Frequent Chromosomal Translocations Research Articles

Conversion from the frequency of chromosome translocations in T-lymphocytes to the bone marrow dose in the long-term period after internal 89,90 Sr exposure

Cytogenetic Fluorescence In Situ Hybridization studies, that allow assessing the frequency of stable chromosome aberrations in circulating T lymphocytes, are commonly used in retrospective dosimetry in cases of uniform whole-body exposure. In the event of 89,90Sr exposure, interpretation of cytogenetic data is challenging, especially if blood sampling occurs long after the start of exposure. The weighted average dose to T-lymphocytes at the time of donor blood sampling in the long-term period after exposure to 89,90Sr does not coincide with the red bone marrow dose. Previously, we developed a model that allows us to estimate the weighted average doses to T-lymphocytes upon 89,90Sr ingress into the body of people belonging to various age groups. In this study, the modeling results were used to estimate the conversion factors from the frequency of translocations to the red bone marrow dose, which is important for assessing radiobiological effects associated with hematological diseases. The objective of our study is to estimate numerically the conversion factors (Brbm) from the dose to lymphocytes to the dose to red bone marrow for various scenarios of 89,90Sr ingestion depending on age, sex, and time after the start of exposure. The following scenarios are considered: single, uniform chronic for six months, uniform chronic for 1-5 years, non-uniform intake for 5 years (simulates the dynamics of intake in the Techa riverside settlements in 1950-1954). As a result, it has been found that the Brbm values significantly depend on the age at the time of 89,90Sr intake. The older the person is at the start of exposure, the more the cytogenetic dose differs (it is significantly lower) from the dose to the red bone marrow. We can say that the cytogenetic dose corresponds to the red bone marrow dose only in newborns and infants. This is due to the age-related dynamics of T-cell populations. Sex does not have a significant effect on Brbm. The effect of the 89,90Sr intake duration on Brbm is the most pronounced for 15-year-old adolescents. For them, the difference in Brbm values for a single and chronic 5-year ingress reaches 13%. Non-uniform intake of 90Sr over several years does not have a significant effect on Brbm and can be modelled by a uniform intake of the same duration.

Pattern of Translocations in Acute Leukaemia: A Single Centre Experience

A multifaceted approach is the current modality to the diagnoses of acute leukaemia. Given the importance of knowing chromosomal aberrations for rapid diagnosis and better treatment selection, this study assessed the frequency of common chromosomal translocations among acute leukaemia patients. In this retrospective study, both conventional karyotype and RT-PCR detecting translocations (HemaVision®-28N) were utilised in 400 patients with acute leukaemia of all subtypes in King Abdulaziz University, Jeddah (2015-2020). The researchers identified 38 acute leukaemia cases associated with translocations out of 400 new cases (9.5%), 326 samples were negative (81.5%) and 36 resisted PCR (9%). The most frequent observed translocation is t(9;22) (q34;q11.2) P190 (representing 28.9% of the total positive calls), followed by t(15;17) (q24;q21) (PML-RARA) and t(8;21) AML-ETO, each of which represents 13 percent. The resulting acute leukaemia translocation frequencies are similar to that published in the literature both locally and globally

An aptamer-mediated base editing platform for simultaneous knockin and multiple gene knockout for allogeneic CAR-T cells generation

Gene editing technologies hold promise for enabling the next generation of adoptive cellular therapies. Conventional gene editing platforms that rely on nuclease activity, such as Clustered regularly interspaced short palindromic repeats-CRISPR associated protein 9 (CRISPR-Cas9), allow efficient introduction of genetic modifications; however, these modifications occur via the generation of DNA double-strand breaks (DSBs) and can lead to unwanted genomic alterations and genotoxicity. Here, we apply a novel modular RNA aptamer-mediated Pin-point™ base editing platform to simultaneously introduce multiple gene knockouts and site-specific integration of a transgene in human primary T cells. We demonstrate high editing efficiency and purity at all target sites and significantly reduced frequency of chromosomal translocations compared to the conventional CRISPR-Cas9 system. Site-specific knock-in of a chimeric antigen receptor (CAR) and multiplex gene knockout are achieved within a single intervention and without the requirement for additional sequence-targeting components. The ability to perform complex genome editing efficiently and precisely highlights the potential of the Pin-point platform for application in a range of advanced cell therapies.

Abstract 404: LINE-1 retrotransposition promotes chromosomal translocations through RNA-templated DNA repair in human cancers

Abstract Introduction: Approximately 50% of human cancers have somatic integrations of long interspersed element-1 (LINE-1; also known as L1). L1 is a retrotransposon that copies itself through RNA and integrates into new genomic loci. Although L1 sequences comprise approximately 17% of the human genome, only 100-150 L1 loci have retained the ability to retrotranspose. These full-length, retrotransposition-competent L1s are typically repressed in human somatic cells, but there is evidence of their significant reactivation in human cancers. Therefore, L1 overexpression is a hallmark of many human cancers, particularly in highly malignant tumor types such as breast, ovarian, pancreatic, esophageal, lung, head-and-neck, colon, prostate, and liver cancers. Results: In many cancers, chromosomal translocations are fundamental pathogenetic events initiated by the generation of DNA double-strand breaks (DSBs). Although LINE-1 (L1) retrotransposition events have been implicated in chromosomal rearrangements associated with most human cancers, the frequency and mechanisms by which L1 is involved in these rearrangements, including chromosomal translocations, remain poorly characterized. By combining high-throughput genome-wide translocation sequencing (HTGTS) and two sequencing techniques to detect L1 insertion sites (PolyA-seq and CELTICS-seq), we demonstrated that the presence of an active human L1 retrotransposition significantly increases the frequency of chromosomal translocations. By identifying L1-dependent translocation hotspots in HEK293T cells we highlight the requirement for the L1 reverse transcriptase (RT) activity and the crucial role of pre-existing DNA DSBs in promoting L1-mediated chromosomal translocations. L1-dependent translocation hotspots showed a marked preference for transcription end sites (TES) of active genes, early replication timing regions, and accessible chromatin regions. Therefore, while cancer genome analysis provides a static view of chromosomal rearrangements based on canonical L1 integrations, our functional studies reveal an unanticipated predominance of chromosomal translocations facilitated by non-canonical L1 retrotransposition via RNA-templated repair of existing DSBs, largely expanding our knowledge on the mechanism by which L1 retrotransposition induces genomic instability in human cancers. Citation Format: Jianli Tao, Luca Alessandri, Carlos Mendez-Dorantes, Kathleen H. Burns, Qi Wang, Roberto Chiarle. LINE-1 retrotransposition promotes chromosomal translocations through RNA-templated DNA repair in human cancers [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 404.

Genome dosage alteration caused by chromosome pyramiding and shuffling effects on karyotypic heterogeneity, reproductive diversity, and phenotypic variation in Zea-Tripsacum allopolyploids.

We developed an array of Zea-Tripsacum tri-hybrid allopolyploids with multiple ploidies. We unveiled that changes in genome dosage due to the chromosomes pyramiding and shuffling of three species effects karyotypic heterogeneity, reproductive diversity, and phenotypic variation in Zea-Tripsacum allopolyploids. Polyploidy, or whole genome duplication, has played a major role in evolution and speciation. The genomic consequences of polyploidy have been extensively studied in many plants; however, the extent of chromosomal variation, genome dosage, phenotypic diversity, and heterosis in allopolyploids derived from multiple species remains largely unknown. To address this question, we synthesized an allohexaploid involving Zea mays, Tripsacum dactyloides, and Z. perennis by chromosomal pyramiding. Subsequently, an allooctoploid and an allopentaploid were obtained by hybridization of the allohexaploid with Z. perennis. Moreover, we constructed three populations with different ploidy by chromosomal shuffling (allopentaploid × Z. perennis, allohexaploid × Z. perennis, and allooctoploid × Z. perennis). We have observed 3 types of sexual reproductive modes and 2 types of asexual reproduction modes in the tri-species hybrids, including 2n gamete fusion (2n + n), haploid gamete fusion (n + n), polyspermy fertilization (n + n + n) or 2n gamete fusion (n + 2n), haploid gametophyte apomixis, and asexual reproduction. The tri-hybrids library presents extremely rich karyotype heterogeneity. Chromosomal compensation appears to exist between maize and Z. perennis. A rise in the ploidy of the trihybrids was linked to a higher frequency of chromosomal translocation. Variation in the degree of phenotypic diversity observed in different segregating populations suggested that genome dosage effects phenotypic manifestation. These findings not only broaden our understanding of the mechanisms of polyploid formation and reproductive diversity but also provide a novel insight into genome pyramiding and shuffling driven genome dosage effects and phenotypic diversity.

CRISPR-Cas9 Screening Identifies Therapeutic Targets for AML1-ETO Positive Leukemia

Objectives: Targeted therapy has achieved tremendous success in leukemia therapy over the past few decades, especially in those with fusion proteins, such as t(15;17) which generates PML-RARa and t(9;22) which generates BCR-ABL. However, effective targeted therapy for AML1-ETO-positive leukemia, which arises from one of the most frequent chromosomal translocations t(8;21), remains largely elusive. In this study, we performed CRISPR-Cas9 screening on the AML1-ETO-positive Kasumi-1 cell line using an AML-related sgRNA library to identify potential therapeutic targets that could restore normal differentiation in AML1-ETO-positive AML. Methods: To identify critical genes capable of reversing differentiation blockage in AML1-ETO-driven leukemogenesis, we constructed an AML1-related sgRNA library which focused genes and signaling pathways regulated by AML1-ETO. This sgRNA library consist of (1) coding genes of proteins interacting with AML1, (2) genes activated by AML1-ETO, and (3) genes downregulated upon knockdown of AML1-ETO as observed in CHIP-seq results. This sgRNA library comprises 4130 sgRNAs targeting 929 human genes (~4 sgRNA/gene), along with 100 control sgRNAs. CD13 high and CD13 low populations were collected by flow cytometry at 10th day post-transduction of sgRNA library. The enrichment of gRNAs between CD13 high and CD13 low group was analyzed using the MAGeCK program, and the candidate genes were identified based on the log2 fold change of sgRNA abundance. To make the screening results more reliable, we used CD11b as another screening marker to repeat aforementioned process. We further preformed single candidate gene knockout in Kasumi-1 and SKNO-1 cell line to validate the screening phenotype. The regulatory function of candidate gene in AML1-ETO positive leukemia was explored through various in vitro assays, including cell apoptosis, cell proliferation, morphological evaluation, flow cytometry analysis, quantitative real-time PCR (qPCR), and Western blot. Results: The gene set enriched in the CD13 high group is considered to be positive hit. Silence of these genes may reverse blockage of differentiation, making them potential therapeutic targets for AML1-ETO leukemia. Additionally, genes such as CBFB, MTA2, DOT1L, PRMT1, RUNX1 and KDM1A, which had been previously reported to promote myeloid differentiation when down-regulated, were also significantly enriched in the CD13 high group, these findings demonstrated the credibility of our screening strategy and results. Clathrin Heavy Chain (CLTC) emerged as one of the top-ranking genes in our study. CLTC is a crucial protein involved in the regulation of clathrin-mediated endocytosis, which plays a critical role in various cellular processes including cell signaling, proliferation, and differentiation. Expression of CD13 and CD16 were upregulated in CLTC knockout cells, further validating our screening results. Besides, morphological analysis displayed a more mature cell morphology with a decrease in nucleus-to-cytoplasm ratio and indented shaped nuclei, suggesting that repression of CLTC promotes terminal differentiation of AML blasts. Cell biology experiments indicated that knockout of CLTC remarkably inhibited the proliferation of Kasumi-1 and SKNO-1 cells, meanwhile, apoptosis of these cells was accelerated. Therefore, these results collectively suggested that the down-regulation of CLTC exhibited significant tumor-suppressive effect in AML1-ETO leukemia. Furthermore, Western blot and RT-qPCR analyses revealed that CLTC is highly expressed in AML1-ETO-positive leukemia, whereas its expression is downregulated upon deletion of AML1-ETO fusion protein. This suggested that CLTC might be regulated by AML1-ETO fusion protein and contribute to its oncogenic activity. Conclusions: Our results revealed a possible novel mechanism underlying the blockage of myeloid differentiation in AML1-ETO leukemia, and have identified CLTC as a promising therapeutic target for AML1-ETO-driven leukemogenesis.

Current Testing Practices for t(11;14) Rearrangements in Patients with Newly Diagnosed Multiple Myeloma in the United States

Background: Despite an improvement in the awareness and use of precision medicine and molecular testing in hematological cancers, there are still significant disparities in biomarker testing. This ultimately leads to inequality in molecular testing access and can lead to suboptimal medical care for some patients, who do not receive the most appropriate and effective therapy. Venetoclax is a selective BCL-2 inhibitor and has shown promising antimyeloma activity in patients with t(11;14) multiple myeloma (MM). t(11;14) is the most frequent chromosomal translocation in MM reported in approximately 15-20% of newly diagnosed MM patients (NDMM) (Kumar et al. Blood 2017). In this study, we assessed current t(11;14)(q13;q32) testing practices in patients with NDMM in the United States (US) to gain insights on challenges for biomarker testing and equitable access to precision medicine. Methods: A retrospective, real-world evidence study was conducted between January and December 2021 using the Diaceutics DXRX Data Repository database. DXRX is a patient-level claims- and laboratory-linked dataset covering more than 4000 laboratories and 360 million patient lives between 2011 and 2022 in the US. Eligible patients were identified using International Classification of Disease (ICD) codes for NDMM (ICD-10 code C90.0). A 2-year lookback was utilized to ensure patients were not in remission or relapse (ICD-10 codes C90.01, C90.02). Percentages were used to describe study population characteristics. t(11;14) and plasma cell enrichment (PCE) testing rates were estimated using descriptive statistics for the entire cohort as well as for race/ethnicity subgroups. PCE testing was considered as it contributes to increasing sensitivity of testing. Results: We identified 27,586 eligible patients with NDMM. The median age at diagnosis was 70 years (interquartile range: 65-75) and 45% were female. Among the eligible patients, 69% (n=19,034) specifically received t(11;14) testing, within 1 month from diagnosis to testing. Fluorescence in situ hybridization (FISH; dual color, dual fusion probe and immunoglobin [IG] break apart) was the most commonly utilized technology (89%; n=16,940) for detecting t(11;14); next-generation sequencing panels were limited (<1%) in utilization. Confirmatory reflex testing with a t(11;14) dual probe following positive IG break apart was not performed in 17% (n=3235) of patients. In patients who were tested with the t(11;14) dual probe FISH assay, less than half (40.9%) were tested for t(11;14) with PCE. Results of the FISH assay were available for 4941 patients. A lower positivity rate was observed with non-PCE testing (13.1%; n=647) compared with those utilizing PCE (16.8%; n=830), p=0.494. Testing rates of t(11;14) in an academic setting were 72% (n=10,659) vs 64% (n=8374) in the community setting, p<0.0001. PCE was performed on only 24.9% (n=2093) of patients in a community setting vs 61% (n=6502) of samples in an academic setting, p<0.0001. For the subgroup analysis, race/ethnicity data were available for 9245 patients with NDMM; 75.7% were White, 15.9% were Black, 2.6% were Asian, 2% were Hispanic, and 3.2% were classified as other. t(11;14) testing rates were higher for patients who were White (72.8%) compared with the minority groups (66.9% for patients who were Black, 68.8% for patients who were Asian, and 65.7% for patients who were Hispanic). The t(11;14) testing setting for minority group patients was community (62%) vs academic (38%). Conclusions: Notable variations in t(11;14) testing patterns were observed among patients with NDMM in different care settings and racial/ethnic groups. There is a clear unmet need for standardization across academic and community settings to mitigate suboptimal testing methodologies that could impact treatment decision-making and patient outcomes. From our study, there is a clear need to improve t(11;14) testing rates as the clinical utility changes from a prognostic to predictive biomarker with the availability of personalized healthcare options. Education of PCE utilization for physicians, especially community-based pathologists and laboratories, will be essential to reduce false negatives and inequalities in optimal testing, especially PCE in ethnic minorities in the US.

DNA replication timing directly regulates the frequency of oncogenic chromosomal translocations.

Chromosomal translocations result from the joining of DNA double-strand breaks (DSBs) and frequently cause cancer. However, the steps linking DSB formation to DSB ligation remain undeciphered. We report that DNA replication timing (RT) directly regulates lymphomagenic Myc translocations during antibody maturation in B cells downstream of DSBs and independently of DSB frequency. Depletion of minichromosome maintenance complexes alters replication origin activity, decreases translocations, and deregulates global RT. Ablating a single origin at Myc causes an early-to-late RT switch, loss of translocations, and reduced proximity with the immunoglobulin heavy chain (Igh) gene, its major translocation partner. These phenotypes were reversed by restoring early RT. Disruption of early RT also reduced tumorigenic translocations in human leukemic cells. Thus, RT constitutes a general mechanism in translocation biogenesis linking DSB formation to DSB ligation.

Sporadic chromosome translocation frequencies in lymphocyte cultures - a retrospective study in a cohort of patients from Bosnia and Herzegovina.

Aim Chromosome translocations are considered as one of the most severe forms of genome defects. Because of the clinical significance of chromosome translocations and scarce data on the incidence of sporadic translocations in population of Bosnia and Herzegovina, we aimed to report sporadic translocation frequencies in samples karyotyped in our laboratory. Methods The study group consisted of 108 samples. Whole blood was cultivated in complete medium for 72 hours with the thymidine application at 48th hour to synchronize the cell culture. Metaphases were arrested by colcemid 60 minutes before harvesting. Following hypotonic treatment, cells were fixed and cell suspension was dropped on coded slides. Dried slides were subjected to conventional GTG (G-banding with trypsin-Giemsa) banding and analyzed under 1000x magnification in the accordance with ISCN (International System for Human Cytogenetic Nomenclature) and E.C.A. Cytogenetic Guidelines and Quality Assurance. Results The incidence of all detected sporadic translocations was 27.81 x 10-4 per metaphase. The incidence of sporadic translocations involving chromosomes 7 and 14, being considered as the most frequent sporadic translocations of the human karyotype in phytohaemagglutinin (PHA) stimulated lymphocytes, was 15.89 x 10-4 per metaphase. The most frequent breakpoints were 7p21, 14q11 and 14q21. Other detected sporadic translocation breakpoints were: 1q25, 3p22, 7p13, 7q11.22, 7q33, 14q23 and 19q13.4. Conclusion Higher incidence of sporadic translocations compared to the similar studies was registered. Since potential explanations for this issue are smaller sample size and higher exposure of examined population to genotoxic agents, further monitoring of sporadic translocation incidences is recommended.

Polymorphisms Within DNA Double-Strand Breaks Repair-Related Genes Contribute to Structural Chromosome Abnormality in Recurrent Pregnancy Loss.

Background: Structural chromosome abnormality (SCA) is an important cause of human diseases, including recurrent pregnancy loss (RPL). DNA double-strand breaks (DSBs) repair-related genes play critical roles in SCA. The present study aims to investigate the potential contribution of DSBs repair-related gene polymorphisms to SCA. Methods: Fifty-four affected RPL individuals with SCA, 88 affected RPL individuals without SCA, and 84 controls were analyzed. Targeted whole-exome sequencing (WES) was used for screening single nucleotide polymorphisms in six DSBs repair-related genes (EP300, XRCC6, LIG4, XRCC4, PRKDC, and DCLRE1C), and validation was performed by Sanger sequencing. Finally, we detected the frequency of radiation-induced chromosome translocations in no SCA samples with significant polymorphisms by fluorescence in situ hybridization (FISH). Results: A total of 35 polymorphisms have been identified and confirmed. Frequencies of EP300 rs20551, XRCC6 rs132788, and LIG4 rs1805388 were significantly different between SCA RPL and no SCA RPL (p = 0.030, 0.031, and 0.040 respectively). Frequencies of those three gene polymorphisms between SCA RPL and controls also were significantly different (p = 0.017, 0.028, and 0.029 respectively). Moreover, the frequency of the G allele at rs20551 locus, the T allele at rs132788 locus and the A allele at rs1805388 locus was significantly higher in SCA RPL than no SCA RPL (OR = 3.227, p = 0.005; OR = 1.978, p = 0.008 and OR = 1.769, p = 0.036 respectively) and controls (OR = 7.130, p = 0.000; OR = 2.157, p = 0.004; OR = 2.397, p = 0.003 respectively). Additionally, the frequency of radiation-induced translocation in no SCA samples with rs20551, rs132788 or rs1805388 was significantly higher compared with the wild type samples (p = 0.015, 0.012, and 0.007 respectively). Conclusion: Our results suggest that rs20551, rs132788, and rs1805388 might be associated with the risk of SCA. Larger scales of genetic variations studies and functional experiments are necessary to further confirm these findings.

Frequency of Chromosomal Translocations Are Significantly Higher in Therapy Related Myeloid Neoplasm As Compared to Primary MDS

Background: Myelodysplastic syndromes (MDS) are a heterogeneous group of disorders with variable outcomes. Acquired chromosome abnormalities in patients with myelodysplastic syndromes (MDS) are among the most valuable determinants of prognosis. However, chromosomal translocations are rare in MDS, and their prognostic implication is not well known. To elucidate factors driving chromosomal translocations in MDS, we compared the frequency of MDS patients with and without prior exposure to DNA damaging cytotoxic therapies.Methods: We evaluated diagnostic bone marrow metaphase cytogenetic data of MDS patients enrolled in South Australian MDS/AML registry data. Appropriate Institutional Review Board approval was obtained. Diagnosis and subclassification of MDS were done according to World Health Organization (WHO) 2016 criteria and risk stratified according to the revised International Prognostic Scoring System (R-IPSS) (Greenberg et al., 2012). Standard G-banding method was used for cytogenetic analysis.To decipher changes induced by cytotoxic therapy (CT) from that of myeloid neoplasm in general, we compared cytogenetic profile of three carefully selected cohorts: (i) tMN, in which a myeloid neoplasm occurred in a cancer survivor following exposure to cytotoxic (n = 206, 15.5%); (ii) myeloid neoplasm developing in unrelated cancer survivors with NO prior exposure to CT (a diagnosis of primary MN and another cancer; pMN+Ca) (n =148, 12%). This would include myelodysplastic syndrome or acute myeloid leukemia diagnosed in patients managed with surgical resection of breast cancer and NO exposure to CT; (iii) primary MDS without preceding independent cancer and/or exposure to CT (pMDS) (n = 893,72.5%)Results: The median age of 1247 patients analyzed was 72.50 (IQR 64.9 to 79) and 64% patients were male. Majority of patients were diagnosed with pMDS (n=893; 72.5%), while 206 (15.5%) and 148 (12%) were classified as t-MN and pMN+Ca respectively.Ten percent (114/1247) patients harbored translocations at the time of diagnosis. The most frequent chromosomes involved in translocation are chromosome 1 (37/114, 34.5%), 3 (15/114, 13.8%), 5 (6/114= 5.3%) (Fig.1A). Most common chromosome partners for translocation with chromosome 1 were chromosome 3, 7 and 21.The frequency of chromosomal translocations in patients with monsomal (55/114, 48%) and complex (70/114, 61%) karyotype were higher than patients without. There is a clear relationship in incidence of chromosomal translocations with increasing IPSS-R scores. The frequency of translocations in the Very high risk IPSS-R risk category was significantly higher compared to patients with Very low risk category (27% vs.1.1%).Importantly, frequency of chromosomal translocations was significantly higher in t-MN as compared pMN+Ca and P-MN patients who were not exposed to DNA damaging cytotoxic therapies prior to their diagnosis (17% vs. 4% vs. 8%, P=0.0004; Fig 1B). Notably, the survival of patients with chromosomal translocation was significantly poorer as compared to patients without translocation (Fig.1C). Poor OS of patients with translocation is most probably due to association with complex karyotype (Fig.1D).Conclusion: This comprehensive analysis demonstrates that chromosomal translocations are observed in 10% of MDS patients. Chromosomal translocations are significantly higher in patients who had prior exposure to cytotoxic therapy as compared to patients without. [Display omitted] DisclosuresHiwase: Novartis: Membership on an entity's Board of Directors or advisory committees; AbbVie: Membership on an entity's Board of Directors or advisory committees.

The CDK7 Inhibitor THZ1 Alters RNA Polymerase Dynamics at the 5‘ and 3‘ Ends of Genes

The t(8;21) is one of the most frequent chromosomal translocations in acute myeloid leukemia (AML). This translocation encodes a fusion protein containing the DNA binding domain of RUNX1, a master regulator of hematopoiesis, linked to the majority of the myeloid translocation gene on chromosome 8 (MTG8, also known as eight-twenty-one or ETO; gene name RUNX1T1). This chimeric fusion protein binds to the RUNX1 DNA elements to control gene expression by recruiting transcriptional cofactors via the MTG8/ETO moiety. In addition, MTG/ETO family proteins co-purified in a complex that also contained “E proteins” and the cyclin dependent kinase CDK9, a component of the positive transcription elongation factor b (P-TEFb).P-TEFb contains Cyclin T1 and CDK9 and several potential CDK9 inhibitors have shown promise in the clinics for t(8;21) AML, such as flavopiridol (alvocidib). Transcription initiation, promoter-proximal pausing of RNA polymerase II (RNAPII), and transcription elongation are events that are highly regulated for genes involved in proliferation and differentiation such as MYC and BCL2 . CDK7 phosphorylates Ser5 of the C-terminal domain of RNAPII to trigger promoter-proximal pausing of RNA polymerase II, whereas CDK9 phosphorylates Ser2 of RNAPII and the negative elongation factors DSIF and NELF to release the polymerase into the body of the gene.In this study, we used inhibitors of CDK7 and CDK9 to probe for transcriptional vulnerabilities in t(8;21) AML. We used both broad spectrum (flavopiridol, dinacicilib) and a specific CDK9 inhibitor PHA767491 along with THZ1 (CDK7 inhibitor). Since CDK7 is also a CAK (CDK activating kinase) that activates cell-cycle CDKs and mutations in Cyclin D2 are common in t(8;21) AML, we also tested the highly selective CDK4/6 inhibitor palbociclib (PD-0332991). We observed that the t(8;21)-containing AML cell lines SKNO-1 and Kasumi-1, as well as primary AML patient cells, were extremely sensitive to all the CDK7/9 inhibitors, but not palbociclib. We used precision global run-on transcription sequencing (PROseq) to define the mechanism of action of these compounds. This technique creates high resolution genomic maps of the active RNA polymerases to define the effects on RNA polymerase dynamics. CDK9 inhibitors caused wide spread RNA Polymerase II promoter proximal pausing at nearly 80% of the expressed genes, as well as at enhancers where there was a general impairment of production of eRNAs and lncRNAs. Conversely, inhibition of CDK7, a critical component of TFIIH caused a loss of paused RNA polymerase II at promoters, which was associated with an increase of polymerases in the body of genes. While RUNX1 was reported to be regulated by CDK7 in T-ALL, there was no impact on the expression of RUNX1 or the fusion protein in t(8;21)-containing cells. Although enhancers were not affected, super enhancers were modestly affected by THZ1. Interestingly, within a subset of genes that showed increased RNA polymerase accumulation within the gene body, CDK7 inhibition altered 3' end transcription termination dynamics within 1 hr and this effect remained even at 2 hr. A time course of THZ1 treatment at 0, 15', 30', and 60' suggested that CDK7 inhibition altered RNA polymerase dynamics at 5'ends of the genes, and it's these effects that eventually affected transcription termination at the 3' ends of the genes. DisclosuresSavona:Amgen: Membership on an entity's Board of Directors or advisory committees; Sunesis: Research Funding; Takeda: Research Funding; Karyopharm: Consultancy, Equity Ownership; TG Therapeutics: Membership on an entity's Board of Directors or advisory committees, Research Funding; Astex: Membership on an entity's Board of Directors or advisory committees, Research Funding; Incyte Corporation: Consultancy, Research Funding; Gilead: Membership on an entity's Board of Directors or advisory committees; Celgene: Membership on an entity's Board of Directors or advisory committees.

Chromosomal translocations inactivating CDKN2A support a single path for malignant peripheral nerve sheath tumor initiation.

Malignant peripheral nerve sheath tumors (MPNST) are aggressive soft tissue sarcomas with poor prognosis, developing either sporadically or in persons with neurofibromatosis type 1 (NF1). Loss of CDKN2A/B is an important early event in MPNST progression. However, many reported MPNSTs exhibit partial or no inactivation of CDKN2A/B, raising the question of whether there is more than one molecular path for MPNST initiation. We present here a comprehensive genomic analysis of MPNST cell lines and tumors to explore in depth the status of CDKN2A. After accounting for CDKN2A deletions and point mutations, we uncovered a previously unnoticed high frequency of chromosomal translocations involving CDKN2A in both MPNST cell lines and primary tumors. Most identified translocation breakpoints were validated by PCR amplification and Sanger sequencing. Many breakpoints clustered in an intronic 500bp hotspot region adjacent to CDKN2A exon 2. We demonstrate the bi-allelic inactivation of CDKN2A in all tumors (n = 15) and cell lines (n = 8) analyzed, supporting a single molecular path for MPNST initiation in both sporadic and NF1-related MPNSTs. This general CDKN2A inactivation in MPNSTs has implications for MPNST diagnostics and treatment. Our findings might be relevant for other tumor types with high frequencies of CDKN2A inactivation.

Concept of T-Cell Genus as a Basis for Analysis of the Results of Cytogenetic Studies after Local Bone Marrow Exposure

Evaluation of the frequency of chromosome translocations in peripheral blood T-lymphocytes is a generally accepted method of retrospective biodosimetry. Accidental contamination of the Techa River (Chelyabinsk Oblast) in 1950s with bone-seeking long-lived strontium-90 gave an opportunity to evaluate the effect of local red bone marrow (RBM) exposure on translocation formation in the peripheral T-lymphocytes of local inhabitants. The studies of the inhabitants using fluorescent in situ hybridization (FISH) showed that RBM doses calculated based on FISH results were lower than those estimated based on 90Sr body burden measurements. The current study presents analytical review of the published data dealing with the most important processes of the T-lymphocyte development and formation of chromosome aberrations: characteristics of the main compartments where the exposure of T-cell occurs; assessment of the time spent by T-lymphocytes and their progenitors in these compartments; analysis of the dynamics of T-cell populations (proliferation and death); age-related aspects. The paper presents a concept of T-cell Genus (TG) united all the progeny of T progenitor with inheritable specific aberrations that could have developed in bone marrow.

Evolution and structure of clinically relevant gene fusions in multiple myeloma

Multiple myeloma is a plasma cell blood cancer with frequent chromosomal translocations leading to gene fusions. To determine the clinical relevance of fusion events, we detect gene fusions from a cohort of 742 patients from the Multiple Myeloma Research Foundation CoMMpass Study. Patients with multiple clinic visits enable us to track tumor and fusion evolution, and cases with matching peripheral blood and bone marrow samples allow us to evaluate the concordance of fusion calls in patients with high tumor burden. We examine the joint upregulation of WHSC1 and FGFR3 in samples with t(4;14)-related fusions, and we illustrate a method for detecting fusions from single cell RNA-seq. We report fusions at MYC and a neighboring gene, PVT1, which are related to MYC translocations and associated with divergent progression-free survival patterns. Finally, we find that 4% of patients may be eligible for targeted fusion therapies, including three with an NTRK1 fusion.

Routine Karyotyping Reveals Frequent Mosaic Reciprocal Chromosome Translocations in Swine: Prevalence, Pedigree, and Litter Size

In the routine commercial karyotype analysis on 5,481 boars, we identified 32 carriers of mosaic reciprocal translocations, half of which were carrying a specific recurrent translocation, mos t(7;9). An additional 7 mosaic translocations were identified through lymphocyte karyotype analysis from parents and relatives of mosaic carriers (n = 45), a control group of non-carrier boars (n = 73), and a mitogen assessment study (n = 20), bringing the total number of mosaic carriers to 39 cases. Mosaic translocations in all carriers were recognized to be confined to hematopoietic cells as no translocations were identified in fibroblasts cells of the carriers. In addition, negative impact on reproduction was not observed as the fertility of the carriers and their relatives were comparable to breed averages, and cryptic mosaicism was not detected in the family tree. This paper presents the first study of mosaic reciprocal translocations identified in swine through routine screening practices on reproductively unproven breeding boars while presenting evidence that these type of chromosome abnormalities are not associated with any affected phenotype on the carrier animals. In addition, the detection of recurrent mosaic translocations in this study may emphasize the non-random nature of mosaic rearrangements in swine and the potential role of genomic elements in their formation.

Detection of Simple, Complex, and Clonal Chromosome Translocations Induced by Internal Radioiodine Exposure: A Cytogenetic Follow-Up Case Study after 25 Years

Here, we report the findings of a 25-year cytogenetic follow-up study on a male patient who received 2 rounds of radioiodine treatment within a span of 26 months (1.78 GBq in 1992 and 14.5 GBq in 1994). The patient was 34 years old with a body mass index of 25 at the time of the first radioiodine treatment. Multicolor FISH and multicolor banding (mBAND) techniques performed on the patient detected inter- and intrachromosomal exchanges. Although the frequency of chromosome translocations remained essentially the same as reported in our earlier study (0.09/cell), the percentage of reciprocal (balanced) translocations increased from 54.38 to 80.30% in the current study. In addition to simple chromosome translocations, complex exchanges (0.29%) involving more than 2 chromosomes were detected for the first time in this patient. Strikingly, a clonal translocation involving chromosomes 14 and 15, t(14p;15q), was found in 7 of the 677 cells examined (1.03%). The presence of complex and clonal translocations indicates the onset of chromosomal instability induced by internal radioiodine exposure. mBAND analysis using probes specific for chromosomes 1, 2, 4, 5, and 10 revealed 5 inversions in a total of 717 cells (0.69%), and this inversion frequency is several-fold higher than the baseline frequency reported in healthy individuals using the classical G-banding technique. Collectively, our study suggests that stable chromosome aberrations such as translocations and inversions can be useful not only for retrospective biodosimetry but also for long-term monitoring of chromosomal instability caused by past radioiodine exposure.

Investigation of the cumulative number of chromosome aberrations induced by three consecutive CT examinations in eight patients.

In our previous study, we found that chromosomes were damaged by the radiation exposure from a single computed tomography (CT) examination, based on an increased number of dicentric chromosomes (Dics) formed in peripheral blood lymphocytes after a CT examination. We then investigated whether a cumulative increase in the frequency of Dics and chromosome translocations (Trs) formation could be observed during three consecutive CT examinations performed over the course of 3–4 years, using lymphocytes in peripheral bloods of eight patients (five males and three females; age range 27–77 years; mean age, 64 years). The effective radiation dose per CT examination estimated from the computational dosimetry system was 22.0–73.5 mSv, and the average dose per case was 40.5 mSv. The frequency of Dics formation significantly increased after a CT examination and tended to decrease before the next examination. Unlike Dics analysis, we found no significant increase in the frequency of Trs formation before and after the CT examination, and we observed no tendency for the frequency to decrease before the next CT examination. The frequency of Trs formation was higher than that of Dics formation regardless of CT examination. Furthermore, neither analysis of Dics nor Trs showed a cumulative increase in the frequency of formation following three consecutive CT examinations.

Identification of a novel long non-coding RNA within RUNX1 intron 5

BackgroundRUNX1 gene, a master regulator of the hematopoietic process, participates in pathological conditions as a partner for several genes in chromosomal translocations. One of the most frequent chromosomal translocations found in acute myeloid leukemia patients is the t(8;21), in which RUNX1 and ETO genes recombine. In RUNX1 gene, the DNA double-strand breaks that originate the t(8;21) are generated in the intron 5, specifically within three regions designated as BCR1, BCR2, and BCR3. To date, what determines that these regions are more susceptible to DNA double-strand breaks is not completely clear. In this report, we characterized RUNX1 intron 5, by analyzing DNase-seq and ChIP-seq data, available in the ENCODE Project server, to evaluate DNaseI hypersensitivity and the presence of the epigenetic mark H3K4me3 in 124 and 51 cell types, respectively.ResultsOur results show that intron 5 exhibits an epigenetic mark distribution similar to known promoter regions. Moreover, using the online tool YAPP and available CAGE data from the ENCODE Project server, we identified several putative transcription start sites within intron 5 in regions BCR2 and BCR3. Finally, available EST data was analyzed, identifying a novel uncharacterized long non-coding RNA, which is expressed in hematopoietic cell lines as shown by RT-PCR. Our data suggests that the core promoter of the novel long non-coding RNA locates within the region BCR3.ConclusionWe identified a novel long non-coding RNA within RUNX1 intron 5, transcribed from a promoter located in the region BCR3, one of the chromosomal breakpoints of RUNX1 gene.

Abstract 2571: Role of XRCC4 downregulation in bioflavonoid-induced chromosomal translocations

Abstract The faithful repair of DNA double strand breaks (DSBs) is crucial for genome integrity, and aberrant repair can result in chromosomal translocations, including those associated with infant leukemia. Evidence from our lab and others suggests that environmental and dietary compounds such as bioflavonoids have the potential to promote chromosomal translocations in utero. DSBs can be repaired by either classical non-homologous end joining (C-NHEJ) that is mostly accurate or by microhomology-mediated alternative end joining (Alt-EJ) that is more error prone and can cause chromosomal translocations. Ku70/80, Ligase 4 (LIG4), X-Ray Repair Cross-Complementing factor 4 (XRCC4), and XRCC4 like factor (XLF) are central to C-NHEJ. Poly ADP Ribose 1 (PARP 1) and C terminal binding protein interacting protein (CtIP) participate in Alt-EJ. CtIP favors Alt-EJ pathway by promoting the resection of DNA ends to uncover microhomologies supporting the formation of large deletions and chromosomal translocations. Studies suggest that loss of efficient activity in the C-NHEJ repair pathway may promote the use of the other more error-prone pathway such as Alt-EJ. The purpose of the study is to understand the relationship between bioflavonoid exposure, induction of DNA repair proteins, and repair pathway choice to understand the underlying mechanisms of bioflavonoid-induced infant leukemias. Embryonic stem (ES) cells were exposed to genistein 1 hr at doses 0μM-100μM based on determined LD50 values. Following exposure, cells were recovered 4hr, 24hr and 48 hr, followed by protein extraction and Western blotting. Protein levels of γH2AX, Ku70, XRCC4, XLF, CtIP and PARP-1 were measured by densitometry and analyzed using one way ANOVA. CRISPR-Cas9 was used to downregulate C-NHEJ DNA repair protein XRCC4. XRCC4-/- cells will subsequently be exposed to genistein, recovered, followed by protein extraction and Western blotting. Protein levels of γH2AX, Ku70, XRCC4, XLF, CtIP and PARP-1 will measured by densitometry. Protein levels before and after gene editing of XRCC4 will be compared and analyzed using two way ANOVA. We have downregulated the XRCC4 gene in ES cells and anticipate that following exposure to genistein in the absence of XRCC4, we will detect elevated chromosomal translocation frequency in those stem cells by stimulating the Alt-EJ pathway. This research will be highly impactful in understanding how bioflavonoid-induced DNA damage is repaired by cells and whether these compounds promote genome instability analogous to that observed in infant leukemia. Citation Format: Anindita Ghosh, Christine A. Richardson. Role of XRCC4 downregulation in bioflavonoid-induced chromosomal translocations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2571.