Expresión génica en mieloma múltiple: análisis de datos de RNA-seq y microarrays en combinación con estudios de metaanálisis y predicción de respuesta al tratamiento

[ES] El mieloma múltiple (MM) es una neoplásia hematológica que presenta una gran variabilidad clínica como consecuencia de su heterogeneidad genética. Así, desde las etapas precursoras del MM conviven en la médula ósea múltiples clones celulares genéticamente distintos y por tanto, con capacidad diferente para sobrevivir y resistir a la acción de factores externos como son los tratamientos. Esta diversidad, ha conducido en los últimos 20 años al desarrollo de nuevos fármacos con mecanismos de acción muy diferentes a la quimioterapia clásica, lo que ha contribuído a prolongar notablemente la supervivencia global de las personas afectadas por esta patología. Igualmente, en las últimas décadas ha habido grandes progresos en el descubrimiento de los procesos biológicos implicados en el MM, derivados, principalmente, de la inmensa información aportada en campos como la transcriptómica gracias a tecnologías de análisis masivo de datos como los microarrays o la RNA-seq. Con estos antecedentes, en el presente trabajo se ha procedido a la búsqueda de las firmas de expresión génica de diferentes compuestos utilizados en el tratamiento del MM, así como a la determinación de genes implicados en la respuesta de estos fármacos en pacientes con esta patología. Para ello, se propuso en un primer lugar, una guía para el análisis de datos de RNA-seq mediante el desarrollo de un flujo de análisis o pipeline, en el que se determinaron los métodos y algoritmos más adecuados para el procesamiento de datos de esta tecnología. Así, se llevó a cabo la evaluación del rendimiento de 192 pipelines a nivel de expresión génica cruda y de 17 métodos a nivel de expresión génica diferencial, de manera que finalmente fueron establecidos los pipelines y algoritmos con mejores índices de precisión y exactitud a la hora de la determinación de la expresión génica a ambos niveles. En una siguiente etapa se realizó un estudio comparativo entre la RNA-seq y el microarray transcriptómico HTA 2.0 de Affymetrix, para establecer cuál de las dos tecnologías muestra un mayor rendimiento en estudios de expresión génica. Tras el establecimiento de las metodologías óptimas de análisis, se procedió a la determinación de los perfiles de expresión génica asociados a 12 fármacos antimieloma mediante técnicas de metaanálisis en líneas celulares. Esto condujo a la especificación de una firma génica para cada uno de los compuestos analizados, que fue asociada posteriormente a posibles mecanismos de acción o de quimiorresistencia. Adicionalmente, también se llevó a cabo la definición de los perfiles de expresión génica asociados a la respuesta a tres esquemas de tratamiento en pacientes con MM al momento del diagnóstico, siendo comprobada, en un último paso, la eficiencia de estos perfiles de expresión en la predicción de la respuesta propuestos a través del uso de modelos estadísticos predictivos

Polymorphisms in receptors involved in opsonic and nonopsonic phagocytosis, and correlation with risk of infection in oncohematology patients

Producción CientíficaHigh-risk hematological malignancies are a privileged setting for infection by opportunistic microbes, with invasive mycosis being one of the most serious complications. Recently, genetic background has emerged as an unanticipated risk factor. For this reason, polymorphisms for genes encoding archetypal receptors involved in the opsonic and nonopsonic clearance of microbes, pentraxin-3 (PTX3) and Dectin-1, respectively, were studied and correlated with the risk of infection. Fungal, bacterial, and viral infections were registered for a group of 198 patients with highrisk hematological malignancies. Polymorphisms for the pentraxin-3 gene (PTX3) showed a significant association with the risk of fungal infection by Candida spp. and, especially, by Aspergillus spp. This link remained even for patients undergoing antifungal prophylaxis, thus demonstrating the clinical relevance of PTX3 in the defense against fungi. CLEC7A polymorphisms did not show any definite correlation with the risk of invasive mycosis, nor did they influence the expression of Dectin-1 isoforms generated by alternative splicing. The PTX3 mRNA expression level was significantly lower in samples from healthy volunteers who showed these polymorphisms, although no differences were observed in the extents of induction elicited by bacterial lipopolysaccharide and heat-killed Candida albicans, thus suggesting that the expression of PTX3 at the start of infection may influence the clinical outcome. PTX3 mRNA expression can be a good biomarker to establish proper antifungal prophylaxis in immunodepressed patients

Effects on respiratory pressures, spirometry biomarkers, and sports performance after inspiratory muscle training in a physically active population by Powerbreath®: A systematic review and meta-analysis

Producción CientíficaSimple Summary: There is currently a growing interest in respiratory muscle training in athletes, so we set out to systematically assess with meta-analyses the effects of IMT with PowerBretah® (PwB), a threshold work device for IMT, on respiratory parameters and athletic performance in healthy physically active adults. Eleven studies were included in the systematic review and nine in the meta-analysis. IMT by PwB significantly increased maximal inspiratory pressure (MIP) and substantial improvements in forced vital capacity (FVC) in the results of the meta-analysis, and sports performance was significantly increased. In conclusion, the IMT with PwB would improve respiratory, MIP, FVC, and sports performance.Sports performance in athletes can be limited by respiratory factors, so it is understandable to propose that inspiratory muscle training (IMT) can improve respiratory function and exercise performance. Power-Breathe® (PwB) is a sectorized respiratory muscle training tool that uses a resistive load to train IMT. There is currently a growing interest in respiratory muscle training, so we set out to systematically assess the effects of IMT with PwB on respiratory parameters and athletic performance in physically active, healthy adults. Based on the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guideline, the Cochrane and PEDro scales to assess methodological quality, effect size using the Rosenthal formula, and the Cochrane tool for estimation of risk of bias, studies searchable in Medline, Web of Science, and Cochrane. In addition, for the performance of the meta-analysis, the documentation and quantification of the heterogeneity in each meta-analysis were directed through the Cochran’s Q test and the I2 statistic; in addition, a publication bias analysis was performed using funnel plots. Of the total of 241 studies identified in the search, 11 studies for the systematic review and nine for the meta-analysis met the exclusion and/or inclusion criteria. IMT, with PwB, showed significant improvements in maximal inspiratory pressure (MIP) and substantial improvements in forced vital capacity (FVC) in the meta-analysis results. Also, sports performance was significantly increased by IMT with PwB. In conclusion, the use of PwB is an IMT tool that improves respiratory and sports performance

Integrated Genomic Analysis of Chromosomal Alterations and Mutations in B-Cell Acute Lymphoblastic Leukemia Reveals Distinct Genetic Profiles at Relapse

The clonal basis of relapse in B-cell precursor acute lymphoblastic leukemia (BCP-ALL) is complex and not fully understood. Next-generation sequencing (NGS), array comparative genomic hybridization (aCGH), and multiplex ligation-dependent probe amplification (MLPA) were carried out in matched diagnosis-relapse samples from 13 BCP-ALL patients to identify patterns of genetic evolution that could account for the phenotypic changes associated with disease relapse. The integrative genomic analysis of aCGH, MLPA and NGS revealed that 100% of the BCP-ALL patients showed at least one genetic alteration at diagnosis and relapse. In addition, there was a significant increase in the frequency of chromosomal lesions at the time of relapse (p = 0.019). MLPA and aCGH techniques showed that IKZF1 was the most frequently deleted gene. TP53 was the most frequently mutated gene at relapse. Two TP53 mutations were detected only at relapse, whereas the three others showed an increase in their mutational burden at relapse. Clonal evolution patterns were heterogeneous, involving the acquisition, loss and maintenance of lesions at relapse. Therefore, this study provides additional evidence that BCP-ALL is a genetically dynamic disease with distinct genetic profiles at diagnosis and relapse. Integrative NGS, aCGH and MLPA analysis enables better molecular characterization of the genetic profile in BCP-ALL patients during the evolution from diagnosis to relapse

The kinesin spindle protein inhibitor filanesib enhances the activity of pomalidomide and dexamethasone in multiple myeloma

[EN]Kinesin spindle protein inhibition is known to be an effective therapeutic approach in several malignancies. Filanesib (ARRY-520), an inhibitor of this protein, has demonstrated activity in heavily pre-treated multiple myeloma patients. The aim of the work herein was to investigate the activity of filanesib in combination with pomalidomide plus dexamethasone backbone, and the mechanisms underlying the potential synergistic effect. The ability of filanesib to enhance the activity of pomalidomide plus dexamethasone was studied in several in vitro and in vivo models. Mechanisms of this synergistic combination were dissected by gene expression profiling, immunostaining, cell cycle and short interfering ribonucleic acid studies. Filanesib showed in vitro, ex vivo, and in vivo synergy with pomalidomide plus dexamethasone treatment. Importantly, the in vivo synergy observed in this combination was more evident in large, highly proliferative tumors, and was shown to be mediated by the impairment of mitosis transcriptional control, an increase in monopolar spindles, cell cycle arrest and the induction of apoptosis in cells in proliferative phases. In addition, the triple combination increased the activation of the proapoptotic protein BAX, which has previously been associated with sensitivity to filanesib, and could potentially be used as a predictive biomarker of response to this combination. Our results provide preclinical evidence for the potential benefit of the combination of filanesib with pomalidomide and dexamethasone, and supported the initiation of a recently activated trial being conducted by the Spanish Myeloma group which is investigating this combination in relapsed myeloma patients.Array BioPharma, the Spanish ISCIII-FIS and FEDER, the Spanish RTICC, Spanish Association Against Cancer (AECC) and the Regional Council of Castilla y León (Consejería de Medicina y Educación)

Prognostic stratification of adult primary glioblastoma multiforme patients based on their tumor gene amplification profiles

[EN]everal classification systems have been proposed to address genomic heterogeneity of glioblastoma multiforme, but they either showed limited prognostic value and/or are difficult to implement in routine diagnostics. Here we propose a prognostic stratification model for these primary tumors based on tumor gene amplification profiles, that might be easily implemented in routine diagnostics, and potentially improve the patients management. Gene amplification profiles were prospectively evaluated in 80 primary glioblastoma multiforme tumors using singlenucleotide polymorphism arrays and the results obtained validated in publicly available data from 267/347 cases. Gene amplification was detected in 45% of patients, and chromosome 7p11.2 including the EGFR gene, was the most frequently amplified chromosomal region - either alone (18%) or in combination with amplification of DNA sequences in other chromosomal regions (10% of cases). Other frequently amplified DNA sequences included regions in chromosomes 12q(10%), 4q12(7%) and 1q32.1(4%). Based on their gene amplification profiles, glioblastomas were subdivided into: i) tumors with no gene amplification (55%); ii) tumors with chromosome 7p/EGFR gene amplification (with or without amplification of other chromosomal regions) (38%); and iii) glioblastoma multiforme with a single (11%) or multiple (6%) amplified DNA sequences in chromosomal regions other than chromosome 7p

Targeting of PI3K/AKT/mTOR pathway to inhibit T cell activation and prevent graft-versus-host disease development

Producción CientíficaBackground: Graft-versus-host disease (GvHD) remains the major obstacle to successful allogeneic hematopoietic stem cell transplantation, despite of the immunosuppressive regimens administered to control T cell alloreactivity. PI3K/AKT/mTOR pathway is crucial in T cell activation and function and, therefore, represents an attractive therapeutic target to prevent GvHD development. Recently, numerous PI3K inhibitors have been developed for cancer therapy. However, few studies have explored their immunosuppressive effect. Methods: The effects of a selective PI3K inhibitor (BKM120) and a dual PI3K/mTOR inhibitor (BEZ235) on human T cell proliferation, expression of activation-related molecules, and phosphorylation of PI3K/AKT/mTOR pathway proteins were analyzed. Besides, the ability of BEZ235 to prevent GvHD development in mice was evaluated. Results: Simultaneous inhibition of PI3K and mTOR was efficient at lower concentrations than PI3K specific targeting. Importantly, BEZ235 prevented naïve T cell activation and induced tolerance of alloreactive T cells, while maintaining an adequate response against cytomegalovirus, more efficiently than BKM120. Finally, BEZ235 treatment significantly improved the survival and decreased the GvHD development in mice. Conclusions: These results support the use of PI3K inhibitors to control T cell responses and show the potential utility of the dual PI3K/mTOR inhibitor BEZ235 in GvHD prophylaxis.Asociación Española Contra el Cáncer (Proyecto AIOA110296BLAN).Gerencia Regional de Salud de Castilla y León (Proyecto GRS 726/A13

Mesenchymal Stromal Cell Irradiation Interferes with the Adipogenic/Osteogenic Differentiation Balance and Improves Their Hematopoietic-Supporting Ability

[EN]Bone marrow mesenchymal stromal cells (MSCs) are precursors of adipocytes and osteoblasts and key regulators of hematopoiesis. Irradiation is widely used in conditioning regimens. Although MSCs are radioresistant, the effects of low-dose irradiation on their behavior have not been extensively explored. Our aim was to evaluate the effect of 2.5 Gy on MSCs. Cells from 25 healthy donors were either irradiated or not (the latter were used as controls). Cells were characterized following International Society for Cellular Therapy criteria, including in vitro differentiation assays. Apoptosis was evaluated by annexin V/7-amino-actinomycin staining. Gene expression profiling and reverse transcriptase (RT)-PCR of relevant genes was also performed. Finally, long-term bone marrow cultures were performed to test the hematopoietic-supporting ability. Our results showed that immunophenotypic characterization and viability of irradiated cells was comparable with that of control cells. Gene expression profiling showed 50 genes differentially expressed. By RT-PCR, SDF-1 and ANGPT were overexpressed, whereas COL1A1 was downregulated in irradiated cells (P = .015, P = .007, and P = .031, respectively). Interestingly, differentiation of irradiated cells was skewed toward osteogenesis, whereas adipogenesis was impaired. Higher expression of genes involved in osteogenesis as SPP1 (P = .039) and lower of genes involved in adipogenesis, CEBPA and PPARG (P = .003 and P = .019), together with an increase in the mineralization capacity (Alizarin Red) was observed in irradiated cells. After differentiation, adipocyte counts were decreased in irradiated cells at days 7, 14, and 21 (P = .018 P = .046, and P = .018, respectively). Also, colony-forming unit granulocyte macrophage number in long-term bone marrow cultures was signifi- cantly higher in irradiated cells after 4 and 5 weeks (P = .046 and P = .007). In summary, the irradiation of MSCs with 2.5 Gy improves their hematopoietic-supporting ability by increasing osteogenic differentiation and decreasing adipogenesis

Integrated genomic analysis of chromosomal alterations and mutations in B-cell acute lymphoblastic leukemia reveals distinct genetic profiles at relapse

© 2020 by the authors.The clonal basis of relapse in B-cell precursor acute lymphoblastic leukemia (BCP-ALL) is complex and not fully understood. Next-generation sequencing (NGS), array comparative genomic hybridization (aCGH), and multiplex ligation-dependent probe amplification (MLPA) were carried out in matched diagnosis–relapse samples from 13 BCP-ALL patients to identify patterns of genetic evolution that could account for the phenotypic changes associated with disease relapse. The integrative genomic analysis of aCGH, MLPA and NGS revealed that 100% of the BCP-ALL patients showed at least one genetic alteration at diagnosis and relapse. In addition, there was a significant increase in the frequency of chromosomal lesions at the time of relapse (p = 0.019). MLPA and aCGH techniques showed that IKZF1 was the most frequently deleted gene. TP53 was the most frequently mutated gene at relapse. Two TP53 mutations were detected only at relapse, whereas the three others showed an increase in their mutational burden at relapse. Clonal evolution patterns were heterogeneous, involving the acquisition, loss and maintenance of lesions at relapse. Therefore, this study provides additional evidence that BCP-ALL is a genetically dynamic disease with distinct genetic profiles at diagnosis and relapse. Integrative NGS, aCGH and MLPA analysis enables better molecular characterization of the genetic profile in BCP-ALL patients during the evolution from diagnosis to relapse.This work was supported in part by a grant from the Consejería de Educación, Junta de Castilla y León, Fondos FEDER (SA085U16, SA271P18), Proyectos de Investigación de la Gerencia Regional de Sanidad, SACYL, (GRS 1847/A/18; GRS 2062/A/19), SYNtherapy. Synthetic Lethality for Personalized Therapy-based Stratification In Acute Leukemia (ERAPERMED2018-275); ISCIII (AC18/00093), co-funded by ERDF/ESF, “Investing in your future”, Fundación Castellano Leonesa de Hematología y Hemoterapia (FUCALHH 2017), and Centro de Investigación Biomédica en Red de Cáncer (CIBERONC CB16/12/00233). A grant to AM from the Junta Provincial de Salamanca of the Asociación Española Contra el Cáncer (AECC), a grant to MFC from the Universidad Pedagógica y Tecnológica de Colombia—Vicerrectoría de Investigación y Extensión (Grupo de Investigación en Ciencias Biomédicas UPTC—GICBUPTC, Escuela de Ciencias Biológicas). M. Hernández-Sánchez holds a Sara Borrell post-doctoral contract (CD19/00222) from the Instituto de Salud Carlos III (ISCIII). co-founded by Fondo Social Europeo (FSE) “El Fondo Social Europeo invierte en tu futuro”, MM is currently supported by an “Ayuda predoctoral de la Junta de Castilla y León” by the Fondo Social Europeo (JCYL- EDU/556/2019 PhD scholarship) and a grant to JR and JMR from Instituto Carlos III (PI14/01971)

Integrated Genomic Analysis of Chromosomal Alterations and Mutations in B-Cell Acute Lymphoblastic Leukemia Reveals Distinct Genetic Profiles at Relapse

The clonal basis of relapse in B-cell precursor acute lymphoblastic leukemia (BCP-ALL) is complex and not fully understood. Next-generation sequencing (NGS), array comparative genomic hybridization (aCGH), and multiplex ligation-dependent probe amplification (MLPA) were carried out in matched diagnosis-relapse samples from 13 BCP-ALL patients to identify patterns of genetic evolution that could account for the phenotypic changes associated with disease relapse. The integrative genomic analysis of aCGH, MLPA and NGS revealed that 100% of the BCP-ALL patients showed at least one genetic alteration at diagnosis and relapse. In addition, there was a significant increase in the frequency of chromosomal lesions at the time of relapse (p = 0.019). MLPA and aCGH techniques showed that IKZF1 was the most frequently deleted gene. TP53 was the most frequently mutated gene at relapse. Two TP53 mutations were detected only at relapse, whereas the three others showed an increase in their mutational burden at relapse. Clonal evolution patterns were heterogeneous, involving the acquisition, loss and maintenance of lesions at relapse. Therefore, this study provides additional evidence that BCP-ALL is a genetically dynamic disease with distinct genetic profiles at diagnosis and relapse. Integrative NGS, aCGH and MLPA analysis enables better molecular characterization of the genetic profile in BCP-ALL patients during the evolution from diagnosis to relapse