Detection of kinase domain mutations in BCR::ABL1 leukemia by ultra-deep sequencing of genomic DNA

The screening of the BCR::ABL1 kinase domain (KD) mutation has become a routine analysis in case of warning/failure for chronic myeloid leukemia (CML) and B-cell precursor acute lymphoblastic leukemia (ALL) Philadelphia (Ph)-positive patients. In this study, we present a novel DNA-based next-generation sequencing (NGS) methodology for KD ABL1 mutation detection and monitoring with a 1.0E−4 sensitivity. This approach was validated with a well-stablished RNA-based nested NGS method. The correlation of both techniques for the quantification of ABL1 mutations was high (Pearson r = 0.858, p < 0.001), offering DNA-DeepNGS a sensitivity of 92% and specificity of 82%. The clinical impact was studied in a cohort of 129 patients (n = 67 for CML and n = 62 for B-ALL patients). A total of 162 samples (n = 86 CML and n = 76 B-ALL) were studied. Of them, 27 out of 86 harbored mutations (6 in warning and 21 in failure) for CML, and 13 out of 76 (2 diagnostic and 11 relapse samples) did in B-ALL patients. In addition, in four cases were detected mutation despite BCR::ABL1 < 1%. In conclusion, we were able to detect KD ABL1 mutations with a 1.0E−4 sensitivity by NGS using DNA as starting material even in patients with low levels of disease.Tis project was funded in part by CRIS CANCER FOUNDATION

Is There a Seamount Effect on Microbial Community Structure and Biomass? The Case Study of Seine and Sedlo Seamounts (Northeast Atlantic)

Seamounts are considered to be “hotspots” of marine life but, their role in oceans primary productivity is still under discussion. We have studied the microbial community structure and biomass of the epipelagic zone (0–150 m) at two northeast Atlantic seamounts (Seine and Sedlo) and compared those with the surrounding ocean. Results from two cruises to Sedlo and three to Seine are presented. Main results show large temporal and spatial microbial community variability on both seamounts. Both Seine and Sedlo heterotrophic community (abundance and biomass) dominate during winter and summer months, representing 75% (Sedlo, July) to 86% (Seine, November) of the total plankton biomass. In Seine, during springtime the contribution to total plankton biomass is similar (47% autotrophic and 53% heterotrophic). Both seamounts present an autotrophic community structure dominated by small cells (nano and picophytoplankton). It is also during spring that a relatively important contribution (26%) of large cells to total autotrophic biomass is found. In some cases, a “seamount effect” is observed on Seine and Sedlo microbial community structure and biomass. In Seine this is only observed during spring through enhancement of large autotrophic cells at the summit and seamount stations. In Sedlo, and despite the observed low biomasses, some clear peaks of picoplankton at the summit or at stations within the seamount area are also observed during summer. Our results suggest that the dominance of heterotrophs is presumably related to the trapping effect of organic matter by seamounts. Nevertheless, the complex circulation around both seamounts with the presence of different sources of mesoscale variability (e.g. presence of meddies, intrusion of African upwelling water) may have contributed to the different patterns of distribution, abundances and also changes observed in the microbial community

Phosphoinositide 3-kinase p85beta regulates invadopodium formation

The acquisition of invasiveness is characteristic of tumor progression. Numerous genetic changes are associated with metastasis, but the mechanism by which a cell becomes invasive remains unclear. Expression of p85β, a regulatory subunit of phosphoinositide-3-kinase, markedly increases in advanced carcinoma, but its mode of action is unknown. We postulated that p85β might facilitate cell invasion. We show that p85β localized at cell adhesions in complex with focal adhesion kinase and enhanced stability and maturation of cell adhesions. In addition, p85β induced development at cell adhesions of an F-actin core that extended several microns into the cell z-axis resembling the skeleton of invadopodia. p85β lead to F-actin polymerization at cell adhesions by recruiting active Cdc42/Rac at these structures. In accordance with p85β function in invadopodium-like formation, p85β levels increased in metastatic melanoma and p85β depletion reduced invadopodium formation and invasion. These results show that p85β enhances invasion by inducing cell adhesion development into invadopodia-like structures explaining the metastatic potential of tumors with increased p85β levels

Factors of the epidemiological triad that influence the persistence of human papilloma virus infection in women with systemic lupus erythematosus

We studied the epidemiologic triad-related factors influencing human papilloma virus (HPV) persistence in Mexican women with systemic lupus erythematosus (SLE). Patients aged ?18 years with SLE (American College of Rheumatology criteria), with and without HPV persistence, were selected. Groups were analyzed by (1) host: clinical disease characteristics; (2) agent: (I) infectious (prevalence, incidence, HPV genotype and co-infections (?2 HPV genotypes or mycoplasmas)), (II) chemical (contraceptives and immunosuppressive drugs) and (III) physical (vitamin D deficiency) and (3) environment. A total of 121 SLE patients were selected over a two-year period. (1) Host: mean age 45.8 years and disease duration 12.7 years. (2) Agent: (I) infectious. HPV infection prevalence in the second sample was 26.4%, high-risk HPV genotypes 21.5% and co-infections 7.4%. HPV infection incidence was 13.2%, persistence 13.2% and clearance 15.7%. (II) Chemical: use of oral hormonal contraceptives 5% and immunosuppressive treatment 97.5%. (III) Physical: Vitamin D levels were similar in both groups. (3) Environment: (I) natural. A total of 60.6% of patients were residents of Puebla City. (II) Social: The mean education level was 10.9. Poverty levels were: III degree 52.4%, IV degree 28% and II degree 17%. (III) Cultural behavioral: Onset of sexual life was 20.5 years, 10% had ?3 sexual partners and 51.2% were postmenopausal. In conclusion, no factor of the epidemiologic triad was associated with HPV infection prevalence. © The Author(s) 2018

Sofosbuvir-velpatasvir en pacientes mexicanos con hepatitis C: una revisión retrospectiva

Resumen: Introducción: La combinación de sofosbuvir-velpatasvir (SOF/VEL) es una terapia antiviral de acción directa que está autorizada y disponible en México. Esto hace que la evaluación de la respuesta virológica sostenida (RVS) 12 semanas después del tratamiento, por medio de la realización de una revisión multicentro en el mundo real, sea una tarea relevante. Métodos: Se efectuó una revisión retrospectiva de los registros de 241 casos de pacientes atendidos en 20 hospitales en México para evaluar el tratamiento contra la hepatitis C con la combinación SOF/VEL (n = 231) y sofosbuvir/velpatasvir/ribavirin (SOF/VEL/RBV) (n = 10). El objetivo de eficacia primario fue el porcentaje de pacientes que lograron la RVS 12 semanas posterior a la finalización del tratamiento. Resultados: En general, la RVS fue de 98.8% (IC 95% 97.35 a 100%). Solo tres pacientes no lograron la RVS, de los cuales dos padecían cirrosis y una tenía historia previa de tratamiento con interferón pegilado (peg-IFN). De los subgrupos analizados, todos los casos con infección de virus de la inmunodeficiencia humana (VIH), tres con genotipo 3 y aquellos tratados con la combinación SOF/VEL/RBV, lograron RVS. Los subgrupos con tasas menores de éxito fueron los pacientes que tenían experiencia con tratamiento (96.8%) y pacientes con fibrosis F1 (95.5%). Los eventos adversos más frecuentes fueron fatiga, cefalea e insomnio. No se reportaron eventos adversos graves. Conclusión: Los tratamientos con SOF/VEL y SOF/VEL/RBV fueron altamente seguros y efectivos y los resultados coinciden con los de otros estudios internacionales realizados en el mundo real. Abstract Introduction: The sofosbuvir-velpatasvir (SOF/VEL) combination is a direct-acting antiviral therapy that is authorized and available in Mexico, making the performance of a real-world multicenter study that evaluates the sustained virologic response at 12 weeks post-treatment a relevant undertaking. Methods: A retrospective review of the case records of 241 patients seen at 20 hospitals in Mexico was conducted to assess hepatitis C treatment with the SOF/VEL combination (n = 231) and the sofosbuvir/velpatasvir/ribavirin (SOF/VEL/RBV) combination (n = 10). The primary efficacy endpoint was the percentage of patients that achieved SVR at 12 weeks after the end of treatment. Results: Overall SVR was 98.8% (95% CI 97.35-100%). Only three patients did not achieve SVR, two of whom had cirrhosis and a history of previous treatment with peg-IFN. Of the subgroups analyzed, all the patients with HIV coinfection, three patients with genotype 3, and the patients treated with the SOF/VEL/RBV combination achieved SVR. The subgroups with the lower success rates were patients that were treatment-experienced (96.8%) and patients with F1 fibrosis (95.5%). The most frequent adverse events were fatigue, headache, and insomnia. No serious adverse events were reported. Conclusion: Treatments with SOF/VEL and SOF/VEL/RBV were highly safe and effective, results coinciding with those of other international real-world studies

K-polystability of Q-Fano varieties admitting Kahler-Einstein metrics

It is shown that any, possibly singular, Fano variety X admitting a Kahler-Einstein metric is K-polystable, thus confirming one direction of the Yau-Tian-Donaldson conjecture in the setting of Q-Fano varieties equipped with their anti-canonical polarization. The proof is based on a new formula expressing the Donaldson-Futaki invariants in terms of the slope of the Ding functional along a geodesic ray in the space of all bounded positively curved metrics on the anti-canonical line bundle of X. One consequence is that a toric Fano variety X is K-polystable iff it is K-polystable along toric degenerations iff 0 is the barycenter of the canonical weight polytope P associated to X. The results also extend to the logarithmic setting and in particular to the setting of Kahler-Einsteinmetrics with edge-cone singularities. Applications to geodesic stability, bounds on the Ricci potential and Perelman\u27s lambda-entropy functional on K-unstable Fano manifolds are also given