Higher Incidence of Co-Expression of BCR-ABL Fusion Transcripts in an Eastern Indian Population

Background Chronic myeloid leukaemia (CML) is a hematopoietic stem cell disorder, caused by a balanced reciprocal translocation (t(9;22) (q34;q11))that lead to the formation of BCR (Break point Cluster Region)-ABL (Abelson) fusion transcripts known as Philadelphia (Ph) chromosome. Prevalence of BCR-ABL fusion transcripts in Indian CML population is poorly understood and few studies have been reported from India. The aim of present study was to determine the frequencies as well as prognostic effects of the three fusion transcripts i.e. b2a2, b3a2 and e1a2 in an Indian population. Methods RNA was isolated from total 123 sample 27 bone marrow (BM) sample and 96 Peripheral blood (PB) sample of CML patient followed by cDNA synthesis. Real-time quantitative reverse-transcription polymerase chain reaction (qRT-PCR) was performed using TaqMan→ assay (ABI, CA, USA) to monitor BCR-ABL transcript. Results Ph' chromosome was observed in 103 patients whereas it was not detected in 20 cases. qRT-PCR revealed that the b3a2 fusion transcripts was the most common transcript in CML patients (63.41%) while b2a2 fusion transcript was present in 16.26% cases. Co-expression of b3a2+b2a2 fusion transcript was observed in 0.81% cases whereas co-expression of b3a2+e1a2 fusion transcript was found in 1.63% cases. There was no co-relation observed between b3a2 fusion transcript and platelet count. The fusion transcript b2a2 was observed in relatively younger patients compared to b3a2 fusion transcript. Although this correlation was not statistically significant. Conclusion The co-expression of BCR-ABL fusion transcripts was higher (63.41% aggregate of b3a2) in the present population in contrast to other populations reported. This finding was consistent with the frequency data reported from Sudan.

Genomic Copy Number Variants in CML Patients With the Philadelphia Chromosome (Ph+): An Update

BackgroundSubmicroscopic segmental imbalances detected by array-comparative genomic hybridization (array-CGH) were discovered to be common in chronic myeloid leukemia (CML) patients with t(9;22) as the sole chromosomal anomaly. To confirm the findings of the previous study and expand the investigation, additional CML patients with t(9;22) as the sole chromosomal anomaly were recruited and copy number variants (CNVs) were searched for.MethodsKaryotyping tests were performed on 106 CML patients during January 2010–September 2019 in our Genetics Laboratory. Eighty-four (79.2%) patients had the Philadelphia (Ph) chromosome as the sole chromosomal anomaly. Only 49(58.3%) of these 84 patients had sufficient marrow or leukemia blood materials to additionally be included in the array-CGH analysis. Fluorescence in situ hybridization (FISH) was carried out to confirm the genes covered by the deleted or duplicated regions of the CNVs.Results11(22.4%) out of the 49 patients were found to have one to three somatic segmental somatic segmental (CNVs), including fourteen deletions and three duplications. The common region associated with deletions was on 9q33.3-34.12. Identified in five (45.5%) of the 11 positive patients with segmental CNVs, the deletions ranged from 106 kb to 4.1 Mb in size. Two (18.2%) cases had a deletion in the ABL1-BCR fusion gene on der (9), while three (27.3%) cases had a deletion in the ASS1 gene. The remaining CNVs were randomly distributed on different autosomes.ConclusionSubtle genomic CNVs are relatively common in CML patients without cytogenetically visible additional chromosomal aberrations (ACAs). Long-term studies investigating the potential impact on patient prognosis and treatment outcome is underway.

Dasatinib—A Generation Ahead

Dasatinib is a highly potent second-generation (2G) tyrosine kinase inhibitor (TKI) used in the management of Philadelphia (Ph) chromosome-positive leukemias, chronic myeloid leukemia (CML) and acute lymphoblastic leukemia (ALL). In CML, dasatinib produces higher rates of early and deeper molecular responses compared with imatinib. The drug has its share of toxicities, namely, cytopenias, cardiovascular, and pleural effusion. This review describes the pharmacological aspects of dasatinib, clinically relevant toxicities, and their management.

Expression of genes involved in immune regulation in chronic myeloid leukemia

Chronic myeloid leukemia (CML) is a blood cancer involved in abnormal proliferation of myeloid cells at all stages of differentiation. Translocation of regions of the BCR and ABL genes, leading to the fusion gene BCR-ABL, which forms the Philadelphia (Ph) chromosome, is the cause of more than 90% of CML. The BCR-ABL protein shows abnormal tyrosine kinase activity, leading to changes in proliferation signals including signal transducer and activator of transcriptions (STATs) and nuclear factor kappa-light-chain-enhancer of activated B (NF-κB) and resulting in uncontrolled proliferation of myeloid cells. CTLA-4, PD-1 and LAG3 genes are known as immunosuppressive receptors playing important roles in controlling immune response by inhibiting activity of T helper cells. Klotho gene has anti-aging, anti-inflammatory and anti-cancer functions. STAT signaling pathway genes regulate cancer cell functions by their phosphorylation and IκB-α gene by degradation of its expression. In this study, we conducted experiments to determine mRNA expression of these genes on immune cells in CML patients by using realtime-PCR. Results showed a marked increase in the expression of STAT-1 and STAT-6 signaling genes and a decreased LAG3 expression in CML patients as compared with healthy controls. In addition, other gene expressions such as CTLA4, PD1, klotho, IκB-α, STAT3 and STAT5 were unaltered in CML cells. The abnormal increased expression of STAT1 and STAT6 genes indicated an important role of these signaling genes in regulating activity of immune cells, leading to pathogenesis and development of CML disease. The evidence suggested that STAT-1 and STAT-6 genes could be important and potential markers in early prognosis of CML.

Nursing Care Management of Chronic Myeloid Leukemia – A Case Report

Excessive growth of mature granulocytes in the bone marrow induces chronic myeloid leukemia. The excess neoplastic granulocytes travel massively into the peripheral blood and in the end invade the liver and spleen. The protein encoded on the Philadelphia chromosome by the newly created BCR-ABL gene interferes with normal cell cycle activities, including regulating cell proliferation. Philadelphia chromosome is present in 90 - 95 percent of chronic myeloid leukemia (CML) patients. Their involvement is often a vital indicator of persistent disease or posttreatment relapse. However, for the diagnosis of CML, the presence of the Philadelphia chromosome is not specific since it is also present in acute lymphocytic leukemia (ALL) and rarely in acute myeloid leukemia (AML). 1 Chronic myeloid leukemia is a myeloproliferative neoplasm (MPN) characterised by involvement of the fusion gene BCRABL1 located in the Philadelphia chromosome. In reactive neutrophilia or chronic neutrophilic leukemia, the Ph chromosome is pathognomonic to CML and is never registered.2,3

BCR/ABL1 fluorescence in situ hybridization fusion signals on both copies of chromosome 22 in a Philadelphia-masked chronic myeloid leukemia case: implication for the therapy

The cytogenetic hallmark of Chronic Myeloid Leukemia (CML) is the presence of Philadelphia (Ph) chromosome, which results from a reciprocal translocation t(9;22)(q34;q11). In this report, we describe a CML patient with no evidence of Ph chromosome but trisomy of chromosome 8 as single cytogenetic abnormality and a typical e14a2 (b3a2) BCR-ABL1 fusion transcript. Fluorescence In Situ Hybridization (FISH) analysis revealed an uncommon signal pattern: the fusion signals were located on both copies of chromosome 22. During the course of the disease the appearance of the p.(Tyr315Ile) mutation was recorded. To the best of our knowledge this is the first Ph chromosome-negative CML case with e14a2 (b3a2) BCR-ABL1 transcript and p.(Tyr315Ile) mutation.

Identification of the motifs of beta-turns and mutated amino acids studies on BCR (Breakpoint cluster region) protein using Insilico techniques

Recent investigations have rapidly added crucial new insights into the complex functions of the normal BCR gene and of the BCR-ABL chimaera. They are yielding potential therapeutic breakthroughs in the treatment of Philadelphia (Ph) chromosome-positive leukemias. The objective of the present in silico research investigation is to find out whether the functional part (beta-turns) is present in the mutated amino acids of BCR (Breakpoint cluster region) protein. Two significant steps are involved in this study. First, we performed protein sequence modeling of BCR using automated protein modeling servers and the 3D structure was visualized using molecular visualization software and tools. In the second step, the function domains and motifs regions of BCR gene-coded protein is predicted using “PDBsum generate” tool in order to show where exactly the beta-turns lie on the clinically-proven mutated amino acids of BCR protein. The results of our investigation can be used as potential drug binding sites in the field of drug docking studies. It can act as a potential therapeutic agent for Chronic Myeloid Leukemia (CML) type of Leukemia.

"Detection of BCR-ABL1-like Subtype in Adult Acute Lymphoblastic Leukemia Using Digital Ncounter Nanostring Technology"

Introduction A new provisional entity of "B-lymphoblastic leukaemia/lymphoma, BCR-ABL1-like" has been introduced in the 2017 revised edition of WHO classification of tumours of haematopoietic and lymphoid tissues. BCR-ABL1-like cases are negative for Ph chromosome or t(9:22)(q34;q11.2) translocation, do not express the fusion BCR-ABL1 RNA transcripts and proteins resulting from the Ph chromosome,and are characterized by similar gene expression profiles as that of BCR-ABL1-positive acute lymphoblastic leukemia (BCR-ABL1-positive ALL).There is no 'short-cut approach' for making an accurate diagnosis of BCR-ABL1-like ALL. Two approaches namely Gene expression profiling (GEP) or Next-generation sequencing (NGS) and TLDA (TaqMan low-density array) are used for the detection of BCR-ABL1-like ALL cases. NGS is very costly and data interpretation requires a lot of bioinformatics skills and TLDA is not commercially available in India. Aims We planned to study the whole transcriptome of BCR-ABL1-positive ALL cases using microarray GEP, followed by customizing targeted gene panel using nCounter NanoString technology, for the detection of BCR-ABL1-like cases. METHODS Flow cytometric immunophenotying (FCM-IP) and multiplex RT-PCR were performed on 200 B-ALL cases to detect BCR-ABL1 chimeric fusion transcripts. Further, 12 BCR-ABL1-positive cases were subjected to transcriptome profiling using Affymetrix microarray (Gene Chip Human Genome U133 Plus 2.0 Array). The results were analyzed using TAC 4.0 software. Finally, a targeted panel of 50 differentially expressed genes [including 5 Housekeeping genes (HKGs)] was constructed according to our microarray findings and previously published data (Harvey RC et al.ASH 2013). A total of 96 B-ALL cases (16 BCR-ABL1-positive cases & 80 BCR-ABL1-negative cases) were subjected to GEP using nCounter Platform. The results were analyzed using nSolver4.0 software. RESULTS In the study cohort of 200 adult B-ALL cases, BCR-ABL1 chimeric fusion transcripts were detected in 34% (b2a2 and b3a2=18.05% & e1a2=15.5%), as revealed by multiplex assay. Global transcriptome profiling of 12 BCR-ABL1 RNA transcripts revealed a total of 1574 as DE genes (460 genes in e1a2, 515 genes in b2a2 and 599 genes in b3a2). DE genes were further filtered through hierarchical clustering analysis and a total of 45 DE genes with 10- to -86-fold change were identified. These genes were further analyzed using nCounter NanoString. To further identify the best classifier genes, log2 normalized expression values were analyzed using penalized logistic regression. Based on previous literature and regression coefficient values, 15 genes were finally selected whose performance was individually analyzed using receiver operating characteristic curve (ROC) and area under the curve (AUC). Optimal thresholds for these genes were estimated as the values with maximum sensitivity and specificity. Out of 78 examined BCR-ABL1-negative cases, 33(42.30%) BCR-ABL1-negative cases were clustered together with 15 BCR-ABL1-positive cases and were attributed as BCR-ABL1-like ALL cases in principal component analysis. Further, we categorized CRLF2 in two categories; high CRLF2 cases 25/33 (75.75%) & low 8/33 (24.24%) in BCR-ABL1-like ALL cases. JAK2p.R683G mutation was screened in CRLF2 high cases and showed positivity in 19/24 (79.16%) by the Amplification Refractory Mutation (ARMS) PCR. In 25 cases, the average log fold change of -0.80 &-5.83 was seen in P2YR8 & CSF2RA respectively by qPCR. In CRLF2 low expressing cases, the average log fold change of 11 kinase genes showed -0.75 in CENPC, -0.66 FOXP1, -0.16 NUP153, 1.04 RCSD1, 1.50 PAX5, 1.12 FLT3, -5.65 EPOR, -4.03 ILR2B, -3.46 PDGRFB, -7.49 NTRK3 &-2.83 ZNF274 respectively. The average log fold change of IKZF1 in 80 BCR-ABL1-negative cases was found to be 1.07. DISCUSSION & CONCLUSION We have devised a method that includes 15 genes according to AUC/ROC for the detection of BCR-ABL1-like ALL cases, using nCounter NanoString technology for the first time in Indian patients. Furthermore, we are planning to validate this model in future, on 50 BCR-ABL1-positive and 150 BCR-ABL1-negative cases and devise a simple, efficient, cost-effective qPCR method. It is very important to detect BCR-ABL1-like ALL cases to start the desirable TKI therapy & aid in treatment stratification, prognostication, and improve the overall survival of these patients. Figure Disclosures No relevant conflicts of interest to declare.

Chronic myeloid leukaemia with pulmonary leucostasis in a young Down syndrome patient

We reported a rare case of chronic myeloid leukaemia (CML) complicated with pulmonary leucostasis in an 11-year-old Down syndrome (DS) patient who presented with respiratory distress. His peripheral blood investigation showed features of CML with 17% circulating blast, with immunophenotyping showing positivity towards myeloid markers. Peripheral blood polymerase chain reaction for BCR–ABL fusion transcripts was positive, and cytogenetic studies showed Ph chromosome with trisomy 21. Despite cytoreduction therapy with hydroxyurea and leukapheresis, the patient succumbed due to shock, with multiple organ failure. Our case highlights the need for early detection and rapid referral for aggressive treatment in DS patients with CML, as the combination is associated with a poor outcome.