22 results on '"Beatriz Antelo Rodríguez"'
Search Results
2. Evaluation of the Stellae-123 prognostic gene expression signature in acute myeloid leukemia
- Author
-
Adrián Mosquera Orgueira, Andrés Peleteiro Raíndo, José Ángel Díaz Arias, Beatriz Antelo Rodríguez, Mónica López Riñón, Claudio Cerchione, Adolfo de la Fuente Burguera, Marta Sonia González Pérez, Giovanni Martinelli, Pau Montesinos Fernández, and Manuel Mateo Pérez Encinas
- Subjects
leukemia ,transcriptome ,machine learning ,survival ,risk ,prediction ,Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Abstract
Risk stratification in acute myeloid leukemia (AML) has been extensively improved thanks to the incorporation of recurrent cytogenomic alterations into risk stratification guidelines. However, mortality rates among fit patients assigned to low or intermediate risk groups are still high. Therefore, significant room exists for the improvement of AML prognostication. In a previous work, we presented the Stellae-123 gene expression signature, which achieved a high accuracy in the prognostication of adult patients with AML. Stellae-123 was particularly accurate to restratify patients bearing high-risk mutations, such as ASXL1, RUNX1 and TP53. The intention of the present work was to evaluate the prognostic performance of Stellae-123 in external cohorts using RNAseq technology. For this, we evaluated the signature in 3 different AML cohorts (2 adult and 1 pediatric). Our results indicate that the prognostic performance of the Stellae-123 signature is reproducible in the 3 cohorts of patients. Additionally, we evidenced that the signature was superior to the European LeukemiaNet 2017 and the pediatric clinical risk scores in the prediction of survival at most of the evaluated time points. Furthermore, integration with age substantially enhanced the accuracy of the model. In conclusion, Stellae-123 is a reproducible machine learning algorithm based on a gene expression signature with promising utility in the field of AML.
- Published
- 2022
- Full Text
- View/download PDF
3. Prognostic Stratification of Multiple Myeloma Using Clinicogenomic Models: Validation and Performance Analysis of the IAC-50 Model
- Author
-
Adrián Mosquera Orgueira, Marta Sonia González Pérez, José Ángel Díaz Arias, Beatriz Antelo Rodríguez, and María-Victoria Mateos
- Subjects
Diseases of the blood and blood-forming organs ,RC633-647.5 - Abstract
A growing need to evaluate risk-adapted treatments in multiple myeloma (MM) exists. Several clinical and molecular scores have been developed in the last decades, which individually explain some of the variability in the heterogeneous clinical behavior of this neoplasm. Recently, we presented Iacobus-50 (IAC-50), which is a machine learning-based survival model based on clinical, biochemical, and genomic data capable of risk-stratifying newly diagnosed MM patients and predicting the optimal upfront treatment scheme. In the present study, we evaluated the prognostic value of the IAC-50 gene expression signature in an external cohort composed of patients from the Total Therapy trials 3, 4, and 5. The prognostic value of IAC-50 was validated, and additionally we observed a better performance in terms of progression-free survival and overall survival prediction compared with the UAMS70 gene expression signature. The combination of the IAC-50 gene expression signature with traditional prognostic variables (International Staging System [ISS] score, baseline B2-microglobulin, and age) improved the performance well above the predictability of the ISS score. IAC-50 emerges as a powerful risk stratification model which might be considered for risk stratification in newly diagnosed myeloma patients, in the context of clinical trials but also in real life.
- Published
- 2022
- Full Text
- View/download PDF
4. Prognostic Stratification of Diffuse Large B-cell Lymphoma Using Clinico-genomic Models: Validation and Improvement of the LymForest-25 Model
- Author
-
Adrián Mosquera Orgueira, Jose Ángel Díaz Arías, Miguel Cid López, Andrés Peleteiro Raíndo, Alberto López García, Rosanna Abal García, Marta Sonia González Pérez, Beatriz Antelo Rodríguez, Carlos Aliste Santos, Manuel Mateo Pérez Encinas, Máximo Francisco Fraga Rodríguez, and José Luis Bello López
- Subjects
Diseases of the blood and blood-forming organs ,RC633-647.5 - Abstract
Diffuse large B-cell lymphoma (DLBCL) is the most common type of non-Hodgkin lymphoma. Despite notable therapeutic advances in the last decades, 30%–40% of affected patients develop relapsed or refractory disease that frequently precludes an infamous outcome. With the advent of new therapeutic options, it becomes necessary to predict responses to the standard treatment based on rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP). In a recent communication, we presented a new machine learning model (LymForest-25) that was based on 25 clinical, biochemical, and gene expression variables. LymForest-25 achieved high survival prediction accuracy in patients with DLBCL treated with upfront immunochemotherapy. In this study, we aimed to evaluate the performance of the different features that compose LymForest-25 in a new UK-based cohort, which contained 481 patients treated with upfront R-CHOP for whom clinical, biochemical and gene expression information for 17 out of 19 transcripts were available. Additionally, we explored potential improvements based on the integration of other gene expression signatures and mutational clusters. The validity of the LymForest-25 gene expression signature was confirmed, and indeed it achieved a substantially greater precision in the estimation of mortality at 6 months and 1, 2, and 5 years compared with the cell-of-origin (COO) plus molecular high-grade (MHG) classification. Indeed, this signature was predictive of survival within the MHG and all COO subgroups, with a particularly high accuracy in the “unclassified” group. Integration of this signature with the International Prognostic Index (IPI) score provided the best survival predictions. However, the increased performance of molecular models with the IPI score was almost exclusively restricted to younger patients (
- Published
- 2022
- Full Text
- View/download PDF
5. Improved personalized survival prediction of patients with diffuse large B-cell Lymphoma using gene expression profiling
- Author
-
Adrián Mosquera Orgueira, José Ángel Díaz Arias, Miguel Cid López, Andrés Peleteiro Raíndo, Beatriz Antelo Rodríguez, Carlos Aliste Santos, Natalia Alonso Vence, Ángeles Bendaña López, Aitor Abuín Blanco, Laura Bao Pérez, Marta Sonia González Pérez, Manuel Mateo Pérez Encinas, Máximo Francisco Fraga Rodríguez, and José Luis Bello López
- Subjects
DLBCL ,Lymphoma ,Survival ,Prediction ,Transcriptomics ,Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Abstract
Abstract Background Thirty to forty percent of patients with Diffuse Large B-cell Lymphoma (DLBCL) have an adverse clinical evolution. The increased understanding of DLBCL biology has shed light on the clinical evolution of this pathology, leading to the discovery of prognostic factors based on gene expression data, genomic rearrangements and mutational subgroups. Nevertheless, additional efforts are needed in order to enable survival predictions at the patient level. In this study we investigated new machine learning-based models of survival using transcriptomic and clinical data. Methods Gene expression profiling (GEP) of in 2 different publicly available retrospective DLBCL cohorts were analyzed. Cox regression and unsupervised clustering were performed in order to identify probes associated with overall survival on the largest cohort. Random forests were created to model survival using combinations of GEP data, COO classification and clinical information. Cross-validation was used to compare model results in the training set, and Harrel’s concordance index (c-index) was used to assess model’s predictability. Results were validated in an independent test set. Results Two hundred thirty-three and sixty-four patients were included in the training and test set, respectively. Initially we derived and validated a 4-gene expression clusterization that was independently associated with lower survival in 20% of patients. This pattern included the following genes: TNFRSF9, BIRC3, BCL2L1 and G3BP2. Thereafter, we applied machine-learning models to predict survival. A set of 102 genes was highly predictive of disease outcome, outperforming available clinical information and COO classification. The final best model integrated clinical information, COO classification, 4-gene-based clusterization and the expression levels of 50 individual genes (training set c-index, 0.8404, test set c-index, 0.7942). Conclusion Our results indicate that DLBCL survival models based on the application of machine learning algorithms to gene expression and clinical data can largely outperform other important prognostic variables such as disease stage and COO. Head-to-head comparisons with other risk stratification models are needed to compare its usefulness.
- Published
- 2020
- Full Text
- View/download PDF
6. Correction: Gene expression profiling identifies FLT3 mutation-like cases in wild-type FLT3 acute myeloid leukemia
- Author
-
Adrián Mosquera Orgueira, Andrés Peleteiro Raíndo, Miguel Cid López, Beatriz Antelo Rodríguez, José Ángel Díaz Arias, Roi Ferreiro Ferro, Natalia Alonso Vence, Ángeles Bendaña López, Aitor Abuín Blanco, Laura Bao Pérez, Paula Melero Valentín, Marta Sonia González Pérez, Claudio Cerchione, Giovanni Martinelli, Pau Montesinos Fernández, Manuel Mateo Pérez Encinas, and José Luis Bello López
- Subjects
Medicine ,Science - Published
- 2022
7. Personally Tailored Survival Prediction of Patients With Follicular Lymphoma Using Machine Learning Transcriptome-Based Models
- Author
-
Adrián Mosquera Orgueira, Miguel Cid López, Andrés Peleteiro Raíndo, Aitor Abuín Blanco, Jose Ángel Díaz Arias, Marta Sonia González Pérez, Beatriz Antelo Rodríguez, Laura Bao Pérez, Roi Ferreiro Ferro, Carlos Aliste Santos, Manuel Mateo Pérez Encinas, Máximo Francisco Fraga Rodríguez, Claudio Cerchione, Pablo Mozas, and José Luis Bello López
- Subjects
machine learning ,lymphoma ,follicular ,gene expression ,survival ,Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Abstract
Follicular Lymphoma (FL) has a 10-year mortality rate of 20%, and this is mostly related to lymphoma progression and transformation to higher grades. In the era of personalized medicine it has become increasingly important to provide patients with an optimal prediction about their expected outcomes. The objective of this work was to apply machine learning (ML) tools on gene expression data in order to create individualized predictions about survival in patients with FL. Using data from two different studies, we were able to create a model which achieved good prediction accuracies in both cohorts (c-indexes of 0.793 and 0.662 in the training and test sets). Integration of this model with m7-FLIPI and age rendered high prediction accuracies in the test set (cox c-index 0.79), and a simplified approach identified 4 groups with remarkably different outcomes in terms of survival. Importantly, one of the groups comprised 27.35% of patients and had a median survival of 4.64 years. In summary, we have created a gene expression-based individualized predictor of overall survival in FL that can improve the predictions of the m7-FLIPI score.
- Published
- 2022
- Full Text
- View/download PDF
8. The association of germline variants with chronic lymphocytic leukemia outcome suggests the implication of novel genes and pathways in clinical evolution
- Author
-
Adrián Mosquera Orgueira, Beatriz Antelo Rodríguez, Natalia Alonso Vence, José Ángel Díaz Arias, Nicolás Díaz Varela, Manuel Mateo Pérez Encinas, Catarina Allegue Toscano, Elena María Goiricelaya Seco, Ángel Carracedo Álvarez, and José Luis Bello López
- Subjects
Chronic lymphocytic leukemia ,Germline ,Polymorphism ,Association ,Prognosis ,Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Abstract
Abstract Background Chronic Lymphocytic Leukemia (CLL) is the most frequent lymphoproliferative disorder in western countries and is characterized by a remarkable clinical heterogeneity. During the last decade, multiple genomic studies have identified a myriad of somatic events driving CLL proliferation and aggressivity. Nevertheless, and despite the mounting evidence of inherited risk for CLL development, the existence of germline variants associated with clinical outcomes has not been addressed in depth. Methods Exome sequencing data from control leukocytes of CLL patients involved in the International Cancer Genome Consortium (ICGC) was used for genotyping. Cox regression was used to detect variants associated with clinical outcomes. Gene and pathways level associations were also calculated. Results Single nucleotide polymorphisms in PPP4R2 and MAP3K4 were associated with earlier treatment need. A gene-level analysis evidenced a significant association of RIPK3 with both treatment need and survival. Furthermore, germline variability in pathways such as apoptosis, cell-cycle, pentose phosphate, GNα13 and Nitric oxide was associated with overall survival. Conclusion Our results support the existence of inherited conditionants of CLL evolution and points towards genes and pathways that may results useful as biomarkers of disease outcome. More research is needed to validate these findings.
- Published
- 2019
- Full Text
- View/download PDF
9. Personalized Survival Prediction of Patients With Acute Myeloblastic Leukemia Using Gene Expression Profiling
- Author
-
Adrián Mosquera Orgueira, Andrés Peleteiro Raíndo, Miguel Cid López, José Ángel Díaz Arias, Marta Sonia González Pérez, Beatriz Antelo Rodríguez, Natalia Alonso Vence, Laura Bao Pérez, Roi Ferreiro Ferro, Manuel Albors Ferreiro, Aitor Abuín Blanco, Emilia Fontanes Trabazo, Claudio Cerchione, Giovanni Martinnelli, Pau Montesinos Fernández, Manuel Mateo Pérez Encinas, and José Luis Bello López
- Subjects
acute myeloid leukemia ,cancer ,survival ,machine learning ,gene expression ,prognosis ,Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Abstract
Acute Myeloid Leukemia (AML) is a heterogeneous neoplasm characterized by cytogenetic and molecular alterations that drive patient prognosis. Currently established risk stratification guidelines show a moderate predictive accuracy, and newer tools that integrate multiple molecular variables have proven to provide better results. In this report, we aimed to create a new machine learning model of AML survival using gene expression data. We used gene expression data from two publicly available cohorts in order to create and validate a random forest predictor of survival, which we named ST-123. The most important variables in the model were age and the expression of KDM5B and LAPTM4B, two genes previously associated with the biology and prognostication of myeloid neoplasms. This classifier achieved high concordance indexes in the training and validation sets (0.7228 and 0.6988, respectively), and predictions were particularly accurate in patients at the highest risk of death. Additionally, ST-123 provided significant prognostic improvements in patients with high-risk mutations. Our results indicate that survival of patients with AML can be predicted to a great extent by applying machine learning tools to transcriptomic data, and that such predictions are particularly precise among patients with high-risk mutations.
- Published
- 2021
- Full Text
- View/download PDF
10. Detection of new drivers of frequent B-cell lymphoid neoplasms using an integrated analysis of whole genomes.
- Author
-
Adrián Mosquera Orgueira, Roi Ferreiro Ferro, José Ángel Díaz Arias, Carlos Aliste Santos, Beatriz Antelo Rodríguez, Laura Bao Pérez, Natalia Alonso Vence, Ággeles Bendaña López, Aitor Abuin Blanco, Paula Melero Valentín, And Res Peleteiro Raindo, Miguel Cid López, Manuel Mateo Pérez Encinas, Marta Sonia González Pérez, Máximo Francisco Fraga Rodríguez, and José Luis Bello López
- Subjects
Medicine ,Science - Abstract
B-cell lymphoproliferative disorders exhibit a diverse spectrum of diagnostic entities with heterogeneous behaviour. Multiple efforts have focused on the determination of the genomic drivers of B-cell lymphoma subtypes. In the meantime, the aggregation of diverse tumors in pan-cancer genomic studies has become a useful tool to detect new driver genes, while enabling the comparison of mutational patterns across tumors. Here we present an integrated analysis of 354 B-cell lymphoid disorders. 112 recurrently mutated genes were discovered, of which KMT2D, CREBBP, IGLL5 and BCL2 were the most frequent, and 31 genes were putative new drivers. Mutations in CREBBP, TNFRSF14 and KMT2D predominated in follicular lymphoma, whereas those in BTG2, HTA-A and PIM1 were more frequent in diffuse large B-cell lymphoma. Additionally, we discovered 31 significantly mutated protein networks, reinforcing the role of genes such as CREBBP, EEF1A1, STAT6, GNA13 and TP53, but also pointing towards a myriad of infrequent players in lymphomagenesis. Finally, we report aberrant expression of oncogenes and tumor suppressors associated with novel noncoding mutations (DTX1 and S1PR2), and new recurrent copy number aberrations affecting immune check-point regulators (CD83, PVR) and B-cell specific genes (TNFRSF13C). Our analysis expands the number of mutational drivers of B-cell lymphoid neoplasms, and identifies several differential somatic events between disease subtypes.
- Published
- 2021
- Full Text
- View/download PDF
11. Gene expression profiling identifies FLT3 mutation-like cases in wild-type FLT3 acute myeloid leukemia.
- Author
-
Adrián Mosquera Orgueira, Andrés Peleteiro Raíndo, Miguel Cid López, Beatriz Antelo Rodríguez, José Ángel Díaz Arias, Roi Ferreiro Ferro, Natalia Alonso Vence, Ángeles Bendaña López, Aitor Abuín Blanco, Laura Bao Pérez, Paula Melero Valentín, Marta Sonia González Pérez, Claudio Cerchione, Giovanni Martinelli, Pau Montesinos Fernández, Manuel Mateo Pérez Encinas, and José Luis Bello López
- Subjects
Medicine ,Science - Abstract
BackgroundFLT3 mutation is present in 25-30% of all acute myeloid leukemias (AML), and it is associated with adverse outcome. FLT3 inhibitors have shown improved survival results in AML both as upfront treatment and in relapsed/refractory disease. Curiously, a variable proportion of wild-type FLT3 patients also responded to these drugs.MethodsWe analyzed 6 different transcriptomic datasets of AML cases. Differential expression between mutated and wild-type FLT3 AMLs was performed with the Wilcoxon-rank sum test. Hierarchical clustering was used to identify FLT3-mutation like AMLs. Finally, enrichment in recurrent mutations was performed with the Fisher's test.ResultsA FLT3 mutation-like gene expression pattern was identified among wild-type FLT3 AMLs. This pattern was highly enriched in NPM1 and DNMT3A mutants, and particularly in combined NPM1/DNMT3A mutants.ConclusionsWe identified a FLT3 mutation-like gene expression pattern in AML which was highly enriched in NPM1 and DNMT3A mutations. Future analysis about the predictive role of this biomarker among wild-type FLT3 patients treated with FLT3 inhibitors is envisaged.
- Published
- 2021
- Full Text
- View/download PDF
12. New Recurrent Structural Aberrations in the Genome of Chronic Lymphocytic Leukemia Based on Exome-Sequencing Data
- Author
-
Adrián Mosquera Orgueira, Beatriz Antelo Rodríguez, José Ángel Díaz Arias, Marta Sonia González Pérez, and José Luis Bello López
- Subjects
copy number aberration ,chronic lymphocytic leukemia ,driver ,time to treatment ,overall survival ,Genetics ,QH426-470 - Abstract
Chronic lymphocytic leukemia (CLL) is the most frequent lymphoproliferative syndrome in Western countries, and it is characterized by recurrent large genomic rearrangements. During the last decades, array techniques have expanded our knowledge about CLL’s karyotypic aberrations. The advent of large sequencing databases expanded our knowledge cancer genomics to an unprecedented resolution and enabled the detection of small-scale structural aberrations in the cancer genome. In this study, we have performed exome-sequencing-based copy number aberration (CNA) and loss of heterozygosity (LOH) analysis in order to detect new recurrent structural aberrations. We describe 54 recurrent focal CNAs enriched in cancer-related pathways, and their association with gene expression and clinical evolution. Furthermore, we discovered recurrent large copy number neutral LOH events affecting key driver genes, and we recapitulate most of the large CNAs that characterize the CLL genome. These results provide “proof-of-concept” evidence supporting the existence of new genes involved in the pathogenesis of CLL.
- Published
- 2019
- Full Text
- View/download PDF
13. Time to Treatment Prediction in Chronic Lymphocytic Leukemia Based on New Transcriptional Patterns
- Author
-
Adrián Mosquera Orgueira, Beatriz Antelo Rodríguez, Natalia Alonso Vence, Ángeles Bendaña López, José Ángel Díaz Arias, Nicolás Díaz Varela, Marta Sonia González Pérez, Manuel Mateo Pérez Encinas, and José Luis Bello López
- Subjects
chronic lymphocytic leukemia ,time to treatment prediction ,gene expression ,RNAseq ,machine learning ,prognostic factors ,Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Abstract
Chronic lymphocytic leukemia (CLL) is the most frequent lymphoproliferative syndrome in western countries. CLL evolution is frequently indolent, and treatment is mostly reserved for those patients with signs or symptoms of disease progression. In this work, we used RNA sequencing data from the International Cancer Genome Consortium CLL cohort to determine new gene expression patterns that correlate with clinical evolution.We determined that a 290-gene expression signature, in addition to immunoglobulin heavy chain variable region (IGHV) mutation status, stratifies patients into four groups with notably different time to first treatment. This finding was confirmed in an independent cohort. Similarly, we present a machine learning algorithm that predicts the need for treatment within the first 5 years following diagnosis using expression data from 2,198 genes. This predictor achieved 90% precision and 89% accuracy when classifying independent CLL cases. Our findings indicate that CLL progression risk largely correlates with particular transcriptomic patterns and paves the way for the identification of high-risk patients who might benefit from prompt therapy following diagnosis.
- Published
- 2019
- Full Text
- View/download PDF
14. Detection of Rare Germline Variants in the Genomes of Patients with B-Cell Neoplasms
- Author
-
Adrián Mosquera Orgueira, Miguel Cid López, Andrés Peleteiro Raíndo, José Ángel Díaz Arias, Beatriz Antelo Rodríguez, Laura Bao Pérez, Natalia Alonso Vence, Ángeles Bendaña López, Aitor Abuin Blanco, Paula Melero Valentín, Roi Ferreiro Ferro, Carlos Aliste Santos, Máximo Francisco Fraga Rodríguez, Marta Sonia González Pérez, Manuel Mateo Pérez Encinas, and José Luis Bello López
- Subjects
germline ,rare variant ,cancer ,lymphoid ,B-cell ,lymphoma ,Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Abstract
There is growing evidence indicating the implication of germline variation in cancer predisposition and prognostication. Here, we describe an analysis of likely disruptive rare variants across the genomes of 726 patients with B-cell lymphoid neoplasms. We discovered a significant enrichment for two genes in rare dysfunctional variants, both of which participate in the regulation of oxidative stress pathways (CHMP6 and GSTA4). Additionally, we detected 1675 likely disrupting variants in genes associated with cancer, of which 44.75% were novel events and 7.88% were protein-truncating variants. Among these, the most frequently affected genes were ATM, BIRC6, CLTCL1A, and TSC2. Homozygous or germline double-hit variants were detected in 28 cases, and coexisting somatic events were observed in 17 patients, some of which affected key lymphoma drivers such as ATM, KMT2D, and MYC. Finally, we observed that variants in six different genes were independently associated with shorter survival in CLL. Our study results support an important role for rare germline variation in the pathogenesis and prognosis of B-cell lymphoid neoplasms.
- Published
- 2021
- Full Text
- View/download PDF
15. Identification of new putative driver mutations and predictors of disease evolution in chronic lymphocytic leukemia
- Author
-
José Luis Bello López, Adrian Mosquera Orgueira, José Ángel Díaz Arias, Beatriz Antelo Rodríguez, and Universidade de Santiago de Compostela. Departamento de Psiquiatría, Radioloxía, Saúde Pública, Enfermaría e Medicina
- Subjects
Chronic lymphocytic leukaemia ,Chronic lymphocytic leukemia ,lcsh:RC254-282 ,Clonal Evolution ,Evolution, Molecular ,Correspondence ,medicine ,Cancer genomics ,Humans ,B-Lymphocytes ,business.industry ,Computational Biology ,High-Throughput Nucleotide Sequencing ,Hematology ,Sequence Analysis, DNA ,medicine.disease ,lcsh:Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,Leukemia, Lymphocytic, Chronic, B-Cell ,Disease evolution ,Oncology ,Immunology ,Mutation ,Disease Progression ,Identification (biology) ,business ,Genes, Neoplasm - Abstract
SI
- Published
- 2019
16. The association of germline variants with chronic lymphocytic leukemia outcome suggests the implication of novel genes and pathways in clinical evolution
- Author
-
Ángel Carracedo Álvarez, Nicolás Díaz Varela, Beatriz Antelo Rodríguez, Adrián Mosquera Orgueira, Catarina Allegue Toscano, Elena María Goiricelaya Seco, José Ángel Díaz Arias, Manuel Mateo Pérez Encinas, Natalia Alonso Vence, José Luis Bello López, Universidade de Santiago de Compostela. Departamento de Bioquímica e Bioloxía Molecular, and Universidade de Santiago de Compostela. Departamento de Psiquiatría, Radioloxía, Saúde Pública, Enfermaría e Medicina
- Subjects
0301 basic medicine ,Male ,Cancer Research ,Germline ,Chronic lymphocytic leukemia ,Single-nucleotide polymorphism ,Biology ,Bioinformatics ,GTP-Binding Protein alpha Subunits, G12-G13 ,MAP Kinase Kinase Kinase 4 ,lcsh:RC254-282 ,Association ,03 medical and health sciences ,0302 clinical medicine ,Surgical oncology ,Exome Sequencing ,Genetics ,medicine ,Biomarkers, Tumor ,Phosphoprotein Phosphatases ,Humans ,Gene Regulatory Networks ,Genetic Predisposition to Disease ,Polymorphism ,Genotyping ,Gene ,Exome sequencing ,Germ-Line Mutation ,Proportional hazards model ,medicine.disease ,Prognosis ,lcsh:Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,Leukemia, Lymphocytic, Chronic, B-Cell ,Survival Analysis ,030104 developmental biology ,Oncology ,030220 oncology & carcinogenesis ,Female ,Research Article - Abstract
Background Chronic Lymphocytic Leukemia (CLL) is the most frequent lymphoproliferative disorder in western countries and is characterized by a remarkable clinical heterogeneity. During the last decade, multiple genomic studies have identified a myriad of somatic events driving CLL proliferation and aggressivity. Nevertheless, and despite the mounting evidence of inherited risk for CLL development, the existence of germline variants associated with clinical outcomes has not been addressed in depth. Methods Exome sequencing data from control leukocytes of CLL patients involved in the International Cancer Genome Consortium (ICGC) was used for genotyping. Cox regression was used to detect variants associated with clinical outcomes. Gene and pathways level associations were also calculated. Results Single nucleotide polymorphisms in PPP4R2 and MAP3K4 were associated with earlier treatment need. A gene-level analysis evidenced a significant association of RIPK3 with both treatment need and survival. Furthermore, germline variability in pathways such as apoptosis, cell-cycle, pentose phosphate, GNα13 and Nitric oxide was associated with overall survival. Conclusion Our results support the existence of inherited conditionants of CLL evolution and points towards genes and pathways that may results useful as biomarkers of disease outcome. More research is needed to validate these findings. Electronic supplementary material The online version of this article (10.1186/s12885-019-5628-y) contains supplementary material, which is available to authorized users.
- Published
- 2019
17. Detection of Rare Germline Variants in the Genomes of B Cell Neoplasms
- Author
-
Jose Luis Bello Lopez, Adrian Mosquera Orgueira, Roi Ferreiro Ferro, Miguel Cid López, José Ángel Díaz Arias, Beatriz Antelo Rodríguez, Laura Bao Pérez, Carlos Aliste Santos, Manuel Mateo Pérez Encinas, Natalia Alonso Vence, Ángeles Bendaña López, Maximo Francisco Fraga Martinez, Aitor Abuin Blanco, Paula Melero Valentín, Andrés Peleteiro Raíndo, and Marta Sonia González Pérez
- Subjects
Genetics ,medicine.anatomical_structure ,allergology ,medicine ,Cancer ,Biology ,medicine.disease ,Genome ,Germline ,B cell - Abstract
Growing evidence has revealed the implication of germline variation in cancer predisposition and prognostication. Here, we describe an analysis of putatively disruptive rare variants across the genomes of 726 patients with B-cell lymphoid neoplasms. We discovered a significant enrichment of 26 genes in germline protein truncating variants (PTVs), affecting cell signaling (MET, JAK2, ANGPT2), energy metabolism (ACO1) and nucleic acid metabolism and repair pathways (NT5E, DCK). Interestingly, some of these variants were restricted to either chronic lymphocytic leukemia (CLL) (i.e., ANGPT2 and AKR1C3) or B-cell lymphoma cases (PNMT, TPT1 and IGHMBP2). Additionally, we detected 1,675 likely disrupting variants in genes associated with cancer, of which 44.75% were novel events and 7.88% were PTVs. Among these, the most frequently affected genes were ATM, BIRC6, CLTCL1A and TSC2. Homozygous or compound heterozygous variants were detected in 28 cases; and coexisting somatic events were observed in 17 patients, some of which affected key lymphoma drivers such as ATM, KMT2D and MYC. Finally, we observed that variants in the helicase gene WRN were independently associated with shorter survival in CLL. Our study results support an important role for rare germline variation in the pathogenesis, clinical presentation and disease outcome of B-cell lymphoid neoplasms.
- Published
- 2021
18. Gene expression profiling identifies FLT3 mutation-like cases in wild-type FLT3 acute myeloid leukemia
- Author
-
Aitor Abuin Blanco, Ángeles Bendaña López, Adrián Mosquera Orgueira, Giovanni Martinelli, Andrés Peleteiro Raíndo, Laura Bao Pérez, Natalia Alonso Vence, José Luis Bello López, Marta Sonia González Pérez, Roi Ferreiro Ferro, Miguel Cid López, José Ángel Díaz Arias, Pau Montesinos Fernández, Claudio Cerchione, Paula Melero Valentín, Beatriz Antelo Rodríguez, and Manuel Mateo Pérez Encinas
- Subjects
Myeloid ,Mutant ,Cancer Treatment ,Gene Expression ,medicine.disease_cause ,DNA Methyltransferase 3A ,Hematologic Cancers and Related Disorders ,Database and Informatics Methods ,Mathematical and Statistical Techniques ,fluids and secretions ,hemic and lymphatic diseases ,Medicine and Health Sciences ,Cluster Analysis ,DNA (Cytosine-5-)-Methyltransferases ,Mutation ,Leukemia ,Multidisciplinary ,Nuclear Proteins ,Myeloid leukemia ,hemic and immune systems ,Hematology ,Genomics ,Myeloid Leukemia ,Leukemia, Myeloid, Acute ,medicine.anatomical_structure ,Oncology ,embryonic structures ,Biomarker (medicine) ,Medicine ,Nucleophosmin ,Transcriptome Analysis ,Research Article ,Acute Myeloid Leukemia ,NPM1 ,Science ,Biology ,Research and Analysis Methods ,Genetics ,medicine ,Humans ,Hierarchical Clustering ,Gene Expression Profiling ,Cancers and Neoplasms ,Biology and Life Sciences ,Computational Biology ,Staurosporine ,Genome Analysis ,medicine.disease ,Gene expression profiling ,Biological Databases ,fms-Like Tyrosine Kinase 3 ,Mutation Databases ,Cancer research ,Biomarkers - Abstract
Background FLT3 mutation is present in 25–30% of all acute myeloid leukemias (AML), and it is associated with adverse outcome. FLT3 inhibitors have shown improved survival results in AML both as upfront treatment and in relapsed/refractory disease. Curiously, a variable proportion of wild-type FLT3 patients also responded to these drugs. Methods We analyzed 6 different transcriptomic datasets of AML cases. Differential expression between mutated and wild-type FLT3 AMLs was performed with the Wilcoxon-rank sum test. Hierarchical clustering was used to identify FLT3-mutation like AMLs. Finally, enrichment in recurrent mutations was performed with the Fisher’s test. Results A FLT3 mutation-like gene expression pattern was identified among wild-type FLT3 AMLs. This pattern was highly enriched in NPM1 and DNMT3A mutants, and particularly in combined NPM1/DNMT3A mutants. Conclusions We identified a FLT3 mutation-like gene expression pattern in AML which was highly enriched in NPM1 and DNMT3A mutations. Future analysis about the predictive role of this biomarker among wild-type FLT3 patients treated with FLT3 inhibitors is envisaged.
- Published
- 2021
19. Survival prediction and treatment optimization of multiple myeloma patients using machine-learning models based on clinical and gene expression data
- Author
-
Maria Victoria Mateos Manteca, Ángeles Bendaña López, Beatriz Antelo Rodríguez, José Ángel Díaz Arias, Laura Bao Pérez, Adrián Mosquera Orgueira, Marta Sonia González Pérez, Andrés Peleteiro Raíndo, Miguel Cid López, Aitor Abuin Blanco, José Luis Bello López, Natalia Alonso Vence, and Manuel Mateo Pérez Encinas
- Subjects
0301 basic medicine ,Male ,Cancer Research ,Concordance ,Myeloma ,Disease ,Machine learning ,computer.software_genre ,Cohort Studies ,Machine Learning ,03 medical and health sciences ,0302 clinical medicine ,Text mining ,Antineoplastic Combined Chemotherapy Protocols ,medicine ,Biomarkers, Tumor ,Humans ,Stage (cooking) ,Multiple myeloma ,Dexamethasone ,business.industry ,Bortezomib ,Gene Expression Profiling ,Hematology ,Translational research ,Middle Aged ,medicine.disease ,Prognosis ,Gene expression profiling ,Gene Expression Regulation, Neoplastic ,Survival Rate ,030104 developmental biology ,Oncology ,030220 oncology & carcinogenesis ,Female ,Artificial intelligence ,business ,Multiple Myeloma ,computer ,Algorithms ,medicine.drug ,Follow-Up Studies - Abstract
Multiple myeloma (MM) remains mostly an incurable disease with a heterogeneous clinical evolution. Despite the availability of several prognostic scores, substantial room for improvement still exists. Promising results have been obtained by integrating clinical and biochemical data with gene expression profiling (GEP). In this report, we applied machine learning algorithms to MM clinical and RNAseq data collected by the CoMMpass consortium. We created a 50-variable random forests model (IAC-50) that could predict overall survival with high concordance between both training and validation sets (c-indexes, 0.818 and 0.780). This model included the following covariates: patient age, ISS stage, serum B2-microglobulin, first-line treatment, and the expression of 46 genes. Survival predictions for each patient considering the first line of treatment evidenced that those individuals treated with the best-predicted drug combination were significantly less likely to die than patients treated with other schemes. This was particularly important among patients treated with a triplet combination including bortezomib, an immunomodulatory drug (ImiD), and dexamethasone. Finally, the model showed a trend to retain its predictive value in patients with high-risk cytogenetics. In conclusion, we report a predictive model for MM survival based on the integration of clinical, biochemical, and gene expression data with machine learning tools.
- Published
- 2020
20. FLT3 inhibitors in the treatment of acute myeloid leukemia: current status and future perspectives
- Author
-
Giovanni Martinelli, José Luis Bello López, Adrián Mosquera Orgueira, Alicia Mosquera Torre, Natalia Alonso Vence, Marta Sonia González Pérez, Claudio Cerchione, Beatriz Antelo Rodríguez, Laura Bao Pérez, Manuel Mateo Pérez Encinas, Andrés Peleteiro Raíndo, José Ángel Díaz Arias, Manuel Albors Ferreiro, Roi Ferreiro Ferro, and Miguel Cid López
- Subjects
Myeloid ,chemistry.chemical_compound ,fluids and secretions ,0302 clinical medicine ,Piperidines ,Recurrence ,hemic and lymphatic diseases ,Midostaurin ,Aniline Compounds ,Lestaurtinib ,Hematopoietic Stem Cell Transplantation ,Imidazoles ,Myeloid leukemia ,hemic and immune systems ,General Medicine ,Sorafenib ,Drug Resistance, Multiple ,Pyridazines ,Leukemia, Myeloid, Acute ,Leukemia ,medicine.anatomical_structure ,Pyrazines ,030220 oncology & carcinogenesis ,embryonic structures ,030211 gastroenterology & hepatology ,medicine.drug ,Crenolanib ,Carbazoles ,Antineoplastic Agents ,Maintenance Chemotherapy ,03 medical and health sciences ,medicine ,Humans ,Point Mutation ,Benzothiazoles ,Furans ,Protein Kinase Inhibitors ,Quizartinib ,business.industry ,Phenylurea Compounds ,Staurosporine ,medicine.disease ,fms-Like Tyrosine Kinase 3 ,chemistry ,Drug Resistance, Neoplasm ,Mutation ,Cancer research ,Benzimidazoles ,business ,Forecasting - Abstract
Mutations in the FMS-like tyrosine kinase 3 (FLT3) gene arise in 25-30% of all acute myeloid leukemia (AML) patients. These mutations lead to constitutive activation of the protein product and are divided in two broad types: internal tandem duplication (ITD) of the juxtamembrane domain (25% of cases) and point mutations in the tyrosine kinase domain (TKD). Patients with FLT3 ITD mutations have a high relapse risk and inferior cure rates, whereas the role of FLT3 TKD mutations still remains to be clarified. Additionally, growing research indicates that FLT3 status evolves through a disease continuum (clonal evolution), where AML cases can acquire FLT3 mutations at relapse - not present in the moment of diagnosis. Several FLT3 inhibitors have been tested in patients with FLT3-mutated AML. These drugs exhibit different kinase inhibitory profiles, pharmacokinetics and adverse events. First-generation multi-kinase inhibitors (sorafenib, midostaurin, lestaurtinib) are characterized by a broad-spectrum of drug targets, whereas second-generation inhibitors (quizartinib, crenolanib, gilteritinib) show more potent and specific FLT3 inhibition, and are thereby accompanied by less toxic effects. Notwithstanding, all FLT3 inhibitors face primary and acquired mechanisms of resistance, and therefore the combinations with other drugs (standard chemotherapy, hypomethylating agents, checkpoint inhibitors) and its application in different clinical settings (upfront therapy, maintenance, relapsed or refractory disease) are under study in a myriad of clinical trials. This review focuses on the role of FLT3 mutations in AML, pharmacological features of FLT3 inhibitors, known mechanisms of drug resistance and accumulated evidence for the use of FLT3 inhibitors in different clinical settings.
- Published
- 2020
21. Improved personalized survival prediction of patients with diffuse large B-cell Lymphoma using gene expression profiling
- Author
-
Andrés Peleteiro Raíndo, Laura Bao Pérez, Aitor Abuin Blanco, José Ángel Díaz Arias, Adrián Mosquera Orgueira, Natalia Alonso Vence, Carlos Aliste Santos, José Luis Bello López, Beatriz Antelo Rodríguez, Miguel Cid López, Manuel Mateo Pérez Encinas, Ángeles Bendaña López, Marta Sonia González Pérez, and Máximo Francisco Fraga Rodríguez
- Subjects
0301 basic medicine ,Oncology ,Male ,Cancer Research ,medicine.medical_specialty ,Prognostic variable ,Lymphoma ,Survival ,bcl-X Protein ,Biology ,lcsh:RC254-282 ,03 medical and health sciences ,Tumor Necrosis Factor Receptor Superfamily, Member 9 ,0302 clinical medicine ,Internal medicine ,Genetics ,medicine ,Biomarkers, Tumor ,Humans ,Stage (cooking) ,Transcriptomics ,Survival analysis ,Adaptor Proteins, Signal Transducing ,Retrospective Studies ,Proportional hazards model ,Gene Expression Profiling ,Computational Biology ,RNA-Binding Proteins ,Middle Aged ,medicine.disease ,lcsh:Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,Microarray Analysis ,Prognosis ,Survival Analysis ,Baculoviral IAP Repeat-Containing 3 Protein ,Random forest ,Gene expression profiling ,Gene Expression Regulation, Neoplastic ,030104 developmental biology ,030220 oncology & carcinogenesis ,Test set ,DLBCL ,Female ,Lymphoma, Large B-Cell, Diffuse ,Prediction ,Diffuse large B-cell lymphoma ,Research Article ,Unsupervised Machine Learning - Abstract
Background Thirty to forty percent of patients with Diffuse Large B-cell Lymphoma (DLBCL) have an adverse clinical evolution. The increased understanding of DLBCL biology has shed light on the clinical evolution of this pathology, leading to the discovery of prognostic factors based on gene expression data, genomic rearrangements and mutational subgroups. Nevertheless, additional efforts are needed in order to enable survival predictions at the patient level. In this study we investigated new machine learning-based models of survival using transcriptomic and clinical data. Methods Gene expression profiling (GEP) of in 2 different publicly available retrospective DLBCL cohorts were analyzed. Cox regression and unsupervised clustering were performed in order to identify probes associated with overall survival on the largest cohort. Random forests were created to model survival using combinations of GEP data, COO classification and clinical information. Cross-validation was used to compare model results in the training set, and Harrel’s concordance index (c-index) was used to assess model’s predictability. Results were validated in an independent test set. Results Two hundred thirty-three and sixty-four patients were included in the training and test set, respectively. Initially we derived and validated a 4-gene expression clusterization that was independently associated with lower survival in 20% of patients. This pattern included the following genes: TNFRSF9, BIRC3, BCL2L1 and G3BP2. Thereafter, we applied machine-learning models to predict survival. A set of 102 genes was highly predictive of disease outcome, outperforming available clinical information and COO classification. The final best model integrated clinical information, COO classification, 4-gene-based clusterization and the expression levels of 50 individual genes (training set c-index, 0.8404, test set c-index, 0.7942). Conclusion Our results indicate that DLBCL survival models based on the application of machine learning algorithms to gene expression and clinical data can largely outperform other important prognostic variables such as disease stage and COO. Head-to-head comparisons with other risk stratification models are needed to compare its usefulness.
- Published
- 2020
22. A Three-Gene Expression Signature Identifies a Cluster of Patients with Short Survival in Chronic Lymphocytic Leukemia
- Author
-
Nicolás Díaz Varela, Beatriz Antelo Rodríguez, José Luis Bello López, Adrián Mosquera Orgueira, José Ángel Díaz Arias, Universidade de Santiago de Compostela. Centro de Investigación en Medicina Molecular e Enfermidades Crónicas, and Universidade de Santiago de Compostela. Departamento de Psiquiatría, Radioloxía, Saúde Pública, Enfermaría e Medicina
- Subjects
Oncology ,medicine.medical_specialty ,Article Subject ,Chronic lymphocytic leukemia ,tirosina ,leucemia linfocítica crónica de células b ,Disease ,Disease cluster ,lcsh:RC254-282 ,Transcriptome ,Internal medicine ,hemic and lymphatic diseases ,Gene expression ,medicine ,aberraciones cromosómicas ,Short survival ,leucemia ,Chromosome Aberrations ,Leukemia ,business.industry ,Retrospective cohort study ,lcsh:Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,Prognosis ,medicine.disease ,Leukemia, Lymphocytic, Chronic, B-Cell ,pronóstico ,KLF4 ,Leucemia linfocítica crónica ,Tyrosine ,business ,Research Article - Abstract
Chronic lymphocytic leukemia (CLL) is a lymphoproliferative disorder characterized by its heterogeneous clinical evolution. Despite the discovery of the most frequent cytogenomic drivers of disease during the last decade, new efforts are needed in order to improve prognostication. In this study, we used gene expression data of CLL samples in order to discover novel transcriptomic patterns associated with patient survival. We observed that a 3-gene expression signature composed of SCGB2A1, KLF4, and PPP1R14B differentiate a group of circa 5% of cases with short survival. This effect was independent of the main cytogenetic markers of adverse prognosis. Finally, this finding was reproduced in an independent retrospective cohort. We believe that this small gene expression pattern will be useful for CLL prognostication and its association with CLL response to novel drugs should be explored in the future.
- Published
- 2019
- Full Text
- View/download PDF
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.