situ hybridization (FISH) if cryptic, or by RNASeq/next generation sequencing. FISH probes are highly specific and sensitive, and have the advantage of faster turn-around-time, are less expensive, and can be used on a variety of specimen types. Therefore, several of these probes are commercially available, and are incorporated to screen diagnostic specimens.

Impact of Variants in the ATIC and ARID5B Genes on Therapeutic Failure with Imatinib in Patients with Chronic Myeloid Leukemia.

Chronic myeloid leukemia (CML) is a myeloproliferative neoplasm derived from the balanced reciprocal translocation of chromosomes 9 and 22 t (9q34 and 22q11), which leads to the formation of the Philadelphia chromosome and fusion of the BCR-ABL genes. The first-line treatment for CML is imatinib, a tyrosine kinase inhibitor that acts on the BCR-ABL protein. However, even though it is a target-specific drug, about 25% of patients do not respond to this treatment. The resistance mechanisms involved in this process have been investigated and studies have shown that germinal alterations can influence this mechanism. The aim of this work was to investigate 32 polymorphisms in 24 genes of carcinogenic pathway to verify the influence of these genetic variants on the response to treatment with imatinib. Our results demonstrated that individuals with the recessive GG genotype for the rs2372536 variant in the ATIC gene are approximately three times more likely to experience treatment failure with imatinib (p = 0.045, HR = 2.726, 95% CI = 0.9986–7.441), as well as individuals with the TT genotype for the rs10821936 variant in the ARID5B gene, who also have a higher risk for treatment failure with imatinib over time (p = 0.02, HR = 0.4053, IC 95% = 0.1802–0.911). In conclusion, we show that variants in the ATIC and ARIDB5 gene, never screened in previous studies, could potentially influence the therapeutic response to imatinib in patients treated for CML.