Clinical and Prognostic Impact of Copy Number Alterations and Associated Risk Profiles in a Cohort of Pediatric B-cell Precursor Acute Lymphoblastic Leukemia Cases Treated Under ICiCLe Protocol.

Copy number alteration (CNA) status and CNA risk profiles of IKZF1 plus , UK-ALL CNA risk groups and MRplus scores, were evaluated for clinical and prognostic impact in a cohort of 493 B-cell acute lymphoblastic leukemia cases diagnosed and treated under the Indian Collaborative Childhood Leukemia group (ICiCLe) protocol trial. Overall CNA frequency was 59% with 60% of cases showing 2-loci deletion. CDKN2A/B deletion was most common CNA (36.3%), while IKZF1 deletion and IKZF1 plus profile were noted in 19.5% and 13.4% of cases, respectively. IKZF1 deletions and other CNA risk profiles were significantly associated with poor (PR)/high risk (HR) clinical and genetic profile parameters (P < 0.001). In addition, the 3-year OS, event-free survival (EFS) was significantly poor with high relapse rate (RR) of 38.6%, 46.5%, and 35.2% for IKZF1 deletions, IKZF1 plus profiles, and UK-ALL CNA-intermediate risk (IR)+PR risk groups, respectively (P < 0.001). Integrated evaluation of UK-ALL CNA risk profile with ICiCLe trial risk stratification groups revealed a worse overall survival, EFS, and RR of 63.3%, 43.2%, and 35.2% for CNA-IR+PR profile compared to CNA-good risk profile (81.3%, 65.0%, and 21.0%; P < 0.001). Hence, routine CNA testing in our setting is must to identify standard risk and IR cases likely to benefit from HR treatment.

Clinico-hematological and Outcome Profile of Pediatric B-other-ALL and BCR::ABL1-like pre-B-ALL: An Integrated Genomic Study From North India.

PURPOSE: BCR::ABL1-like pre-B-ALL comprises a myriad of genetic lesions making molecular diagnosis challenging and expensive. Its frequency and outcome are less studied in resource-constraint settings. METHODS: 154 pre-B-ALL cases (0-12 years) were enrolled as group 1 (37 cases of B-other-ALL) and group 2 (117 patients with recurrent translocations/ hyperdiploidy). Group 1 was evaluated for BCR::ABL1-like genetic lesions and copy-number abnormalities (CNAs) as per our published PACE approach supplemented with targeted RNA sequencing. RESULTS: BCR::ABL1-like frequency was 5.2% (8 of 154) and 22% (8 of 37) with the PACE approach alone in the whole and B-other-ALL cohort, respectively. The addition of targeted RNA-sequencing had led to the frequency increasing to 9% (14 of 154) and 38% (14 of 37) in the whole and B-other-ALL cohort, respectively. P2RY8::CRLF2, IGH::CRLF2, and RCSD1::ABL1 were noted in 8 (57.1%), 4 (28.6%), and 2 (14.3%) patients, respectively. CNAs were noted in 56.7% (21 of 37) of patients. The BCR::ABL1-like group had a significantly higher initial WBC count of ≥ 50,000/mm3 (71.4%; P < .001) than group 2. The 4-year OS, EFS, RFS of group 1 was not statistically different from group 2, though RFS was borderline poor (84.2%, 51.7%, 56.9% Vs. 82.6%, 62.9%, 78% [P - .42, P - .53, P - .059]). The 4-year EFS and RFS for BCR::ABL1-like cases was 70.7% and 76.6%, respectively. CONCLUSIONS: The sensitivity of detecting BCR::ABL1-like lesions had increased significantly from 22% using the PACE approach alone to 38% in B-other-ALLs with the integrated approach. Although outcomes were not statistically different, a higher percentage of relapses were noted in the B-other-ALL group.

PEST domain NOTCH mutations confer a poor relapse free survival in pediatric T-ALL: Data from a tertiary care centre in India.

A comprehensive genotype-phenotype analysis of pediatric T-ALL data was performed. 33 confirmed pediatric (≤12 y) T-ALL samples were evaluated for oncogenic transcripts: TLX-1, TLX-3, common fusion of STIL-TAL1, NOTCH1 mutations and copy number variations (CNVs). Mean WBC was 235.69 × 103/µL. TLX1 and TLX-3 overexpression detected in 1 (3%) and 7 (21%) patients and STIL-TAL1 in 8 (27%). NOTCH1 mutations were noted in 17 (52%), of which 12 (71%) in HD domain and 6 (35%) in PEST domain (including one case with mutations in all three domains). Commonest CNVs were CDKN2A (85%) and CDKN2B (75%). Relapse occurred in 8 (24%) patients. The median follow-up was 15 months (range: 0.5-36). Bulky liver (p = 0.025), day 35 marrow (p = 0.004) and NOTCH mutation (p = 0.046) were predictive of time to an event. RFS was significantly poor for cases with PEST Vs. HD domain mutations (50% Vs. 85%) (p = 0.0009). Though cases with PEST domain NOTCH mutations had poor RFS, the OS was not influenced by NOTCH mutation positivity.

Optimal Reference Gene Selection for Expression Studies in Human Reticulocytes.

Reference genes are indispensable for normalizing mRNA levels across samples in real-time quantitative PCR. Their expression levels vary under different experimental conditions and because of several inherent characteristics. Appropriate reference gene selection is thus critical for gene-expression studies. This study aimed at selecting optimal reference genes for gene-expression analysis of reticulocytes and at validating them in hereditary spherocytosis (HS) and ß-thalassemia intermedia (ßTI) patients. Seven reference genes (PGK1, MPP1, HPRT1, ACTB, GAPDH, RN18S1, and SDHA) were selected because of published reports. Real-time quantitative PCR was performed on reticulocytes in 20 healthy volunteers, 15 HS patients, and 10 ßTI patients. Threshold cycle values were compared with fold-change method and RefFinder software. The stable reference genes recommended by RefFinder were validated with SLC4A1 and flow cytometric eosin-5'-maleimide binding assay values in HS patients and HBG2 and high performance liquid chromatography-derived percentage of hemoglobin F in ßTI. Comprehensive ranking predicted MPP1 and GAPDH as optimal reference genes for reticulocytes that were not affected in HS and ßTI. This was further confirmed on validation with eosin-5'-maleimide results and percentage of hemoglobin F in HS and ßTI patients, respectively. Hence, MPP1 and GAPDH are good reference genes for reticulocyte expression studies compared with ACTB and RN18S1, the two most commonly used reference genes.

Clozapine associated thrombocytopenia.

Although agranulocytosis as a side effect of clozapine is well known, there is scarcity of data with regard to thrombocytopenia associated with clozapine. In this report we describe a case of clozapine induced thrombocytopenia and review the existing literature. A 22 year old female patient developed thrombocytopenia while on clozapine 187.5 mg/day for 17 weeks. Thrombocytopenia persisted for 24 weeks even after reduction in the dose of clozapine and ultimately clozapine had to be stopped, which led to resolution of thrombocytopenia. Clozapine-induced thrombocytopenia is a less well-known, but potentially serious, adverse effect that should be screened for in practice. The case highlights the fact that besides monitoring the leucocyte count, platelet count of patients receiving clozapine should also be monitored.

Adverse impact of pretransplant polyoma virus infection on renal allograft function.

BACKGROUND: BK polyoma virus (BKV) has emerged as an important cause of acute and chronic allograft injury in renal transplant recipients. Reactivation of latent infection requires reduction in cell-mediated immunity. We hypothesized that BKV could get reactivated in the urinary tract of patients with end-stage renal disease (ESRD) and impact the allograft function after these individuals undergo transplantation. METHODS: We prospectively examined the urine specimens of 68 ESRD patients and their donors for BKV inclusion containing decoy cells with Papanicoulau staining and immunohistochemistry. Polymerase chain reaction was carried out to confirm the presence of viral DNA. Urine examination was repeated 3-9 months after transplantation and during episodes of graft dysfunction. All graft dysfunction episodes were investigated by biopsy. BKV-associated nephropathy was confirmed by immunoperoxidase staining. Graft loss and doubling of serum creatinine were the study end-points. RESULTS: Decoy cells were detected in 22 ESRD patients and four donors (P < 0.0001). All 22 continued decoy cell excretion after transplantation and two fresh excreters were noted. Patients exhibiting decoy cells had more frequent graft dysfunction episodes (67% vs 30%, P = 0.003) and higher serum creatinine value (P < 0.001). About 33% patients achieved the combined end-points in the BK viruria group, compared with 11% in the non-decoy cell excreters (P = 0.03). Histologically proved BKV nephropathy was noted in 7% cases; all decoy cell excreters. CONCLUSION: We conclude that reactivation of latent BKV infection can occur in ESRD and confers an increased risk of graft dysfunction after transplantation. The mechanism of graft dysfunction in decoy cell excreters who do not develop overt nephropathy needs more studies.