RNA Binding Proteins in Breast, Colon, and Rectal Cancer: A Comprehensive Study on Their Influence on Disease Progression and Potential Clinical Applications

Programa Oficial de Doutoramento en Bioloxía Celular e Molecular. 5004V01Tesis por compendio de publicación[Abstract] Breast cancer (BC) and Colorectal adenocarcinoma (COREAD) are major health problems worldwide. While significant progress has been made in understanding their molecular subtypes and genetics, a cure remains elusive. An emerging area of interest is the role of RNA-binding proteins (RBPs) in the development and progression of these cancers. RBPs are critical regulators of every hallmark of cancer and could serve as sensitive biomarkers for diagnosis, prognosis, and potential targets. In COREAD, a multidata integration strategy identified putative roles of NOP56, RBM12, NAT10, FKBP1A, EMG1, and CSE1L in the progression of colon cancer (COAD) and rectal cancer (READ). FKBP1A, NOP56, and NAT10 mRNA expression may predict poor prognosis in COREAD and COAD patients. In BC, integrated in silico analyses of human RBPs in major cancer databases revealed five putative BC RBPs (PUF60, TFRC, KPNB1, NSF, and SF3A3) with robust oncogenic features. PUF60 and SF3A3 were identified as central elements of a spliceosome-related cluster involving RBPs and cancer driver genes (CDGs). RBPs hold significant potential as diagnostic, prognostic, and therapeutic targets in BC, COAD, and READ. Further research on these RBPs is crucial to unveil their molecular mechanisms, validate their clinical potential, and develop novel treatment strategies.[Resumen] El cáncer de mama (BC, por sus siglas en inglés) y el adenocarcinoma colorrectal (COREAD, por sus siglas en inglés) son importantes problemas de salud a nivel mundial. Si bien se ha logrado un progreso significativo en la comprensión de sus subtipos moleculares y su genética, la cura sigue siendo difícil de alcanzar. Un área emergente de interés es el papel de las proteínas de unión al ARN (RBPs, por sus siglas en inglés) en el desarrollo y progresión de estos cánceres. Las RBPs son reguladoras críticas de todas las características del cáncer y podrían servir como biomarcadores sensibles para el diagnóstico, el pronóstico y dianas terapéuticas potenciales. En COREAD, una estrategia de integración de datos múltiples identificó roles putativos de NOP56, RBM12, NAT10, FKBP1A, EMG1 y CSE1L en la progresión del cáncer de colon (COAD, por sus siglas en inglés) y el cáncer de recto (READ, por sus siglas en inglés). La expresión del ARNm de FKBP1A, NOP56 y NAT10 puede predecir un mal pronóstico en pacientes con COREAD y COAD. En BC, los análisis in silico integrados de las RBPs en las principales bases de datos de cáncer revelaron cinco RBPs implicadas en BC (PUF60, TFRC, KPNB1, NSF y SF3A3) con características oncogénicas sólidas. PUF60 y SF3A3 se identificaron como elementos centrales de un grupo relacionado con espliceosoma que involucra RBPs y genes conductores del cáncer (CDG, por sus siglas en inglés). Las RBPs tienen un potencial significativo como dianas diagnósticas, pronósticas y terapéuticas en BC, COAD y READ. La investigación adicional sobre estas RBPs es crucial para revelar sus mecanismos moleculares, validar su potencial clínico y desarrollar nuevas estrategias de tratamiento.[Resumo] O cancro de mama (BC, Breast Cancer em inglês) e o adenocarcinoma colorrectal (COREAD, Colorectal Adenocarcinoma em inglês) son problemas de saúde importantes a nivel mundial. Aínda que se logrou un progreso significativo na comprensión dos seus subtipos moleculares e a súa xenética, a cura segue sendo difícil de alcanzar. Unha área emerxente de interese é o papel das proteínas de unión ao ARN (RBPs, RNA-Binding Proteins en inglés) no desenvolvemento e progresión destes cancros. As RBPs son reguladoras críticas de todas as características do cancro e poderían servir como biomarcadores sensibles para o diagnóstico, o pronóstico e posibles dianas terapéuticas. En COREAD, unha estratexia de integración de datos múltiples identificou roles putativos de NOP56, RBM12, NAT10, FKBP1A, EMG1 e CSE1L na progresión do cancro de colon (COAD em inglês) e o cancro de recto (READ em inglês). A expresión do ARNm de FKBP1A, NOP56 e NAT10 pode predicir un mal pronóstico en pacientes con COREAD e COAD. En BC, os análises in silico integrados das RBPs nas principais bases de datos de cancro revelaron cinco RBPs implicadas en BC (PUF60, TFRC, KPNB1, NSF e SF3A3) con características oncogénicas sólidas. PUF60 e SF3A3 identificáronse como elementos centrais dun grupo relacionado co espliceosoma que involucra RBPs e xenes condutores do cancro (CDG em inglês). As RBPs teñen un potencial significativo como dianas diagnósticas, pronósticos e terapéuticas en BC, COAD e READ. A investigación adicional sobre estas RBPs é crucial para revelar os seus mecanismos moleculares, validar o seu potencial clínico e desenvolver novas estratexias de tratamento

Data mining identifies novel RNA-binding proteins involved in colon and rectal carcinomas

Colorectal adenocarcinoma (COREAD) is the second most deadly cancer and third most frequently encountered malignancy worldwide. Despite efforts in molecular subtyping and subsequent personalized COREAD treatments, multidisciplinary evidence suggests separating COREAD into colon cancer (COAD) and rectal cancer (READ). This new perspective could improve diagnosis and treatment of both carcinomas. RNA-binding proteins (RBPs), as critical regulators of every hallmark of cancer, could fulfill the need to identify sensitive biomarkers for COAD and READ separately. To detect new RBPs involved in COAD and READ progression, here we used a multidata integration strategy to prioritize tumorigenic RBPs. We analyzed and integrated 1) RBPs genomic and transcriptomic alterations from 488 COAD and 155 READ patients, 2) ∼ 10,000 raw associations between RBPs and cancer genes, 3) ∼ 15,000 immunostainings, and 4) loss-of-function screens performed in 102 COREAD cell lines. Thus, we unraveled new putative roles of NOP56, RBM12, NAT10, FKBP1A, EMG1, and CSE1L in COAD and READ progression. Interestingly, FKBP1A and EMG1 have never been related with any of these carcinomas but presented tumorigenic features in other cancer types. Subsequent survival analyses highlighted the clinical relevance of FKBP1A, NOP56, and NAT10 mRNA expression to predict poor prognosis in COREAD and COAD patients. Further research should be performed to validate their clinical potential and to elucidate their molecular mechanisms underlying these malignancies

Cytogenetic and genomic analysis of a patient with turner syndrome and t(2;12): a case report

Background: Turner syndrome is a genetic disorder that afects women. It is caused by an absent or incomplete X chromosome, which can be presented in mosaicism or not. There are 12 cases of Turner syndrome patients who present structural alterations in autosomal chromosomes. Case presentation: The present case report describes a patient with a reciprocal, maternally inherited translocation between chromosomes 2 and 12 with a mosaicism of X monosomy 45,X,t(2;12)(p13;q24)[95]/46,XX,t(2;12)(p13;q24) [5]. Through genetic mapping arrays, altered genes in the patient were determined within the 23 chromosome pairs. These genes were associated with the patient’s clinical features using a bioinformatics tool Conclusion: To our knowledge, this is the frst case in which a translocation (2;12) is reported in a patient with Turner syndrome and confrmed by conventional cytogenetics, FISH and molecular genetics. Clinical features of our patient are closely related with the loss of one X chromosome, however mild intellectual disability can be likely explained by autosomal genes. The presence of familial translocations was a common fnding, thus emphasizing the need for familiar testing for further genetic counselling

A Quick Guide for Using Microsoft Onenote as an Electronic Laboratory Notebook

[Abstract] Scientific data recording and reporting systems are of a great interest for endorsing reproducibility and transparency practices among the scientific community. Current research generates large datasets that can no longer be documented using paper lab notebooks (PLNs). In this regard, electronic laboratory notebooks (ELNs) could be a promising solution to replace PLNs and promote scientific reproducibility and transparency. We previously analyzed five ELNs and performed two survey-based studies to implement an ELN in a biomedical research institute. Among the ELNs tested, we found that Microsoft OneNote presents numerous features related to ELN best functionalities. In addition, both surveyed groups preferred OneNote over a scientifically designed ELN (PerkinElmer Elements). However, OneNote remains a general note-taking application and has not been designed for scientific purposes. We therefore provide a quick guide to adapt OneNote to an ELN workflow that can also be adjusted to other nonscientific ELNs

USO DE MICROSOFT ONENOTE COMO CUADERNO ELECTRÓNICO DE LABORATORIO

Los sistemas de registro y de reporte de datos son de gran interés, puesto que respaldan la reproducibilidad y transparencia científica. La investigación actual genera una gran cantidad de datos que ya no se pueden documentar utilizando cuadernos de laboratorio de papel (CLP). Los cuadernos electrónicos de laboratorio (CEL) podrían ser una solu-ción prometedora para reemplazar los CLP y promover la reproducibilidad científica y su transparencia. Anteriormente analizamos cinco CEL y realizamos dos encuestas para implementar un CEL en un instituto de investigación biomédica. Entre los CEL proba-dos, encontramos que Microsoft OneNote presenta numerosas características relacio-nadas con las mejores funcionalidades del CEL. Además, ambos grupos encuestados prefirieron OneNote sobre un CEL científico (Elements de PerkinElmer). Sin embargo, OneNote es una aplicación general para tomar notas que no ha sido diseñada para fi-nes científicos. Por lo tanto, en este trabajo proporcionamos varias pautas para adaptar OneNote a un flujo de trabajo experimental

In silico Analyses of Immune System Protein Interactome Network, Single-Cell RNA Sequencing of Human Tissues, and Artificial Neural Networks Reveal Potential Therapeutic Targets for Drug Repurposing Against COVID-19

Background: There is pressing urgency to identify therapeutic targets and drugs that allow treating COVID-19 patients effectively.Methods: We performed in silico analyses of immune system protein interactome network, single-cell RNA sequencing of human tissues, and artificial neural networks to reveal potential therapeutic targets for drug repurposing against COVID-19.Results: We screened 1,584 high-confidence immune system proteins in ACE2 and TMPRSS2 co-expressing cells, finding 25 potential therapeutic targets significantly overexpressed in nasal goblet secretory cells, lung type II pneumocytes, and ileal absorptive enterocytes of patients with several immunopathologies. Then, we performed fully connected deep neural networks to find the best multitask classification model to predict the activity of 10,672 drugs, obtaining several approved drugs, compounds under investigation, and experimental compounds with the highest area under the receiver operating characteristics.Conclusion: After being effectively analyzed in clinical trials, these drugs can be considered for treatment of severe COVID-19 patients. Scripts can be downloaded at

Screening exons 16 and 17 of the amyloid precursor protein gene in sporadic early-onset Alzheimer's disease

Early-onset Alzheimer's disease (EOAD) can be familial (FAD) or sporadic EOAD (sEOAD); both have a disease onset ≤65 years of age. A total of 451 sEOAD samples were screened for known causative mutations in exons 16 and 17 of the amyloid precursor protein (APP) gene. Four samples were shown to be heterozygous for 1 of 3 known causative mutations: p.A713T, p.V717I, and p.V717G; this highlights the importance of screening EOAD patients for causative mutations. Additionally, we document an intronic 6 base pair (bp) deletion located 83 bp downstream of exon 17 (rs367709245, IVS17 83-88delAAGTAT), which has a nonsignificantly increased minor allele frequency in our sEOAD cohort (0.006) compared to LOAD (0.002) and controls (0.002). To assess the effect of the 6-bp deletion on splicing, COS-7 and BE(2)-C cells were transfected with a minigene vector encompassing exon 17. There was no change in splicing of exon 17 from constructs containing either wild type or deletion inserts. Sequencing of cDNA generated from cerebellum and temporal cortex of a patient harboring the deletion found no evidence of transcripts with exon 17 remov

Microfiltraciones entre ionómero de vidrio y resina compuesta en lesiones clase-V no cariosas

No standards have been established for the treatment of non-carious cervical cavities; a suitable biomaterial will allow good adaptation and longevity of the restoration. Objective: To determine microfiltration in non-carious class V cavities restored with glass ionomer and nanoparticulate resin. Materials and methods: Class V cavities made on the vestibular surface of 80 healthy premolars (1.5 mm deep x 3 mm high in the occlusion-gingival direction x 2 mm wide in the mesio-distal direction) were randomly restored with two biomaterials (n = 40): 1) glass ionomer and 2) nano-filled resin. Then, the specimens were isolated with varnish and immersed in methylene blue for 24 hours. Subsequently, the samples were subjected to 500 cycles of thermocycling for 8 hours and 45 minutes with thermal changes of 37°, 72° and 75° C, each cycle with a duration of 17 seconds. The samples were washed with distilled water and sectioned longitudinally to determine the degree of microfiltration using a stereoscope (Leica M60 Biosystems). Categorical data were analyzed with the Chi2 test in SPSS 24®. Results: It was observed that filtration is significantly lower in resin than in those restored with glass ionomers (p < 0.001). However, none of the restoration materials tested were able to seal the margins or walls of the teeth completely. Conclusion: As a result of the present experiment, it is determined that class V restorations sealed with nano-filled resin have less marginal microfiltration than those restored with glass ionomer.No se han establecido estándares para el tratamiento de cavidades cervicales no cariosas; un biomaterial adecuado permitirá buena adaptación y longevidad de la restauración. Objetivo: Determinar la microfiltración en cavidades clase V no cariosas restauradas con ionómero de vidrio y resina nanoparticulada. Materiales y métodos: Cavidades clase V realizadas en la superficie vestibular de 80 premolares sanos (1,5 mm de profundidad x 3 mm de altura en sentido ocluso- gingival x 2 mm de ancho en sentido mesio-distal) se restauraron aleatoriamente con dos biomateriales (n = 40): 1) ionómero de vidrio y 2) resina de nano relleno. Después, los especímenes fueron aislados con barniz y sumergidos en azul de metileno por 24 horas. Posteriormente, las muestras se sometieron 500 ciclos de termociclado por 8 horas y 45 minutos con cambios térmicos de 37°, 72° y 75°C, cada ciclo con una duración de 17 segundos. Las muestras fueron lavadas con agua destilada y seccionadas longitudinalmente para determinar el grado de microfiltración utilizando un estereoscopio (Leica M60, Biosystems). Los datos categóricos se analizaron con el test Chi2 en SPSS 24®. Resultados: Se pudo apreciar que la filtración es significativamente menor en resina que con ionómeros de vidrio (p < 0,001). Sin embargo, ninguno de los materiales de restauración probados fue capaz de sellar los márgenes o las paredes de los dientes completamente. Conclusión: como resultado del presente experimento se determina que las restauraciones de clase V obturadas con resina de nano relleno presentan menor microfiltración marginal que las restauradas con ionómero de vidrio

Identification of Key Proteins from the Alternative Lengthening of Telomeres-Associated Promyelocytic Leukemia Nuclear Bodies Pathway

Alternative lengthening of telomeres-associated promyelocytic leukemia nuclear bodies (APBs) are a hallmark of telomere maintenance. In the last few years, APBs have been described as the main place where telomeric extension occurs in ALT-positive cancer cell lines. A different set of proteins have been associated with APBs function, however, the molecular mechanisms behind their assembly, colocalization, and clustering of telomeres, among others, remain unclear. To improve the understanding of APBs in the ALT pathway, we integrated multiomics analyses to evaluate genomic, transcriptomic and proteomic alterations, and functional interactions of 71 APBs-related genes/proteins in 32 Pan-Cancer Atlas studies from The Cancer Genome Atlas Consortium (TCGA). As a result, we identified 13 key proteins which showed distinctive mutations, interactions, and functional enrichment patterns across all the cancer types and proposed this set of proteins as candidates for future ex vivo and in vivo analyses that will validate these proteins to improve the understanding of the ALT pathway, fill the current research gap about APBs function and their role in ALT, and be considered as potential therapeutic targets for the diagnosis and treatment of ALT-positive cancers in the future

Integrated in silico analyses identify PUF60 and SF3A3 as new spliceosome-related breast cancer RNA-binding proteins

More women are diagnosed with breast cancer (BC) than any other type of cancer. Although large-scale efforts have completely redefined cancer, a cure remains unattainable. In that respect, new molecular functions of the cell should be investigated, such as post-transcriptional regulation. RNA-binding proteins (RBPs) are emerging as critical post-transcriptional modulators of tumorigenesis, but only a few have clear roles in BC. To recognize new putative breast cancer RNA-binding proteins, we performed integrated in silico analyses of all human RBPs (n = 1392) in three major cancer databases and identified five putative BC RBPs (PUF60, TFRC, KPNB1, NSF, and SF3A3), which showed robust oncogenic features related to their genomic alterations, immunohistochemical changes, high interconnectivity with cancer driver genes (CDGs), and tumor vulnerabilities. Interestingly, some of these RBPs have never been studied in BC, but their oncogenic functions have been described in other cancer types. Subsequent analyses revealed PUF60 and SF3A3 as central elements of a spliceosome-related cluster involving RBPs and CDGs. Further research should focus on the mechanisms by which these proteins could promote breast tumorigenesis, with the potential to reveal new therapeutic pathways along with novel drug-development strategies.This research received no external fundin