Complex Chromosomal Aberrations Research Articles

Genomic Balancing Act: deciphering DNA rearrangements in the complex chromosomal aberration involving 5p15.2, 2q31.1, and 18q21.32.

Despite extensive research into the genetic underpinnings of neurodevelopmental disorders (NDD), many clinical cases remain unresolved. We studied a female proband with a NDD, mildly dysmorphic facial features, and brain stem hypoplasia on neuroimaging. Comprehensive genomic analyses revealed a terminal 5p loss and aterminal 18q gain in the proband while a diploid copy number for chromosomes 5 and 18 in both parents. Genomic investigations in the proband identified an unbalanced translocation t(5;18) with additional genetic material from chromosome 2 (2q31.3) inserted at the breakpoint, pointing to a complex chromosomal rearrangement (CCR) involving 5p15.2, 2q31.3, and 18q21.32. Breakpoint junction analyses enabled by long-read genome sequencing unveiled the presence of four distinct junctions in the father, who is acarrier of a balanced CCR. The proband inherited from the father both the abnormal chromosome 5 resulting in segmental aneusomies of chr5 (loss) and chr18 (gain) and a der(2) homologue. Evidences suggest a chromoplexy mechanism for this CCR derivation, involving double-strand breaks (DSBs) repaired by non-homologous end joining (NHEJ) or alternative end joining (alt-EJ). The complexity of the CCR and the segregation of homologues elucidate the genetic model for this family. This study demonstrates the importance of combining multiple genomic technologies to uncover genetic causes of complex neurodevelopmental syndromes and to better understand genetic disease mechanisms.

Molecular basis of multiple myeloma.

Multiple myeloma (MM) is aheterogeneous hematological malignancy characterized by clonal expansion of malignant plasma cells in the bone marrow. The disease is accompanied by various clinical manifestations, such as bone lesions, anemia, hypercalcemia, and renal insufficiency. However, despite significant advances in treatment over the last two decades, the disease remains challenging to treat, and most patients relapse. Although its pathogenesis has not yet been elucidated, it is clear that genomic instability plays akey role in its develop-ment or resistance to treatment. In some instances, the cause of this instability is chromothripsis, aform of complex genomic rearrangement that involves shattering and subsequent haphazard reassembly of chromosomes within asingle catastrophic event. The resulting rearrangements involve avariety of structural changes, including deletions, duplications, inversions, and translocations, that lead to genome disruption. Specifically, these changes may result in alteration or inactivation of tumor suppressor genes (TP53and CDKN2C), activation of oncogenes (MAF, FGFR3, and CCND1) or genes involved in key cellular processes. Unraveling the mechanisms that result in chromothripsis provides opportunities to identify critical genes and pathways involved in MM pathogenesis. These findings may serve as abasis for improved dia-gnostic approaches. The goal of this review is to summarize the common primary and secondary chromosomal aberrations in MM with a particular focus on introducing complex chromosomal aberrations, especially chromothripsis in MM.

M-FISH evaluation of chromosome aberrations to examine for historical exposure to ionising radiation due to participation at British nuclear test sites

Veterans of the British nuclear testing programme represent a population of ex-military personnel who had the potential to be exposed to ionising radiation through their participation at nuclear testing sites in the 1950s and 1960s. In the intervening years, members of this population have raised concerns about the status of their health and that of their descendants, as a consequence. Radiation dose estimates based on film badge measurements of external dose recorded at the time of the tests suggest any exposure to be limited for the majority of personnel, however, only ∼20% of personnel were monitored and no measurement for internalised exposure are on record. Here, to in-part address families concerns, we assay for chromosomal evidence of historical radiation exposure in a group of aged nuclear test (NT) veterans, using multiplex in situ hybridisation (M-FISH), for comparison with a matched group of veterans who were not present at NT sites. In total, we analysed 9379 and 7698 metaphase cells using M-FISH (24-colour karyotyping) from 48 NT and 38 control veteran samples, representing veteran servicemen from the army, Royal Airforce and Royal Navy. We observed stable and unstable simple- and complex-type chromosome aberrations in both NT and control veterans’ samples, however find no significant difference in yield of any chromosome aberration type between the two cohorts. We do observe higher average frequencies of complex chromosome aberrations in a very small subset of veterans previously identified as having a higher potential for radiation exposure, which may be indicative of internalised contamination to long-lived radionuclides from radiation fallout. By utilising recently published whole genome sequence analysis data of a sub-set of the same family groups, we examined for but found no relationship between paternal chromosome aberration burden, germline mutation frequency and self-reported concerns of adverse health in family members, suggesting that the previously reported health issues by participants in this study are unlikely to be associated with historical radiation exposure. We did observe a small number of families, representing both control and NT cohorts, showing a relationship between paternal chromosome aberrations and germline mutation sub-types which should be explored in future studies. In conclusion, we find no cytogenetic evidence of historical radiation exposure in the cohort of nuclear veterans sampled here, offering reassurance that attendance at NTs sites by the veterans sampled here, was not associated with significant levels of exposure to radiation.

FISH-Banding for Characterization of Simple and Complex Chromosomal Rearrangements in Cancer.

While interphase and metaphase-directed molecular cytogenetics is a standard technique in routine tumor (cyto)genetics, fluorescence in situ hybridization-based banding (FISH-banding) approaches are less commonly applied. In research FISH-banding showed its excellence in the characterization of simple and complex chromosomal aberrations; however, in routine settings, it is still only little applied. The main argument against FISH-banding is, that it shall be associated with comparatively high costs. However, if applied advisedly FISH-banding can even save costs, as in one or two chromosome-specific FISH experiments; otherwise, cryptic, not resolvable chromosomal rearrangements may be resolved quickly. Here the protocol for the only yet commercially available FISH-banding approach-the multicolor banding (MCB/ mBAND)-is outlined.

MaterniCode: New Bioinformatic Pipeline to Detect Fetal Aneuploidies and Rearrangements Using Next-Generation Sequencing.

Objective: The present study is aimed at introducing and evaluating MaterniCode, a state-of-the-art bioinformatic pipeline for noninvasive prenatal testing (NIPT) that leverages the Ion Torrent semiconductor sequencing platform. The initiative strives to revolutionize prenatal diagnostics by offering a rapid and cost-effective method without sacrificing accuracy. Methods: Two distinct bioinformatic strategies were employed for fetal sex determination, one of which achieved 100% accuracy. We analyzed 1225 maternal blood samples for fetal aneuploidies, benchmarking against the industry standard Illumina VeriSeq™ NIPT Solution v2. The capability of MaterniCode to detect and characterize complex chromosomal anomalies was also assessed. Results: MaterniCode achieved near-perfect accuracy in fetal sex determination through chromosome Y (chrY )-specific gene analysis, whereas the alternative method, employing the ratio of high-quality mapped reads on chrY relative to all reads, delivered 100% accuracy. For fetal aneuploidy detection, both the integrated WisecondorX and NIPTeR algorithms demonstrated a 100% sensitivity and specificity rate, consistent with Illumina VeriSeq™ NIPT Solution v2. The pipeline also successfully identified and precisely mapped significant chromosomal abnormalities, exemplified by a 2.4 Mb deletion on chromosome 13 and a 3 Mb duplication on chromosome 2. Conclusion: MaterniCode has proven to be an innovative and highly efficient tool in the domain of NIPT, demonstrating excellent sensitivity and specificity. Its robust capability to effectively detect a wide range of complex chromosomal aberrations, including rare and subtle variations, positions it as a promising and valuable addition to prenatal diagnostic technologies. This enhancement to diagnostic precision significantly aids clinicians in making informed decisions during pregnancy management.

T Cell Selection Is Not Helpful for Therapeutic Efficacy of CART19 in Relapsed or Refractory B-ALL Patients with Peripheral Blood Leukemia Burden at Time of Apheresis

Abstract Introduction: We have demonstrated peripheral blood (PB) blasts negatively affected chimeric antigen receptor T cells targeting CD19 (CART19) production and the clinical efficacy of CART19 therapy in patients (pts) with refractory/relapsed B cell acute lymphoblastic leukemia (r/r B-ALL) (published in Molecular Therapy: Methods & Clinical Development ,2021). Whether sorting T cells before activation might be helpful for ex-vivo CART19 quality and in-vivo treatment efficacy requires further investigation. Here, we retrospectively analyzed 40 pts with or without upfront T cell purification to evaluate these indexes. Patients and Methods: From July 2021 to June 2023, 40 r/r B-ALL with PB blasts at time of apheresis experienced CART19 therapy. After leukapheresis, all pts' PBMCs were isolated using lymphocyte separation liquid. 30 pts didn't perform T cells selection (group 1) and 10 pts performed T cells selection (group 2). All of cells were activated with CD3 and CD28 antibodies for 24h, then transduced with the lentivirus encoding anti-CD19-CD3zeta-4-1BB CAR and cultured for 5-6 days in serum-free media containing IL2, IL7, IL15, IL21. The baseline characteristics, including age, sex, previous therapy period, blasts in BM, EMD distribution, complex chromosome aberration, poor fusion genes and gene mutations, did not differ between the two groups (Table 1). Cell viability, expanding fold, percentage of CD3 +T and CD3 + CD8 +T cells, transfection efficiency, B cells were all examined pre CART19 infusion. All pts received cyclophosphamide 250 mg/m2/d X 3d, and fludarabine 30 mg/m2/d X 3d, followed by CART19 infusion with a median number of 9.7(0.17-60) X10 5cells/kg in group 1 and 10 (4-16.3) X10 5cells/kg in group 2 ( P=0.99). PB and BM blasts was determined by flow cytometry (FCM). All pts underwent bone marrow (BM) biopsy examination and FCM studies on day 15 or day 30 to determine the response and remission status. Results: At time of apheresis, group 1 and group 2 had a median leukemia cell of 18% (2%-71%) and 19.4% (7%-54.4%) in PB ( P=0.5), respectively. In group 1 and group 2, the median percent of CD3 +T and CD3 + CD8 +T cells were 97.7% (70% - 99.5%) vs. 97.7% (94.8%-99.2%) ( P=0.46) and 66% (24.3% - 88.3%) vs. 64.2% (28% - 84.4%) ( P=0.45), respectively. The median cell viability, transfection efficiency and cell expanding fold in the final products was 82.9%（44.4%-92.2%) vs. 88.6%（76.4%-95.2%）( P=0.09), 31.4%（3.1%-65.5%) vs. 23.6% (12.4%-35.5%) ( P=0.08) and 3.18-fold（0.24-13.6) vs. 2.32-fold（0.48-8.13) ( P=0.83), respectively. Both of normal B and leukemia cells were undetectable pre CART19 infusion in two groups. After CART19 infusion, the median peak CART19/ lymphocyte cells, expanding fold and absolute CART19 count in vivo was 45% (0-79.4%) vs. 57.9% (0-75%) ( P=0.86), 16.7-fold (0-397.3) vs.13.2-fold (0-406)( P=0.96) and 229 (0-4810) X10 6/L blood vs. 242 (0-3220) X10 6/L blood ( P=0.83) in two groups, respectively. In group 1, 28/30 cases were evaluable and 25/28 (89.3%) obtained complete remission (CR)/ incomplete count recovery CR (CRi) and 24/28 (85.7%) obtained minimal residual disease (MRD) - CR. 1/2 patient unevaluable died from pneumonia due to severe and persisted neutropenia. One no-responder was infused at <1 X10 5 cells/kg and his culture failed to expand in vivo, and the other no-responder was infused at 1.16 X10 5 cells/kg (with TEL-AML1 positive). In group 2, 8/10 cases were evaluable and 6/8 (75%) obtained CR/CRi with all MRD - CR (75%). The two non-responders had no detectable CART19 in PB after infusion for one month. Results were shown in Table2. Conclusion: We have demonstrated pts with PB blasts without sorting T cells had poorer ex-vivo CART19 quality and in-vivo treatment efficacy compared to pts without PB blasts (published). Sorting T cells before activation is expected to remove the adverse culture conditions in the system. However, in the present study, upfront T cell purification didn't improve ex vivo cell characteristics and in vivo cell dynamics in r/r B-ALL pts with PB blasts, showing that the negative influence of PB blasts at the time of apheresis could not be reversed by upfront T cell purification. Therefore, leukemia burden in PB is suggested to be reduced before leukapheresis. Absolutely, one of the limitations of our study is that a relatively small number of products was evaluated, and larger samples need to be included to further demonstrated.

Loss of Chromosome 3q Is a Prognostic Marker in Fusion-Negative Rhabdomyosarcoma.

Soft tissue sarcomas (STS) are rare mesenchymal neoplasms that frequently show complex chromosomal aberrations such as amplifications or deletions of DNA sequences or even whole chromosomes. We recently found that gain of chromosome (chr) 8 is associated with worse overall survival (OS) in STS as a group. We therefore aimed to investigate the overall copy number profile of rhabdomyosarcoma (RMS) to evaluate for prognostic signatures. Fluorescence in situ hybridization (FISH) testing was performed on a cohort of STS to assess for chr8 gain. Copy number variation (CNV) data from the National Cancer Institute were analyzed to assess for prognostically significant CNV aberrations in FOXO1 fusion-negative (FN)- versus fusion-positive (FP)-RMS. FISH testing was performed on a cohort of FN-RMS to assess for chr3q loss and correlate with outcomes. Chr8 gain is a highly prevalent CNV in embryonal RMS and shows slightly improved prognosis. Meanwhile, loss of chr3q was associated with worse outcome in FN-RMS compared with FP-RMS. The pathogenesis of STS including FN-RMS remains poorly understood, emphasizing the need for new therapeutic advances and adequate risk stratification. Our data demonstrate that loss of chr3q is associated with poor OS in FN-RMS, supporting it as an important tool for risk stratification.

Optical Genome Mapping for Comprehensive Assessment of Chromosomal Aberrations and Discovery of New Fusion Genes in Pediatric B-Acute Lymphoblastic Leukemia.

To assess the potential added value of Optical Genomic Mapping (OGM) for identifying chromosomal aberrations. We utilized Optical Genomic Mapping (OGM) to determine chromosomal aberrations in 46 children with B-cell Acute lymphoblastic leukemia ALL (B-ALL) and compared the results of OGM with conventional technologies. Partial detection results were verified by WGS and PCR. OGM showed a good concordance with conventional cytogenetic techniques in identifying the reproducible and pathologically significant genomic SVs. Two new fusion genes (LMNB1::PPP2R2B and TMEM272::KDM4B) were identified by OGM and verified by WGS and RT-PCR for the first time. OGM has a greater ability to detect complex chromosomal aberrations, refine complicated karyotypes, and identify more SVs. Several novel fusion genes and single-gene alterations, associated with definite or potential pathologic significance that had not been detected by traditional methods, were also identified. OGM addresses some of the limitations associated with conventional cytogenomic testing. This all-in-one process allows the detection of most major genomic risk markers in one test, which may have important meanings for the development of leukemia pathogenesis and targeted drugs.

LncRNA PVT-1 promotes osteosarcoma cancer stem-like properties through direct interaction with TRIM28 and TSC2 ubiquitination.

Osteosarcoma, the most common pediatric bone tumor, is an aggressive heterogeneous malignancy defined by complex chromosomal aberrations. Overall survival rates remain at ~70%, but patients with chemoresistant or metastatic disease have extremely poor outcomes of <30%. A subgroup of tumors harbor amplification of chromosome 8q24.2 and increased expression of the oncogenic long noncoding RNA (lncRNA) Plasmacytoma Variant Translocation-1 (PVT-1), which is associated with an extremely poor clinical prognosis. This study demonstrates that PVT-1 is critical for osteosarcoma tumor-initiation potential. Chromatin Hybridization by RNA Purification analysis identified Tripartite-Motif Containing Family 28 (TRIM28) as a novel PVT-1 binding partner. Mechanistically, co-immunoprecipitation studies showed the PVT-1/TRIM28 complex binds and increases SUMOylation of phosphatidylinositol 3-kinase catalytic subunit type 3 (Vps34), which leads to enhanced ubiquitination and degradation of tumor suppressor complex 2 (TSC2), thus contributing to increased self-renewal and stem cell phenotypes. Furthermore, we identified that osteosarcoma cells with increased PVT-1 have enhanced sensitivity to the SUMOylation inhibitor, TAK-981. Altogether, this study elucidated a role for PVT-1 in the enhancement of cancer stem-like behaviors, including migration and invasion, in osteosarcoma, and identified the novel PVT-1/TRIM28 axis signaling cascade as a potential therapeutic target for osteosarcoma treatment.

Oxidative Damage Induced Telomere Mediated Genomic Instability in Cells from Ataxia Telangiectasia Patients.

Our cellular genome is susceptible to cytotoxic lesions which include single strand breaks and double strand breaks among other lesions. Ataxia telangiectasia mutated (ATM) protein was one of the first DNA damage sensor proteins to be discovered as being involved in DNA repair and as well as in telomere maintenance. Telomeres help maintain the stability of our chromosomes by protecting the ends from degradation. Cells from ataxia telangiectasia (AT) patients lack ATM and accumulate chromosomal alterations. AT patients display heightened susceptibility to cancer. In this study, cells from AT patients (called as AT -/- and AT +/- cells) were characterized for genome stability status and it was observed that AT -/- cells show considerable telomere attrition. Furthermore, DNA damage and genomic instability were compared between normal (AT +/+ cells) and AT -/- cells exhibiting increased frequencies of spontaneous DNA damage and genomic instability markers. Both AT -/- and AT +/- cells were sensitive to sodium arsenite (1.5 and 3.0 μg/ml) and ionizing radiation-induced (2 Gy, gamma rays) oxidative stress. Interestingly, telomeric fragments were detected in the comet tails as revealed by comet-fluorescence in situ hybridization analysis, suggestive of telomeric instability in AT -/- cells upon exposure to sodium arsenite or radiation. Besides, there was an increase in the number of chromosome alterations in AT -/- cells following arsenite treatment or irradiation. In addition, complex chromosome aberrations were detected by multicolor fluorescence in situ hybridization in AT -/- cells in comparison to AT +/- and normal cells. Telomere attrition and chromosome alterations were detected even at lower doses of sodium arsenite. Peptide nucleic acid - FISH analysis revealed defective chromosome segregation in cells lacking ATM proteins. The data obtained in this study substantiates the role of ATM in telomere stability under oxidative stress.

Alpha-Particle Exposure Induces Mainly Unstable Complex Chromosome Aberrations which do not Contribute to Radiation-Associated Cytogenetic Risk.

The mechanism underlying the carcinogenic potential of α radiation is not fully understood, considering that cell inactivation (e.g., mitotic cell death) as a main consequence of exposure efficiently counteracts the spreading of heritable DNA damage. The aim of this study is to improve our understanding of the effectiveness of α particles in inducing different types of chromosomal aberrations, to determine the respective values of the relative biological effectiveness (RBE) and to interpret the results with respect to exposure risk. Human peripheral blood lymphocytes (PBLs) from a single donor were exposed ex vivo to doses of 0-6 Gy X rays or 0-2 Gy α particles. Cells were harvested at two different times after irradiation to account for the mitotic delay of heavily damaged cells, which is known to occur after exposure to high-LET radiation (including α particles). Analysis of the kinetics of cells reaching first or second (and higher) mitosis after irradiation and aberration data obtained by the multiplex fluorescence in situ hybridization (mFISH) technique are used to determine of the cytogenetic risk, i.e., the probability for transmissible aberrations in surviving lymphocytes. The analysis shows that the cytogenetic risk after α exposure is lower than after X rays. This indicates that the actually observed higher carcinogenic effect of α radiation is likely to stem from small scale mutations that are induced effectively by high-LET radiation but cannot be resolved by mFISH analysis.

Identification of a fetus with complex chromosomal structural aberration by next-generation sequencing and karyotype analysis

To perform prenatal diagnosis for a woman carrying a balanced translocation. Clinical phenotype of the woman and her first child was analyzed. Peripheral blood sample of the woman and amniotic fluid sample from two subsequent pregnancies were subjected to chromosomal karyotyping and copy number variation analysis through next-generation sequencing (NGS). The karyotypes of the woman and her first child were determined as 46,XX,t(5;6)(p15:p23) and 46,XX,?der(5),t(5;6)(p15.32;p22.3), respectively. The karyotype of the amniocyte from her second pregnancy was 46,XN,t(5;6)(p15:p23). No pathogenic copy number variation was detected. The karyotype of her third pregnancy was 46,XN,?der(5),t(5;6)(p15.32;p22. 3), in addition with a 6.04 Mb deletion at 5p15.33p15.32 (20 000 - 6 060 000) and a 18.50 Mb duplication at 6p25.3p22.3 (160 000 - 18 660 000). Combined karyotyping analysis and NGS has enabled detection of fetal copy number variations for a woman carrying a balanced chromosomal translocation.

Acute Myeloid Leukemia and Myelodysplastic Syndromes with TP53 Aberrations - A Distinct Stem Cell Disorder.

The tumor suppressor p53 exerts pivotal roles in hematopoietic stem cell (HSC) homeostasis. Mutations of the TP53 gene have recently been described in individuals with clonal hematopoiesis conferring substantial risk of developing blood cancers. In patients with acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS), TP53 aberrations-mutations, deletions, and a combination thereof-are encountered at a constant frequency of approximately 10%. These aberrations affect HSCs transforming them into preleukemic stem cells, pinpointing their central role in leukemogenesis. AML and MDS with TP53 aberrations are characterized by complex chromosomal aberrations. Respective patients experience a dismal long-term outcome following treatment with both intensive and nonintensive regimens including novel agents like venetoclax combinations or even allogeneic HSC transplantation. However, according to the 2016 WHO classification, AML and MDS with TP53 aberrations are still regarded as separate disease entities. On the basis of their common biological and clinical features, we propose to classify AML and MDS with TP53 aberrations as a single, distinct stem cell disorder with a unique genetic make-up, comparable with the WHO classification of "AML with recurrent genetic abnormalities." This approach will have implications for basic and translational research endeavors, aid in harmonization of current treatment strategies, and facilitate the development of master trials targeting a common deleterious driver event.

Genomic characterization of a newly established esophageal squamous cell carcinoma cell line from China and published esophageal squamous cell carcinoma cell lines

BackgroundEsophageal squamous cell carcinoma (ESCC) is one of the most prevalent malignancies and a major cause of cancer related death worldwide, especially in China. Cell lines are widely used disease models for basic medical research, however, well characterized ESCC cell models from China were seldom reported. Misidentifying and cross-contaminations of cell lines also hamper the way of producing solid and reproductive data.MethodsCSEC216 was originated from a 45-year-old male ESCC patient from Chaoshan littoral, China. Specimens were minced into fragments and seeded in T-25 flask for primary culture. Immunoflourescence staining was performed for identifying the origination and proliferation activity. In vitro migration and invasion abilities was tested by transwell assay. DNA Short Tandem Repeats profiling was implemented for cell authorization. Karyotype was investigated by spectrum karyotyping. Whole genome sequencing was utilized to investigate genomic alterations. Background information and genomic mutation data of published ESCC cell lines were obtained from online databases.ResultsCSEC216 was an uncontaminated cell line, exhibited epithelial cell features with polygonal morphology and adherent growth as monolayer. Immuno staining demonstrated its epithelial origination and high proliferation rate. The Population Doubling time was 29.7 h. The karyotype demonstrated tumor cell patterns with aneuploidy and complex chromosomal aberrations. Mutation signatures, genes with SNA or CNA of CSEC216 and published ESCC cell lines were similar with the mutation spectrum of original ESCC tumors.ConclusionsESCC cell line CSEC216 from high incidence region in China was established with no cross-contamination. Biological features were studied. Genomic mutation features of CSEC216 and 28 ESCC cell lines were characterized which provided thorough cytogenetic background that facilitated future usage.

The Position and Complex Genomic Architecture of Plant T-DNA Insertions Revealed by 4SEE.

The integration of T-DNA in plant genomes is widely used for basic research and agriculture. The high heterogeneity in the number of integration events per genome, their configuration, and their impact on genome integrity highlight the critical need to detect the genomic locations of T-DNA insertions and their associated chromosomal rearrangements, and the great challenge in doing so. Here, we present 4SEE, a circular chromosome conformation capture (4C)-based method for robust, rapid, and cost-efficient detection of the entire scope of T-DNA locations. Moreover, by measuring the chromosomal architecture of the plant genome flanking the T-DNA insertions, 4SEE outlines their associated complex chromosomal aberrations. Applying 4SEE to a collection of confirmed T-DNA lines revealed previously unmapped T-DNA insertions and chromosomal rearrangements such as inversions and translocations. Uncovering such events in a feasible, robust, and cost-effective manner by 4SEE in any plant of interest has implications for accurate annotation and phenotypic characterization of T-DNA insertion mutants and transgene expression in basic science applications as well as for plant biotechnology.

A case of chronic myeloid leukemia with Philadelphia chromosome, BCR-ABL transcript and complex translocation involving four different chromosomes

Such reported cases with the e13a3 transcript showed the Ph chromosome on karyotype analysis. This study reported a rare Ph chromosomepositive CML case with new complex chromosomal aberrations and an e13a3 BCR-ABL transcript that has yet to be established. A four-chromosome translocation involving chromosomal regions 12p11.2, 19q13.3, 9q34.1 and 22q11.2, besides a trisomy 8 and a derivative chromosome 12, were identified using high resolution multicolor banding. Reverse transcription polymerase chain reaction products showed the presence of BCR-ABL fusion transcript e13a3, and this signifies the major BCR breakpoint. The significance of the observed rearrangements and their possible role in the progression of CML was investigated.

Circulating MicroRNAs in Multiple Myeloma: a Literature Review.

Multiple myeloma is a tumour of antibody-secreting plasma cells characterized by clonal expansion and accumulation of monotypic plasma cells in the bone marrow. It is an incurable malignant neoplasm accounting for 10% all hematological malignancies. Globally, the annual percentage of new cancer cases and deaths attributed to multiple myeloma is estimated at about 0.8% and 1%, respectively. Furthermore, its global incidence ranges from 0.5 - 12/100,000 population. It causes hypercalcemia, renal insufficiency, anemia, thrombocytopenia, leucopenia, bone lesions, bone fractures, spinal stenosis, and endorgan damages. This neoplasm occurs due to a complex cytogenetic and chromosomal aberrations. These aberrations affect the expression and functions of microRNAs. Abnormal expression of these microRNAs plays an important role in the pathogenesis and angiogenesis of multiple myeloma and could have a potential role in the diagnosis, prognostic stratification, and treatment of multiple myeloma. This review aimed at summarising the expression of microRNAs and the implication of their dysregulation in the pathogenesis, diagnosis, and treatment of multiple myeloma.

Association of Genetic Factors with Long-Term Outcome in Refractory r/r B-ALL Patients after CAR T-Cell Therapy

Background Although most patients (pts) with refractory or relapsed B acute lymphoblastic leukemia (r/r B-ALL) achieved complete remission (CR) after CD19 or CD22 CAR T-cell therapy, many of them still relapsed during extended observation period. To predict and prevent the occurrence of relapse, it is critical to understand the clinical and biological factors that affect long-term outcome after CAR therapy. Here, with next generation sequencing (NGS) technology, we monitored 339 somatic gene mutations in 90 pts at enrollment and relapse. We tried to determine whether and how the genetic mutation profile will affect the remission duration in patients who received CD19 or (and) CD22 CAR T-cell therapy. Methods During November, 2017 and June, 2019, 90 pediatric r/r B-ALL pts were enrolled in this study including 39 who received CD19 CAR T-cell therapy (Clinical trial #ChiCTR-OIC-17013623), 20 who received CD22 CAR T-cell therapy (Clinical trial #ChiCTR-OIC-17013523), and 31 who received sequential CD19 and CD22 CAR T-cell therapies (Clinical trials #ChiCTR-OIB-17013670 and ChiCTR-ONC-17013648). At enrollment, detailed WHO classification has been evaluated. NGS for 339 somatic gene mutations related to hematological neoplasms has been detected by Illumina sequencing at enrollment and relapse. The average sequencing depth was more than 3000×. Sensitivity of NGS was 0.01% variant allele frequency (VAF). Somatic gene mutations whose frequency in all pts is over 3 times have been involved for analysis. We also analyzed the association of complex chromosome aberrations, high fusion genes with remission duration in these patients Results 85/90 pts had achieved complete remission after CAR T-cell therapy. 18-month EFS rate of all 85 pts was 52.2% (95%CI, 36.5 to 67.9) including 43 pts who were bridged to transplantation. 21/85 pts had relapsed with a median relapse time of 6 (1-12) months. 6/85 pts died from other reasons. 19/85 pts remained sustained remission defined as remaining remission for at least one year, including 11 pts who had been bridged to transplantation after CAR T-cell infusion. 83 somatic gene mutations were identified across 73 pts (median 2 mutations/patient; range, 0-18). 24 types of somatic gene mutations had been identified over 3 times including TP53, NRAS, KRAS, CREBBP, KMT2D, KMT2C, NR3C1, EZH2, IKZF1, PTPN11, NF1, CDKN2A, ETV6, KIT, KDM6A, STAG2, NOTCH1, ANKRD26, TERT, SETD2, KDM6B, ARID1B, SETBP1and VEGFC. We compared the gene mutation between relapsed pts and pts who had sustained remission over 1 year and found the pts who had more than 2 mutated genes have higher risk of relapse (P=0.008). We also foundTP53 mutation was poor indicator sustainable remission (P=0.003). TP53 gene mutation was detectable as a major gene at relapse with AVFs ranging from 0.55% to 95.03%. Many new derived mutated genes were easily observed at relapse, which might be generated under the pressure of CAR T-cells, and contributed to relapse. We found that FCM-MRD+and E2A-HLF fusion gene were poor indicators of sustained remission (P=0.000 and 0.024). In addition, most relapsed pts had B cell function recovery, and was significantly different to pts who remained sustained remission without bridging to transplant (P=0.001), which indicates the loss of the surveillance of CAR T-cells. Conclusion Most r/r B-ALL pts have more than 1 somatic gene mutation before CAR T-cell infusion. Complex gene mutation profile (&amp;gt;2) indicated higher risk of relapse. TP53 mutation was a poor indicator of sustained remission and remained a major genetic feature in blast at relapse. Many new types of gene mutations were detected at relapse. Therefore, monitoring genetic mutations across the procedure of CAR T-Cell therapy may predict the incidence relapse and suggest proper interventions to prevent relapse. Figure Disclosures No relevant conflicts of interest to declare.

Molecular cytogenetic diagnosis of a case with ring chromosome 18 syndrome

To explore the genetic basis for a child with developmental delay and congenital syndactyly. G-banding chromosomal karyotyping and chromosomal microarray analysis (CMA) were performed on peripheral blood sample from the child. The child was ascertained as 46, XY, r(18)[52]/45,XY,?18[3]. A 18q21.32-q23 deletion was identified by CMA with a size of 19.85 Mb, which has encompassed 99 genes including CTDP1, TXNL4A, TSHZ1, PIGN, RTTN, TNFRSF11A, KDSR and CYB5A. Clinical phenotype of the patient with ring chromosome 18 is associated with the size of the euchromatin loss and involved genes. As a useful complement to conventional karyotyping, CMA has provided an powerful tool for delineating complex chromosomal aberrations.

Long-read sequencing for rare human genetic diseases.

During the past decade, the search for pathogenic mutations in rare human genetic diseases has involved huge efforts to sequence coding regions, or the entire genome, using massively parallel short-read sequencers. However, the approximate current diagnostic rate is <50% using these approaches, and there remain many rare genetic diseases with unknown cause. There may be many reasons for this, but one plausible explanation is that the responsible mutations are in regions of the genome that are difficult to sequence using conventional technologies (e.g., tandem-repeat expansion or complex chromosomal structural aberrations). Despite the drawbacks of high cost and a shortage of standard analytical methods, several studies have analyzed pathogenic changes in the genome using long-read sequencers. The results of these studies provide hope that further application of long-read sequencers to identify the causative mutations in unsolved genetic diseases may expand our understanding of the human genome and diseases. Such approaches may also be applied to molecular diagnosis and therapeutic strategies for patients with genetic diseases in the future.