Characterization of 46 patient-specific BCR-ABL1 fusions and detection of SNPs upstream and downstream the breakpoints in chronic myeloid leukemia using next generation sequencing

In chronic myeloid leukemia, the identification of individual BCR-ABL1 fusions is required for the development of personalized medicine approach for minimal residual disease monitoring at the DNA level. Next generation sequencing (NGS) of amplicons larger than 1000 bp simplified and accelerated a process of characterization of patient-specific BCR-ABL1 genomic fusions. NGS of large regions upstream and downstream the individual breakpoints in BCR and ABL1 genes, respectively, also provided information about the sequence variants such are single nucleotide polymorphisms

AFLP-AFLP in silico-NGS approach reveals polymorphisms in repetitive elements in the malignant genome.

The increasing interest in exploring the human genome and identifying genetic risk factors contributing to the susceptibility to and outcome of diseases has supported the rapid development of genome-wide techniques. However, the large amount of obtained data requires extensive bioinformatics analysis. In this work, we established an approach combining amplified fragment length polymorphism (AFLP), AFLP in silico and next generation sequencing (NGS) methods to map the malignant genome of patients with chronic myeloid leukemia. We compared the unique DNA fingerprints of patients generated by the AFLP technique approach with those of healthy donors to identify AFLP markers associated with the disease and/or the response to treatment with imatinib, a tyrosine kinase inhibitor. Among the statistically significant AFLP markers selected for NGS analysis and virtual fingerprinting, we identified the sequences of three fragments in the region of DNA repeat element OldhAT1, LINE L1M7, LTR MER90, and satellite ALR/Alpha among repetitive elements, which may indicate a role of these non-coding repetitive sequences in hematological malignancy. SNPs leading to the presence/absence of these fragments were confirmed by Sanger sequencing. When evaluating the results of AFLP analysis for some fragments, we faced the frequently discussed size homoplasy, resulting in co-migration of non-identical AFLP fragments that may originate from an insertion/deletion, SNP, somatic mutation anywhere in the genome, or combination thereof. The AFLP-AFLP in silico-NGS procedure represents a smart alternative to microarrays and relatively expensive and bioinformatically challenging whole-genome sequencing to detect the association of variable regions of the human genome with diseases

Pericardial malignant infiltration as the cause of sudden death of a patient with metastatic urothelial carcinoma treated with atezolizumab

Abstract Background Muscle-infiltrating urothelial carcinoma of the bladder is the most common genitourinary cancer. Immunotherapeutic agents targeting protein-1 programmed death or protein-1 programmed death ligand are currently considered the standard treatment in patients with either inoperable locally advanced or metastatic urothelial carcinoma (MUC) after platinum-based chemotherapy failure. Case presentation Here we report the case of a Caucasian male patient with metastatic urothelial carcinoma treated with second-line atezolizumab within a trial who achieved complete response by computed tomography (CT), but suddenly died due to cardiac tamponade resulting from malignant pericardial infiltration. Histopathology confirmed this as the only site of disease progression. Conclusions Cardiovascular toxicity of atezolizumab was considered within differential diagnoses, however histopathological examination revealed progression of malignancy in the pericardium as the cause of the sudden death. This is the first published case report of a patient treated with second-line atezolizumab in whom the rare disease progression of pericardial infiltration was confirmed. Despite its rarity, the clinicians should always consider the possibility of pericardial metastases

Long-Term Averaged Spectrum Descriptors of Dysarthria in Patients With Parkinson's Disease Treated With Subthalamic Nucleus Deep Brain Stimulation.

PURPOSE This study aimed to evaluate whether long-term averaged spectrum (LTAS) descriptors for reading and monologue are suitable to detect worsening of dysarthria in patients with Parkinson's disease (PD) treated with subthalamic nucleus deep brain stimulation (STN-DBS) with potential effect of ON and OFF stimulation conditions and types of connected speech. METHOD Four spectral moments based on LTAS were computed for monologue and reading passage collected from 23 individuals with PD treated with bilateral STN-DBS and 23 age- and gender-matched healthy controls. Speech performance of patients with PD was compared in ON and OFF STN-DBS conditions. RESULTS All LTAS spectral moments including mean, standard deviation, skewness, and kurtosis across both monologue and reading passage were able to significantly distinguish between patients with PD in both stimulation conditions and control speakers. The spectral mean was the only LTAS measure sensitive to capture better speech performance in STN-DBS ON, as compared to the STN-DBS OFF stimulation condition (p < .05). Standardized reading passage was more sensitive compared to monologue in detecting dysarthria severity via LTAS descriptors with an area under the curve of up to 0.92 obtained between PD and control groups. CONCLUSIONS Our findings confirmed that LTAS is a suitable approach to objectively describe changes in speech impairment severity due to STN-DBS therapy in patients with PD. We envisage these results as an important step toward a continuum development of technological solutions for the automated assessment of stimulation-induced dysarthria. SUPPLEMENTAL MATERIAL https://doi.org/10.23641/asha.21644798

Chromosomal damage in peripheral blood lymphocytes of newly diagnosed cancer patients and healthy controls

Background: The majority of human cancers arise from cells unable to maintain genomic stability. Recent prospective studies indicated that enhanced chromosomal aberrations (CAs) frequencies are predictive of gastrointestinal and lung cancers. However, studies on incident cancer patients are lacking; thus, we investigated chromosomal damage in newly diagnosed cancer patients and healthy individuals. Methods: We analyzed chromosomal damage in peripheral blood lymphocytes in a group of 300 incident cancer patients (with different malignancies) in comparison with 300 healthy controls. Results and Conclusions: The frequencies of aberrant cells (ACs) and CAs were significantly higher in patients (2.38 +/- 1.56 and 2.53 +/- 1.69, respectively) as compared with controls (1.81 +/- 1.31 and 1.94 +/- 1.47, respectively, P < 0.01). The percentual difference in chromatid-type aberrations (CTAs) between patients and controls was moderately significant (1.37 +/- 1.20 and 1.11 +/- 0.99, respectively, P < 0.05), whereas the difference in chromosome-type aberrations (CSAs) was stronger (1.16 +/- 1.24 versus 0.83 +/- 1.12, P < 0.01). Using binomial logistic regression, the estimated odds ratios and 95% confidence interval for ACs were 1.33 (1.18-1.49), P < 0.01; for CAs, 1.27 (1.14-1.41), P < 0.01; for CTA 1.24 (1.07-1.44), P < 0.01 and for CSA, 1.27 (1.10-1.47), P < 0.01. By stratifying patients for distinct neoplasia, markers of chromosomal damage were significantly enhanced in patients with breast, prostate and head/neck cancers, whereas no effect was recorded in patients affected by gastrointestinal cancers. The present study shows for the first time evidence of increased chromosomal damage in lymphocytes of incident cancer patients compared with healthy controls. The effects were observed in different cancer types but as the number of patients was relatively small, further studies are warranted

Interferon-α Revisited: Individualized Treatment Management Eased the Selective Pressure of Tyrosine Kinase Inhibitors on BCR-ABL1 Mutations Resulting in a Molecular Response in High-Risk CML Patients.

Bone marrow transplantation or ponatinib treatment are currently recommended strategies for management of patients with chronic myeloid leukemia (CML) harboring the T315I mutation and compound or polyclonal mutations. However, in some individual cases, these treatment scenarios cannot be applied. We used an alternative treatment strategy with interferon-α (IFN-α) given solo, sequentially or together with TKI in a group of 6 cases of high risk CML patients, assuming that the TKI-independent mechanism of action may lead to mutant clone repression. IFN-α based individualized therapy decreases of T315I or compound mutations to undetectable levels as assessed by next-generation deep sequencing, which was associated with a molecular response in 4/6 patients. Based on the observed results from immune profiling, we assumed that the principal mechanism leading to the success of the treatment was the immune activation induced with dasatinib pre-treatment followed by restoration of immunological surveillance after application of IFN-α therapy. Moreover, we showed that sensitive measurement of mutated BCR-ABL1 transcript levels augments the safety of this individualized treatment strategy