Alternative end-joining originates stable chromosome aberrations induced by etoposide during targeted inhibition of DNA-PKcs in ATM-deficient tumor cells.

ATM and DNA-PKcs coordinate the DNA damage response at multiple levels following the exposure to chemotherapy. The Topoisomerase II poison etoposide (ETO) is an effective chemotherapeutic agent that induces DNA double-strand breaks (DSB), but it is responsible from the chromosomal rearrangements frequently found in therapy-related secondary tumors. Targeted inhibition of DNA-PKcs in ATM-defective tumors combined with radio- or chemotherapy has been proposed as relevant therapies. Here, we explored the DNA repair mechanisms and the genetic consequences of targeting the non-oncogenic addiction to DNA-PKcs of ATM-defective tumor cells after exposure to ETO. We demonstrated that chemical inhibition of DNA-PKcs followed by treatment with ETO resulted in the accumulation of chromatid breaks and decreased mitotic index in both A-T cells and ATM-knocked-down (ATMkd) tumor cells. The HR repair process in DNA-PKcs-inhibited ATMkd cells amplified the RAD51 foci number, with no correlated increase in sister chromatid exchanges. The analysis of post-mitotic DNA lesions presented an augmented number of persistent unresolved DSB, without alterations in the cell cycle progression. Long-term examination of chromosome aberrations revealed a strikingly high number of chromatid and chromosome exchanges. By using genetic and pharmacological abrogation of PARP-1, we demonstrated that alternative end-joining (alt-EJ) repair pathway is responsible for those chromosome abnormalities generated by limiting c-NHEJ activities during directed inhibition of DNA-PKcs in ATM-deficient cells. Targeting the non-oncogenic addiction to DNA-PKcs of ATM-defective tumors stimulates the DSB repair by alt-EJ, which is liable for the origin of cells carrying stable chromosome aberrations that may eventually restrict the therapeutic strategy.

Molecular Diagnosis in an Argentinean Mitochondrial Disorders Cohort

Abstract Mitochondrial diseases are multisystemic disorders characterized by an impairment of the mitochondrial respiratory chain. Diagnosis requires an approach that involves a high index of suspicion, molecular techniques and a careful selection of the tissue to be studied. Our goal was to develop and implement local strategies for diagnosing mitochondrial disorders, by standardizing procedures of molecular biology and nucleic acid sequencing. A prospective, analytical, observational study was conducted in a cohort of, a total of 82 patients with suspected mitochondrial disorder who were treated at our hospital between May 2008 and June 2019. We developed molecular diagnostic tools that included classical monogenic techniques and Next Generation Sequencing. We characterized the neurological and extra neurological manifestations noted in our cohort. Following the proposed algorithm, we obtained a molecular diagnostic performance of 54%, identifying mutations in 44 patients. mtDNA mutations were identified in 34 patients. Structural rearrangements in mitochondrial genome were found in 3 and 7 in nuclear genes, respectively. Our results confirm the utility of the proposed algorithm and the molecular tools used, as evidenced by a high diagnostic performance. This is of great value to a more efficient and comprehensive medical care of patients and families affected by mitochondrial disorders.

The odyssey of complex neurogenetic disorders: From undetermined to positive.

The genetic and phenotypic heterogeneity of neurogenetic diseases forces patients and their families into a "diagnostic odyssey." An increase in the variability of genetic disorders and the corresponding gene-disease associations suggest the need to periodically re-evaluate the significance of variants of undetermined pathogenicity. Here, we report the diagnostic and clinical utility of Targeted Gene Panel Sequencing (TGPS) and Whole Exome Sequencing (WES) in 341 patients with suspected neurogenetic disorders from centers in Buenos Aires and Cincinnati over the last 4 years, focusing on the usefulness of reinterpreting variants previously classified as of uncertain significance. After a mean of ±2years (IC 95:0.73-3.27), approximately 30% of the variants of uncertain significance were reclassified as pathogenic. The use of next generation sequencing methods has facilitated the identification of both germline and mosaic pathogenic variants, expanding the diagnostic yield. These results demonstrate the high clinical impact of periodic reanalysis of undetermined variants in clinical neurology.

Identification of a somatic mutation in the RHEB gene through high depth and ultra-high depth next generation sequencing in a patient with Hemimegalencephaly and drug resistant Epilepsy.

Malformations of cortical development are a frequent cause of drug-resistant Epilepsy and developmental delay. Hemimegalencephaly is a Malformation of cortical development characterized by enlargement of all or a part of one cerebral hemisphere. Germline and somatic mutation in genes belonging to the Mammalian Target of Rapamycin (mTOR) pathway has been identified in patients suffering from epilepsy secondary to Hemimegalencephaly and focal cortical dysplasia. We present here a patient suffering from severe neonatal Epilepsy since 3 h of life secondary to Hemimegalencephaly, requiring an anatomic hemispherectomy surgical procedure for seizure control, where by means of next-generation sequencing at an ultra-high depth coverage, we were able to identify a novel somatic mutation in the RHEB gene (NM_005614: c.119A > T: p. Glu40Val). The histopathological diagnosis was Cortical Dysplasia type IIB determined by the presence of dysmorphic neurons of variable size with nuclear alteration and balloon cells in the context of Hemimegalencephaly, which are similar to that have been demonstrated in hyperactivating RHEB models. This is the first report of a somatic mutation in RHEB gene in a patient suffering from Epilepsy secondary to Hemimegalencephaly. It highlights different current topics in the fields of genetics of Malformations of cortical development: a-somatic mosaicism is not uncommon in these neurodevelopmental disorders; b-the molecular diagnostic approach should involve the use of state-of-the-art methods and the sampling of different tissues; c-new findings might facilitate therapeutics discoveries while providing an improved understanding of normal brain development.

Whole exome sequencing in neurogenetic odysseys: An effective, cost- and time-saving diagnostic approach.

BACKGROUND: Diagnostic trajectories for neurogenetic disorders frequently require the use of considerable time and resources, exposing patients and families to so-called "diagnostic odysseys". Previous studies have provided strong evidence for increased diagnostic and clinical utility of whole-exome sequencing in medical genetics. However, specific reports assessing its utility in a setting such as ours- a neurogeneticist led academic group serving in a low-income country-are rare. OBJECTIVES: To assess the diagnostic yield of WES in patients suspected of having a neurogenetic condition and explore the cost-effectiveness of its implementation in a research group located in an Argentinean public hospital. METHODS: This is a prospective study of the clinical utility of WES in a series of 40 consecutive patients selected from a Neurogenetic Clinic of a tertiary Hospital in Argentina. We evaluated patients retrospectively for previous diagnostic trajectories. Diagnostic yield, clinical impact on management and economic diagnostic burden were evaluated. RESULTS: We demonstrated the clinical utility of Whole Exome Sequencing in our patient cohort, obtaining a diagnostic yield of 40% (95% CI, 24.8%-55.2%) among a diverse group of neurological disorders. The average age at the time of WES was 23 (range 3-70). The mean time elapsed from symptom onset to WES was 11 years (range 3-42). The mean cost of the diagnostic workup prior to WES was USD 1646 (USD 1439 to 1853), which is 60% higher than WES cost in our center. CONCLUSIONS: WES for neurogenetics proved to be an effective, cost- and time-saving approach for the molecular diagnosis of this heterogeneous and complex group of patients.

Mutaciones en JAK2, MPL y CALR en neoplasias mieloproliferativas: análisis de disociación de alta resolución / Mutations in JAK2, MPL and CALR in myeloproliferative neoplasms: High Resolution Melting analysis / Mutações em JAK2, MPL e CALR em neoplasias mieloproliferativas: análise de dissociação em alta resolução

La policitemia vera (PV), la trombocitemia esencial (TE) y la mielofibrosis idiopática (MI) constituyen las Neoplasias Mieloproliferativas cromosoma Filadelfia negativas (NMP Ph-neg). La mutación V617F en el exón 14 del gen JAK2 ha sido descripta en un 90% de los casos de PV y en un 50% de TE y MI. Recientemente, se identificaron mutaciones en el exón 10 del gen MPL y en el exón 9 del gen CALR, presentes en un 5 y 73% de pacientes con TE y MI sin mutaciones en JAK2, respectivamente. En el presente trabajo se estudió la detección de dichas mutaciones en 52 pacientes con NMP, mediante amplificaciones por PCR en Tiempo Real con posterior análisis por High Resolution Melting (HRM) y secuenciación. La mutación V617F en JAK2 fue registrada en un 83,3% de pacientes con PV y 42,8% con TE y MI. Un 6,25% y 56,25% de pacientes con TE y MI JAK2 negativos resultaron positivos para mutaciones en el exón 10 de gen del receptor de la trombopoyetina (MPL) y el exón 9 de gen de la calreticulina (CALR). El análisis por HRM puede ser considerado como herramienta diagnóstica eficaz para las NMP debido a su alta sensibilidad, bajo costo y tiempo de procesado, teniendo en cuenta el impacto clínico que podría tener en los pacientes la detección temprana de dichas mutaciones.

Polycythemia vera (PV), essential thrombocythemia (TE) and idiopathic myelofibrosis (MI) are Philadelphia chromosome-negative myeloproliferative neoplasms (MPN-Ph. Neg). The presence of the V617F mutation in exon 14 of the JAK2 gene has been described in 90% of cases of PV and 50% of MI and TE. Recently, mutations in exon 10 of the MPL gene and exon 9 of CALR gene have been identified, which are present in 5 to 73% of patients with TE and MI without mutations in JAK2, respectively. In this work, the detection of these mutations was studied in 52 patients with NMP, using real time PCR amplifications with subsequent High Resolution Melting (HRM) analysis and sequencing. A total of 83.3% of patients with PV and 42.8% with MI and TE were recorded as positive for the V617F mutation in JAK2. A total of 6.25% and 56.25% of the patients with MI and TE with non-mutated JAK2 were positive for mutations in MPL exon 10 and CALR exon 9. HRM analysis could be considered an effective diagnostic tool for NMP due to its high sensitivity, low cost and processing time, taking into account the clinical impact that early detection of such mutations could have on patients.

Policitemia vera (PV), trombocitemia essencial (TE) e mielofibrose idiopática (MI) constituem as Neoplasias Mieloproliferativas cromossomo Filadélfia negativas (NMP Ph-neg). A mutação V617F no exon 14 do gene JAK2 foi descrita em 90% dos casos de PV e em 50% de TE e MI. Recentemente, foram identificadas mutações no exon 10 do gene MPL e no exon 9 do gene CALR, presentes em 5 a 73% de pacientes com TE e MI sem mutações em JAK2, respectivamente. Neste trabalho foi estudada a detecção de tais mutações em 52 pacientes com NMP, usando amplificações por PCR em Tempo Real, com posterior análise por High Resolution Melting (HRM) e sequenciamento. 83,3% dos pacientes com PV e 42,8% com TE e MI foram positivos para a mutação V617F em JAK2. 6,25% e 56,25% de pacientes com TE e MI JAK2 negativo foram positivos para mutações no exon 10 de gene do receptor da trombopoietina (MPL) e o exon 9 de gene da calreticulina (CALR). A análise por HRM pode ser considerada como ferramenta de diagnóstico eficaz para as NMP, devido à sua alta sensibilidade, baixo custo e tempo de processamento, tendo em conta o impacto clínico que poderia ter a detecção precoce de tais mutações nos pacientes.