Deep learning analysis on the resulting impacts of weekly load training on students' biological system / Análise do aprendizado profundo nos impactos resultantes dos treinos semanais de carga sobre o sistema biológico dos estudantes / Análisis de aprendizaje profundo sobre los impactos resultantes de los entrenamientos semanales de carga en el sistema biológico de los estudiantes

ABSTRACT Introduction The recent development of the deep learning algorithm as a new multilayer network machine learning algorithm has reduced the problem of traditional training algorithms easily falling into minimal places, becoming a recent direction in the learning field. Objective Design and validate an artificial intelligence model for deep learning of the resulting impacts of weekly load training on students' biological system. Methods According to the physiological and biochemical indices of athletes in the training process, this paper analyzes the actual data of athletes' training load in the annual preparation period. The characteristics of athletes' training load in the preparation period were discussed. The value, significance, composition factors, arrangement principle and method of calculation, and determination of weekly load density using the deep learning algorithm are discussed. Results The results showed that the daily 24-hour random sampling load was moderate intensity, low and high-intensity training, and enhanced the physical-motor system and neural reactivity. Conclusion The research shows that there can be two activities of "teaching" and "training" in physical education and sports training. The sports biology monitoring research proves to be a growth point of sports training research with great potential for expansion for future research. Level of evidence II; Therapeutic studies - investigation of treatment outcomes.

RESUMO Introdução O recente desenvolvimento do algoritmo de aprendizado profundo como um novo algoritmo de aprendizado de máquina de rede multicamadas reduziu o problema dos algoritmos de treinamento tradicionais, que facilmente caiam em locais mínimos, tornando-se uma direção recente no campo do aprendizado. Objetivo Desenvolver e validar um modelo de inteligência artificial para aprendizado profundo dos impactos resultantes dos treinos semanais de carga sobre o sistema biológico dos estudantes. Métodos De acordo com os índices fisiológicos e bioquímicos dos atletas no processo de treinamento, este artigo analisa os dados reais da carga de treinamento dos atletas no período anual de preparação. As características da carga de treinamento dos atletas no período de preparação foram discutidas. O valor, significância, fatores de composição, princípio de arranjo e método de cálculo e determinação da densidade de carga semanal usando o algoritmo de aprendizado profundo são discutidos. Resultados Os resultados mostraram que a carga diária de 24 horas de amostragem aleatória foi de intensidade moderada, treinamento de baixa densidade e alta intensidade, e o sistema físico-motor e a reatividade neural foram aprimorados. Conclusão A pesquisa mostra que pode haver duas atividades de "ensino" e "treinamento" na área de educação física e no treinamento esportivo. A pesquisa de monitoramento da biologia esportiva revela-se um ponto de crescimento da pesquisa de treinamento esportivo com grande potencial de expansão para pesquisas futuras. Nível de evidência II; Estudos terapêuticos - investigação dos resultados do tratamento.

RESUMEN Introducción El reciente desarrollo del algoritmo de aprendizaje profundo como un nuevo algoritmo de aprendizaje automático de red multicapa ha reducido el problema de los algoritmos de entrenamiento tradicionales, que caen fácilmente en lugares mínimos, convirtiéndose en una dirección reciente en el campo del aprendizaje. Objetivo Desarrollar y validar un modelo de inteligencia artificial para el aprendizaje profundo de los impactos resultantes del entrenamiento de la carga semanal en el sistema biológico de los estudiantes. Métodos De acuerdo con los índices fisiológicos y bioquímicos de los atletas en el proceso de entrenamiento, este artículo analiza los datos reales de la carga de entrenamiento de los atletas en el período de preparación anual. Se analizaron las características de la carga de entrenamiento de los atletas en el periodo de preparación. Se analizan el valor, el significado, los factores de composición, el principio de disposición y el método de cálculo y determinación de la densidad de carga semanal mediante el algoritmo de aprendizaje profundo. Resultados Los resultados mostraron que la carga diaria de 24 horas de muestreo aleatorio era de intensidad moderada, de baja densidad y de alta intensidad de entrenamiento, y que el sistema físico-motor y la reactividad neural mejoraban. Conclusión La investigación muestra que puede haber dos actividades de "enseñanza" y "formación" en la educación física y el entrenamiento deportivo. La investigación sobre el seguimiento de la biología del deporte demuestra ser un punto de crecimiento de la investigación sobre el entrenamiento deportivo con un gran potencial de expansión para futuras investigaciones. Nivel de evidencia II; Estudios terapéuticos - investigación de los resultados del tratamiento.

Bioinformatics and expression analysis of the Xeroderma Pigmentosum complementation group C (XPC) of Trypanosoma evansi in Trypanosoma cruzi cells / Análises de bioinformática e da expressão do gene Xeroderma Pigmentosum complementation group C (XPC) de Trypanosoma evansi em células de Trypanosoma cruzi

Abstract Nucleotide excision repair (NER) acts repairing damages in DNA, such as lesions caused by cisplatin. Xeroderma Pigmentosum complementation group C (XPC) protein is involved in recognition of global genome DNA damages during NER (GG-NER) and it has been studied in different organisms due to its importance in other cellular processes. In this work, we studied NER proteins in Trypanosoma cruzi and Trypanosoma evansi, parasites of humans and animals respectively. We performed three-dimensional models of XPC proteins from T. cruzi and T. evansi and observed few structural differences between these proteins. In our tests, insertion of XPC gene from T. evansi (TevXPC) in T. cruzi resulted in slower cell growth under normal conditions. After cisplatin treatment, T. cruzi overexpressing its own XPC gene (TcXPC) was able to recover cell division rates faster than T. cruzi expressing TevXPC gene. Based on these tests, it is suggested that TevXPC (being an exogenous protein in T. cruzi) interferes negatively in cellular processes where TcXPC (the endogenous protein) is involved. This probably occurred due interaction of TevXPC with some endogenous molecules or proteins from T.cruzi but incapacity of interaction with others. This reinforces the importance of correctly XPC functioning within the cell.

Resumo O reparo por excisão de nucleotídeos (NER) atua reparando danos no DNA, como lesões causadas por cisplatina. A proteína Xeroderma Pigmentosum complementation group C (XPC) está envolvida no reconhecimento de danos pela via de reparação global do genoma pelo NER (GG-NER) e tem sido estudada em diferentes organismos devido à sua importância em outros processos celulares. Neste trabalho, estudamos proteínas do NER em Trypanosoma cruzi e Trypanosoma evansi, parasitos de humanos e animais, respectivamente. Modelos tridimensionais das proteínas XPC de T. cruzi e T. evansi foram feitos e observou-se poucas diferenças estruturais entre estas proteínas. Durante testes, a inserção do gene XPC de T. evansi (TevXPC) em T. cruzi resultou em crescimento celular mais lento em condições normais. Após o tratamento com cisplatina, T. cruzi superexpressando seu próprio gene XPC (TcXPC) foi capaz de recuperar as taxas de divisão celular mais rapidamente do que T. cruzi expressando o gene TevXPC. Com base nesses testes, sugere-se que TevXPC (sendo uma proteína exógena em T. cruzi) interfere negativamente nos processos celulares em que TcXPC (a proteína endógena) está envolvida. Isso provavelmente ocorreu pois TevXPC é capaz de interagir com algumas moléculas ou proteínas endógenas de T.cruzi, mas é incapaz de interagir com outras. Isso reforça a importância do correto funcionamento de XPC dentro da célula.

Función biológica de AMPK- ß2 en músculo esquelético y su dinámica estructural después de la activación por SC4 / Biological role of AMPK- ß2 in skeletal muscle and its structural dynamics after activation by SC4

INTRODUCCIÓN: la Proteína Quinasa Activada por AMP (AMPK), es una enzima monitora y reguladora central del estado energético celular, por tanto, es responsable de la respuesta celular al suministro y demanda de energía. El AMP actúa como activador en condiciones de déficit energético, mientras que el ATP la inactiva cuando las condiciones energéticas son más favorables. Debido a su función central en el metabolismo, la AMPK surge como un blanco proteico prometedor para el tratamiento de diferentes enfermedades como la Diabetes Mellitus tipo 2 (DM2), Síndrome Metabólico (SM), Cáncer, entre otros. Existen múltiples isoformas de AMPK que se regulan y expresan diferencialmente en todo el organismo. La isoforma AMPK­ß2 se expresa casi exclusivamente en músculo esquelético y dado que este es el órgano primario para el almacenamiento y eliminación de Glucosa, AMPK­ß2 puede dirigir su homeostasis por una ruta independiente a la Insulina. La molécula activadora SC4 tiene una gran selectividad por AMPK­ß2 y debido a su función biológica, podría servir como modelo farmacológico para coadyuvar el tratamiento de enfermedades metabólicas. OBJETIVO: análisis de la dinámica molecular de activación de la AMPK­ß2. METODOLOGÍA: en el presente estudio, se emplean herramientas bioinformáticas como Chimera 1.15 y Phyton Molecular Viewer. RESULTADOS: el análisis in silico permitió comprender varios aspectos estructurales relacionados con la acción de SC4 sobre la estructura trimérica de la AMPK, los aminoácidos con los que interacciona y cómo su estructura química le otorga gran selectividad. También fue útil para en un futuro, ampliar los criterios de extracción, identificación y/o diseño de compuestos activos a partir de fuentes naturales, con propiedades funcionales similares o aún mejores a SC4, para así poder emplearlos con un enfoque terapéutico que beneficie a nuestra población.

INTRODUCTION: protein Kinase Activated by AMP (AMPK), is a monitor enzyme and a central regulator of the energetic cellular state, therefore, it is responsible for the cellular response to the supply and demand of energy. AMP acts as an activator in conditions of energy deficit, while ATP inactivates it when energy conditions are more favorable. Due to its central role in metabolism, AMPK appears as a promising protein target for the treatment of different diseases such as Diabetes Mellitus type 2 (DM2), Metabolic Syndrome (SM), and Cancer among others. There are multiple isoforms of AMPK that are regulated and differentially expressed throughout the body. The ß2-AMPK isoform is expressed almost exclusively in skeletal muscle and since this is the primary organ for Glucose disposal and storage, ß2-AMPK has an established role as a driver of insulin-independent Glucose clearance. The activator SC4 has a high selectivity for ß2-AMPK and due to its biological function; it could serve as a pharmacological model to aid the treatment of metabolic diseases. OBJETIVE: to analize the molecular dinamic of AMPK- ß2 activation. METHODOLOGY: in the present work we employed bioinformatics, Chimera 1.15 and Phyton Molecular Viewer. RESULTS: the in silico analysis allow us to understand many many structural features related to the action of SC4 on the trimeric structure of AMPK, the specific amino acids involved in the interaction and how its chemical structure gives it high selectivity. Thus, this structural analysis will be useful in order to broaden the criteria for extraction, identification and/or design of active compounds from natural sources, with similar or even better properties than SC4, to use them in a future, with a therapeutic approach that benefits our population.

Clonamiento, expresión y seroreactividad de la proteína recombinante de ensamblaje de lipopolisacáridos - D (LptD) de Bartonella bacilliformis / Cloning, expression and seroreactivity of the recombinant lipopolysaccharide assembly protein - D (LptD) from Bartonella bacilliformis

RESUMEN Objetivo. Evaluar in silico y a nivel serológico el potencial antigénico del dominio extracelular recombinante de la proteína de ensamblaje de lipopolisacáridos - D (LptD) de Bartonella bacilliformis (dexr_LptD). Materiales y métodos. Mediante el análisis in silico se realizó la selección de una proteína de B. bacilliformis con potencial antigénico e inmunogénico. El gen de la proteína seleccionada se clonó en Escherichia coli TOP10 y se expresó en Escherichia coli BL21 (DE3) pLysS. La proteína recombinante fue expresada usando isopropil-β-D-1-tiogalactopiranósido (IPTG) y se optimizaron las condiciones de inducción. Por último, se purificó con resina Ni-IDA (His60 Ni Superflow) y se realizó un ensayo de Western Blot. Resultados. In silico, la proteína seleccionada fue LptD por estar localizada en la membrana externa y ser antigénica e inmunogénica. Las condiciones optimizadas para la inducción del dexr_LptD fueron 0,5 mM IPTG, 16 h, medio TB (Terrific Broth), etanol al 3% (v/v), 28 ºC, OD600: 1-1,5 y 200 r.p.m. La purificación se realizó en condiciones denaturantes a pequeña escala y se obtuvo 2,6 µg/mL de dexr_LptD parcialmente purificada. El ensayo de Western Blot mostró una reacción positiva entre los sueros provenientes de pacientes con la enfermedad de Carrión y dexr_LptD, ello evidencia la antigenicidad del dexr_LptD. Conclusiones. El dexr_LptD muestra antigenicidad in silico y a nivel serológico, estos resultados son base para posteriores estudios sobre candidatos vacunales contra la enfermedad de Carrión.

ABSTRACT Objective. To evaluate in silico and at the serological level the antigenic potential of the recombinant extracellular domain of the lipopolysaccharide assembly protein - D (LptD) of Bartonella bacilliformis (dexr_LptD). Materials and Methods. Through in silico analysis, we selected a B. bacilliformis protein with antigenic and immunogenic potential. The selected protein gene was cloned into Escherichia coli TOP10 and expressed in Escherichia coli BL21 (DE3) pLysS. Recombinant protein was expressed using isopropyl-β-D-1-thiogalactopyranoside (IPTG) and induction conditions were optimized. Finally, it was purified with Ni-IDA resin (His60 Ni Superflow) and a Western Blot assay was conducted. Results. In silico, the selected protein was LptD because it is located in the outer membrane and is antigenic and immunogenic. Optimized conditions for dexr_LptD induction were 0.5 mM IPTG, 16 hours, TB (Terrific Broth) medium, 3% (v/v) ethanol, 28 ºC, OD600: 1-1.5 and 200 rpm. Purification was carried out under denaturating conditions on a small scale and we obtained 2.6 μg/mL of partially purified dexr_LptD. The Western Blot assay showed a positive reaction between the sera from patients with Carrión's Disease and dexr_LptD, which shows the antigenicity of dexr_LptD. Conclusions. The dexr_LptD shows antigenicity both in silico and at the serological level, these results are the basis for further studies on vaccine candidates against Carrion's Disease.

Application of CRISPR-Cas9 to interrogate novel gene functions in cutaneous melanoma

Melanoma accounts for 3% of skin neoplasms and is the leading cause of death from skin disorders worldwide. The high mortality rate associated with this disease stems from the high capacity of melanoma patients to develop metastases and treatment relapse with inhibitors of the MAPK signaling pathway (such as BRAF inhibitors), commonly used in melanoma therapy. Thus, the investigation of genes involved in the mechanisms of melanoma development is essential for new and more effective therapeutic strategies. Hence, we describe in this thesis two projects involving the genes SIN3B and IRF4 as possible biomarkers for cutaneous melanoma. Initially, through bioinformatics analyses performed by our group, an upregulation of SIN3B was found in metastatic melanomas. This result together with the understanding of SIN3B role in regulating gene expression and oncogenic transformation, prompted us to describe in this thesis some mechanisms by which SIN3B may influence melanoma development. We then sought to characterize the gene function using SIN3B-deleted cells, generated by the CRISPR-Cas9 methodology. Initially, we observed increased SIN3B expression in BRAF-mutant metastatic melanomas, where we noted that the long splicing variant of the gene (NM_001297595.1) was effectively prevalent in melanomas. Subsequently, we designed gRNAs between the exons 2 and 3 of the human SIN3B gene and engineered three knockout clones and three control clones (containing empty lentiCRISPRv2 plasmid) from different melanoma cell lines (SKMEL28, A2058, and A375). Through functional analyses, it was observed that the absence of the gene did not interfere in the proliferation of tumor cells; however, it led to a decrease in invasive properties. These results were verified by Boyden chamber assays and transcriptome analysis (total RNA sequencing of deleted cells), where a decrease in migration and motility pathways was observed. Additionally, a screening of synthetically lethal genes with SIN3B was performed with a genome wide CRISPR library. These results showed that USP7 and STK11 genes, which belong to the FoxO signaling pathway, were essential in SIN3B-depleted melanoma cells. Finally, through a collaborative project with the Wellcome Trust Sanger Institute, previous large-scale sequencing analyses demonstrated that deletion of the IRF4 gene was lethal for melanoma cells. Accordingly, we performed IRF4 silencing in vitro and noticed that the lack of IRF4 promotes cell death and apoptosis, independently of MYC and MITF, known in the literature to be downstream targets of this gene. Therefore, these data suggest that IRF4 plays a vital role in melanoma cell survival. Taken together, both works herein described in this thesis demonstrate how CRISPR-Cas9 can be applied to study the functions and mechanisms of genes involved in melanoma progression, collectively helping in the development of more effective therapeutic strategies for this tumor

O melanoma representa 3% dos tipos de neoplasias cutâneas e é a maior causa das mortes por distúrbios de pele no mundo. A alta taxa de mortalidade associada à essa doença advém da alta capacidade de pacientes com melanoma desenvolverem metástases, e apresentarem recidiva após tratamento com inibidores da via de sinalização MAPK (como da proteína BRAF), comumente utilizados no tratamento de pacientes metastáticos. Assim, a investigação de genes envolvidos nos mecanismos de desenvolvimento do melanoma é primordial para novas estratégias terapêuticas mais efetivas. Dessa forma, descrevemos no presente trabalho dois projetos envolvendo os genes SIN3B e IRF4 como possíveis biomarcadores para melanoma cutâneo. Em análises prévias de bioinformática realizados pelo nosso grupo, SIN3B foi identificado tendo maior expressão em melanomas metastáticos. Além disso, diversos estudos mostraram que o gene está envolvido na regulação da expressão gênica e transformação oncogênica. Dessa forma, descrevemos nessa tese alguns mecanismos pelos quais SIN3B pode influenciar no desenvolvimento do melanoma, através da caracterização funcional de células SIN3B-deletadas pela metodologia CRISPR-Cas9. Inicialmente, observamos aumento na expressão de SIN3B em melanomas metastáticos BRAF-mutados, onde notamos que a variante de splicing longa do gene (NM_001297595.1), era efetivamente prevalente em melanomas. Assim, desenhamos sequências de RNA guias entre os éxons 2 e 3 do gene SIN3B humano e, obtivemos três clones knockout e outros três clones controle (contendo plasmídeo vazio) em diferentes linhagens de melanoma (SKMEL28, A2058 e A375), para caracterização funcional. Observou-se que a ausência do gene não interferiu na proliferação das células tumorais, contudo, acarretou na diminuição de processos invasivos. Esses resultados foram averiguados através de ensaios em câmara de Boyden e análises de transcriptoma (sequenciamento de RNA total das células deletadas), onde notou-se diminuição das vias de migração e motilidade. Adicionalmente, um rastreamento de genes sinteticamente letais com SIN3B foi realizado com uma biblioteca de CRISPR capaz de silenciar todo o genoma. Esses resultados mostraram que os genes USP7 e STK11, ambos pertencentes à via de sinalização de FoxO, são essenciais nas células SIN3B deletadas. Por fim, através de um projeto colaborativo com o Wellcome Trust Sanger Institute, análises prévias de sequenciamento de larga escala demonstraram que a deleção do gene IRF4 era letal para células de melanoma. Dessa forma, realizamos o silenciamento de IRF4 in vitro e notamos que a ausência do gene promove morte celular e apoptose, independentemente de MYC e MITF, conhecidos na literatura por serem alvos downstream do gene. Portanto, esses dados sugerem que IRF4 tem um papel importante na sobrevivência de células de melanoma. Em conjunto, ambos trabalhos descritos nessa tese, demonstram como a metodologia CRISPR-Cas9 pode auxiliar no entendimento de processos importantes para a malignidade do melanoma e contribuir para estratégias terapêuticas mais efetivas para esse tumor

sideRETRO: uma ferramenta de bioinformática dedicada à identificação deinserções polimórficas, germinativas ou somáticas, de pseudogenes processados / sideRETRO: a bioinformatics tool for identifying somatic and polymorphic insertions of processed pseudogenes

Os avanços metodológicos e instrumentais decorrentes do Projeto Genoma Humano formaram o arcabouço necessário para o surgimento das tecnologias de sequenciamento de DNA de Nova Geração, as quais se caracterizam por um custo reduzido, uma baixa demanda operacional e a produção de um grande volume de dados por experimento. Concomitantemente a isso, o aumento no poder de processamento computacional permitiu o desenvolvimento de análises genéticas em larga escala, de modo que, atualmente, é possível estudar características genômicas individualizadas e, até então, pouco ou nunca exploradas. Dentre essas características, aquelas relacionadas às variações estruturais em genomas têm recebido bastante atenção. Os pseudogenes processados, ou retrocópias, são variações estruturais causadas pela duplicação de genes codificadores mediante à transposição de seu RNA mensageiro maduro pela maquinaria enzimática de LINE- 1. As retrocópias podem estar fixadas, ou seja, presentes em todos os genomas de uma dada espécie, os quais são representados pela montagem modelo do genoma de referência, ou podem não estar fixadas, sendo polimórficas, germinativas ou somáticas. No entanto, o conhecimento acerca das retrocópias não fixadas ainda é limitado devido à falta de ferramentas de bioinformática dedicadas a sua identificação e anotação em dados de sequenciamento de DNA. Posto isso, este trabalho apresenta o sideRETRO um programa computacional especializado na detecção de pseudogenes processados ausentes do genoma de referência, mas presentes em dados de sequenciamento de genoma completo e exoma de outros indivíduos. Além de apontar para a presença de retrocópias não fixadas, o sideRETRO é capaz de anotar várias outras características relacionadas a esses evento, tais como: a coordenada genômica de inserção do pseudogene processado, a qual constitui o cromossomo, o ponto de inserção e a fita de DNA (líder or retardada); o contexto genômico do evento (exônico, intrônico ou intergênico); a genotipagem (presente ou ausente) e a haplotipagem (em homozigose ou heterozigose). Para atestar a eficiência da ferramenta, o sideRETRO foi executado para dados simulados e para dados reais validados experimentalmente por um grupo independente. Portanto, em resumo, nesta tese são descritos o desenvolvimento e o uso do sideRETRO uma ferramenta computacional robusta e eficiente, designada para identificar e anotar pseudogenes processados não fixados. Por fim, vale destacar que o sideRETRO preenche uma lacuna metodológica e possibilita novas hipóteses e investigações sistemáticas no campo de chamada de variantes estruturais

The methodological and instrumental advances resulting from the Human Genome Project have created the necessary framework to the emergence of Next Generation DNA sequencing technologies, which are characterized by a reduced cost, low operational demand and the generation of a large volume of data per experiment. Concomitantly with this, the increase in computational processing power has driven the development of large-scale genetic analyses, which allowed us to study individualized genomic traits little or never explored before. Among these characteristics, those related to structural variations in genomes have received much attention. Processed pseudogenes, or retrocopies, are structural variations caused by the duplication of coding genes through the transposition of their mature messenger RNA by the LINE-1 enzymatic machinery. Retrocopies can be fixed (i.e., present in all genomes of a given species and included into the assembly of the reference genome) or unfixed, being polymorphic, germinal or somatic. However, knowledge about unfixed retrocopies is still limited due to the lack of bioinformatics tools dedicated to their identification and annotation in DNA sequencing data. Therefore, this work presents sideRETRO a computer program specialized in the detection of processed pseudogenes absent from the reference genome, but present in whole genome and exome sequencing data from other individuals. In addition to pointing out the presence of unfixed retrocopies, sideRETRO is able to annotate several other characteristics related to these events, such as: the genomic coordinate of the processed pseudogene insetion, which constitutes the chromosome, the insertion point and the DNA strand (leader or retard); the genomic context of the event (exonic, intronic or intergenic); genotyping (present or absent) and haplotyping (homozygous or heterozygous). To certify the sideRETRO efficiency, it was run on simulated data and on real data experimentally validated by an independent group. Therefore, in summary, this thesis describes the development and use of sideRETRO a robust and efficient computational tool, designed to identify and annotate unfixed processed pseudogenes. Finally, it is worth noting that sideRETRO fills a methodological gap and allows new hypotheses and systematic investigations in the field of structural variant calling

Bioinformatics analysis of differently expressed genes in osteoblastic sarcoma and screening of key genes / 中华肿瘤杂志

Objective: To screen the different expressed genes between osteosarcoma and normal osteoblasts, and find the key genes for the occurrence and development of osteosarcoma. Methods: The gene expression dataset GSE33382 of normal osteoblasts and osteosarcoma was obtained from Gene Expression Omnibus (GEO) database. The different expressed genes between normal osteoblasts and osteosarcoma were screened by limma package of R language, and the different expressed genes were analyzed by Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analysis. The protein interaction network was constructed by the String database, and the network modules in the interaction network were screened by the molecular complex detection (MCODE) plug-in of Cytoscape software. The different expressed genes contained in the first three main modules screened by MCODE were analyzed by gene ontology (GO) using the BiNGO module of Cytoscape software. The MCC algorithm was used to screen the top 10 key genes in the protein interaction network. The gene expression and survival dataset GSE39055 of osteosarcoma was obtained from GEO database, and the survival analysis was performed by Kaplan-Meier method. The data of 48 patients with osteosarcoma treated in the First Affiliated Hospital of Fujian Medical University from January 2005 to December 2015 were selected for verification. The expression of STC2 protein in osteosarcoma was detected by immunohistochemical method, and the survival analysis was carried out combined with the clinical data of the patients. Results: A total of 874 different expressed genes were identified from GSE33382 dataset, including 402 down-regulated genes and 472 up-regulated genes. KEGG enrichment analysis showed that different expressed genes were mainly related to p53 signal pathway, glutathione metabolism, extracellular matrix receptor interaction, cell adhesion molecules, folate tolerance, and cell senescence. The top 10 key genes in the interaction network were GAS6, IL6, RCN1, MXRA8, STC2, EVA1A, PNPLA2, CYR61, SPARCL1 and FSTL3. STC2 was related to the survival rate of patients with osteosarcoma (P<0.05). The results showed that the expression of STC2 protein was related to tumor size and Enneking stage in 48 cases of osteosarcoma. The median survival time of 25 cases with STC2 high expression was 21.4 months, and that of 23 cases with STC2 low expression was 65.4 months. The survival rate of patients with high expression of STC2 was lower than that of patients with low expression of STC2 (P<0.05). Conclusions: Bioinformatics analysis can effectively screen the different expressed genes between osteosarcoma and normal osteoblasts. STC2 is one of the important predictors for the prognosis of osteosarcoma.

Bioinformatics-based identification of key genes CDC5L and related pathways in osteosarcoma and Ewing's sarcoma / 中国骨伤

OBJECTIVE@#Osteosarcoma(OS) and Ewing's sarcoma (EWS) are the two most common primary malignant bone tumors in children. The aim of the study was to identify key genes in OS and EWS and investigate their potential pathways.@*METHODS@#Expression profiling (GSE16088 and GSE45544) were obtained from GEO DataSets. Differentially expressed genes were identified using GEO2R and key genes involved in the occurrence of both OS and EWS were selected using venn diagram. Gene ontology and pathway enrichment analyses were performed for the ensembl. Protein-protein interaction (PPI) networks were established by STRING. Further, UCSC was used to predict the transcription factors of the cell division cycke 5-like(CDC5L) gene, and GEPIA was used to analyze the correlation between the transcription factors and the CDC5L gene.@*RESULTS@#The results showed that CDC5L gene was the key gene involved in the pathogenesis of OS and EWS. The gene is mainly involved in mitosis, and is related to RNA metabolism, processing of capped intron-containing pre-mRNA, mRNA and pre-mRNA splicing.@*CONCLUSION@#CDC5L, as a key gene, plays a role in development of OS and EWS, which may be reliable targets for diagnosis and treatment of these primary malignant tumors.

Bioinformatics and expression analysis on MYB-related family in Angelica dahurica var. formosana / 中国中药杂志

In recent years, the MYB-related gene family has been found pivotal in plant growth and development. MYB-related gene family in Angelica dahurica var. formosana was systematically investigated based on "Chuanzhi No. 2" through transcriptome database search and bioinformatics and the temporal and spatial expression patterns were analyzed through real-time fluorescence-based quantitative polymerase chain reaction(PCR). The results showed that 122 MYB-related proteins family were identified, mainly including the unstable hydrophilic proteins with good thermal stability. Most of the proteins were located in nuclei. The majority of the proteins had the structures of random coil and α-helix. Five MYB-related proteins family of A. dahurica var. formosana had membrane-binding domains. The conserved domain analysis of MYB-related proteins family of A. dahurica var. formosana showed that the MYB domains of genes in five subgroups, similar to 2 R-, 3 R-, and 4 R-MYB proteins, contained three evenly distributed Trp(W) residues in the MYB repeat sequence. The phylogenetic analysis of MYB-related proteins family in A. dahurica var. formosana and Arabidopsis thaliana showed that the MYB-related members were unevenly distributed in five subgroups, and A. thaliana and A. dahurica var. formosana had almost the same number of genes in the CCA1-like subgroup. There were differences in the number, type, and distribution of motifs contained in 122 encoded proteins. Transcription factors with similar branches had similar domains and motifs. The expression pattern analysis showed that the transcription factors AdMYB53, AdMYB83, and AdMYB89 responded to hormones to varying degrees, and they were highly expressed in leaves and responded quickly in roots. This study lays a foundation for further investigating the function of MYB-related transcription factors of A. dahurica var. formosana and solving the corresponding biological problems such as bolting early.

Screening of differentially expressed genes for colorectal cancer and prediction of potential traditional Chinese medicine: based on bioinformatics / 中国中药杂志

This study screened and analyzed the differentially expressed genes(DEGs) between colorectal cancer(CRC) tissues and normal tissues with bioinformatics techniques to predict biomarkers and Chinese medicinals for the diagnosis and treatment of CRC. The microarray data sets GSE21815, GSE106582, and GSE41657 were downloaded from the Gene Expression Omnibus(GEO), and the DEGs were screened by GEO2 R, followed by the Gene Ontology(GO) tern enrichment and Kyoto Encyclopedia of Genes and Genomes(KEGG) pathway enrichment analysis of the DEGs based on DAVID. The protein-protein interaction network was constructed by STRING, and MCODE and Cytohubba plug-ins were used to screen the significant modules and hub genes in the network. UCSC, cBioPortal, and Oncomine were employed for hierarchical clustering, survival analysis, Oncomine analysis, and correlation analysis of clinical data. Coremine Medical was applied to predict the Chinese medicinals acting on hub genes. A total of 284 DEGs were screened out, with 146 up-regulated and 138 down-regulated. The up-regulated genes were mainly involved in cell cycle, NLRs pathway, and TNF signaling pathway, and the down-regulated genes were related to mineral absorption, nitrogen metabolism, and bicarbonate reabsorption in proximal tubules. The 15 hub genes were CDK1, CDC20, AURKA, MELK, TOP2 A, PTTG1, BUB1, CDCA5, CDC45, TPX2, NEK2, CEP55, CENPN, TRIP13, and GINS2, among which CDK1 and CDC20 were regarded as core genes. The high expression of CDK1 and CDC20 suggested poor prognosis, and they significantly expressed in many cancers, especially breast cancer, lung cancer, and CRC. The expression of CDK1 and CDC20 was correlated with gender, tumor type, TNM stage, and KRAS gene mutation. The potential effective medicinals against CRC were Scutellariae Radix, Scutellariae Barbatae Herba, Arnebiae Radix, etc. The significant expression of CDK1 and CDC20 can help distinguish tumor tissues from normal tissues, and is related to survival prognosis. Thus, the two can be used as biomarkers for the diagnosis and treatment of CRC. This study provides a reference for related drug development.

Análisis clínico, molecular y bioinformático de paciente con enfermedad de Cori-Forbes en el Suroccidente Colombiano / Clinical, molecular and bioinformatic analysis a patient with Cori-Forbes disease in the Southwest of Colombia

Introducción: La enfermedad por almacenamiento del glucógeno tipo III (GSDIII, Glycogen storage disease type III) o Enfermedad de Cori Forbes es un trastorno del proceso de glucogenólisis ocasionado por variantes del gen AGL que codifica la enzima desramificante del glucógeno; se encuentra ubicado en el cromosoma 1p21.2 y su alteración genera una degradación incompleta del glucógeno, llevando a una acumulación de dextrina límite en órganos blanco, ocasionando organomegalia y disfunción. Objetivo: Caracterizar molecularmente un paciente lactante mayor con diagnóstico clínico y bioquímico sospechoso de GSDIII. Materiales y Métodos: Paciente lactante mayor masculino con antecedente de displasia broncopulmonar, infección respiratoria aguda, reflujo gastroesofágico, hepatomegalia e intolerancia a la lactosa. Se realizó estudio molecular mediante secuenciación de exoma completo; las variantes reportadas fueron evaluadas por Software de predicción como: Mutation Tas-ter, PROVEAN, UMD-Predictor, POLYPHEN, SIFT, Human Splicing Finder. Finalmente, se realizó una red de interacción génica mediante el programa GeneMania para determinar asociaciones génicas cercanas. Resultados: Se identifi caron 3 variantes heterocigotas ubicadas en el gen AGL: p.Arg910* que ocasiona pérdida del dominio amilo-1,6 glucosidasa y el dominio de unión al glucógeno, y las variantes p.Trp373Cys, p.Asn565Ser que generan cambios missense en la proteína. El análisis de significancia clínica por medio de métodos in-sílico determinó una clasificación patogénica para todas las variantes. La red de interacción permitió observar asociaciones entre el gen AGL y los genes FOXA2, PPP1R3B, NHLRC1 y GCK, que tienen relación con procesos metabólicos. Conclusión: una sospecha clínica inicial, a través de una buena historia clínica y la pertinencia de estudios bioquímicos-metabólicos-genómicos dirigidos, permite brindar un correcto diagnóstico, tratamiento y seguimiento, acercándonos a la medicina de precisión.

Introduction: Glycogen storage disease type III (GSDIII) or Cori Forbes disease is a disorder of the glycogeno-lysis process caused by variants of the AGL gene that encodes the glycogen debranching enzyme; It is located on chromosome 1p21.2 and its alteration generate an incomplete degradation of glycogen, leading to an accumu-lation of borderline dextrin in target organs, causing organomegaly and dysfunction. Objective: To characterize at the molecular level an elderly male lactating patient from southwestern Colombia with a clinical, biochemical diagnosis suspected of GSDIII. Materials and methods: An elderly male infant with a history of bronchopul-monary dysplasia, acute respiratory infection, gastroesophageal refl ux, hepatomegaly, and lactose intolerance. A molecular study was performed by whole exome sequencing; the reported variants were evaluated by prediction software such as Mutation Taster, PROVEAN, UMD-Predictor, POLYPHEN, SIFT, Human Splicing Finder. Fi-nally, a gene interaction network was performed using the GeneMania program to determine close gene associa-tions. Results: 3 heterozygous variants located in the AGL gene were identifi ed: p.Arg910 * that causes loss of the amyl-1,6 glucosidase domain and the glycogen-binding domain, and the variants p.Trp373Cys, p.Asn565 in the protein. The analysis of clinical signifi cance by means of in-silico methods determined a pathogenic classifi cation for all the variants. The interaction network will observe associations between the AGL gene and the FOXA2, PPP1R3B, NHLRC1 and GCK genes, which are related to metabolic processes. Conclusion: an initial clinical suspicion, through a good clinical history and the relevance of directed biochemical-metabolic-genomic studies, allows us to provide a correct diagnosis, treatment, and follow-up, bringing us closer to precision medicine

Mechanisms of Compound Kushen Injection for the treatment of bladder cancer based on bioinformatics and network pharmacology with experimental validation / 中国天然药物

Bladder cancer is the most common malignancy of the urinary system. Compound Kushen Injection (CKI) is a Chinese medicinal preparation that has been widely used in the treatment of various types of cancers in the past two decades. However, the pharmacological effect of CKI on bladder cancer is not still completely understood. In the current study, network pharmacology combined with bioinformatics was used to elucidate the therapeutic mechanism and potential targets of CKI in bladder cancer. The mechanism by which CKI was effective against bladder cancer was further verified in vitro using human bladder cancer cell line T24. Network pharmacology analysis identified 35 active compounds and 268 target genes of CKI. Bioinformatics data indicated 5500 differentially expressed genes associated with bladder cancer. Common genes of CKI and bladder cancer suggested that CKI exerted anti-bladder cancer effects by regulating genes such as MMP-9, JUN, EGFR, and ERK1. Functional enrichment analysis indicated that CKI exerted therapeutic effects on bladder cancer by regulating certain biological processes, including cell proliferation, cell migration, and cell apoptosis. In addition, Kyoto Encyclopedia of Genes and Genomes enrichment analysis implicated pathways related to cancer, bladder cancer, and the PI3K-Akt signaling pathway. Consistently, cell experiments indicated that CKI inhibited the proliferation and migration of T24 cells, and induced their apoptosis. Moreover, RT-qPCR and Western blot results demonstrated that CKI was likely to treat bladder cancer by down-regulating the gene and protein expression of MMP-9, JUN, EGFR, and ERK1. CKI inhibited the proliferation and migration, and induced the apoptosis of T24 bladder cancer cells through multiple biological pathways and targets. CKI also exhibited significant effects on the regulation of key genes and proteins associated with bladder cancer. Overall, our findings provide solid evidence and deepen current understanding of the therapeutic effects of CKI for bladder cancer, and further support its clinical use.

Construction of endogenous RNA regulatory network for colorectal cancer based on bioinformatics / 中南大学学报(医学版)

OBJECTIVES@#The high morbidity and mortality of colorectal cancer (CRC) have posed great threats to human health. Circular RNA (circRNA) and microRNA (miRNA), acting as competing endogenous RNAs (ceRNAs), have been found to play vital roles in carcinogenesis. This paper aims to construct a circRNA/miRNA/mRNA regulatory network so as to explore the molecular mechanism of CRC.@*METHODS@#The sequencing data of circRNA from CRC were obtained from Gene Expression Omnibus (GEO). The differential circRNA was screened and its structure was identified by Cancer-specific CircRNA Database (CSCD); the sequencing data of miRNA and messenger RNA (mRNAs) were downloaded from The Cancer Genome Atlas (TCGA) database and the differentially expressed genes were screened; the corresponding miRNA of differential circRNAs were predicted by CircInteractome database; DIANA, Miranda, PicTar, and TargetScan databases were used to predict the target genes of different miRNAs; the target genes from Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were enriched by R language; String database combined with Cytoscape 3.7.2 software was used to construct protein-protein interaction (PPI) network and hub genes were screened; the expressions of mRNAs in the Top10 hub genes were verified in CRC. The network diagrams of circRNAs/miRNAs/mRNAs and circRNAs/miRNAs/Top10 hub mRNAs were constructed by Cytoscape3.7.2. Real-time PCR was used to examine the expression levels of hsa_circRNA_0065173, hsa-mir-450b, hsa-mir-582, adenylate cyclase 5 (ADCY5), muscarinic acetylcholine receptor M2 (CHRM2), cannabinoid receptor 1 (CNR1), and lysophosphatidic acid receptor 1 (LPAR1) in the CRC tissues and the adjacent normal tissues.@*RESULTS@#A total of 14 differential circRNAs were identified, and 8 were found in CSCD; 34 miRNAs targeted by circRNAs were obtained. The PPI network was constructed, and the Top10 hub genes were identified, which were CHRM2, melanin concentrating hormone receptor 2 (MCHR2), G-protein gamma 3 subunit (GNG3), neuropeptide Y receptor Y1 (NPY1R), CNR1, LPAR1, ADCY5, adenylate cyclase 2 (ADCY2), gamma 7 (GNG7) and chemokine 12 (CXCL12), respectively. The expressions of Top 10 hub genes were also verified, and the results showed that the Top 10 hub genes were down-regulated in CRC; the constructed network diagram showed that hsa_circRNA_0065173 may regulate ADCY5, CHRM2, and Hsa-mir-450b by modulating hsa-mir-450b and hsa-mir-582. CNR1 and LPAR1 genes might serve as potentially relevant targets for the treatment of CRC. Real-time PCR results showed that the expression levels of hsa_circRNA_0065173, ADCY5, CHRM2, CNR1 and LPAR1 in the CRC tissues were significantly reduced compared with the adjacent normal tissues (all P<0.05); the expression levels of hsa-mir-450b and hsa-miR-582 were significantly increased (both P<0.05).@*CONCLUSIONS@#In this study, a potential circRNAs/miRNAs/mRNAs network is successfully constructed, which provides a new insight for CRC development mechanism through ceRNA mediated by circRNAs.

Bioinformatics Analysis of Microarray Data in Myelodysplastic Syndrome Based on Gene Expression Omnibus Database / 中国实验血液学杂志

OBJECTIVE@#To identify the key genes and explore mechanisms in the development of myelodysplastic syndrome (MDS) by bioinformatics analysis.@*METHODS@#Two cohorts profile datasets of MDS were downloaded from Gene Expression Omnibus (GEO) database. Differentially expressed gene (DEG) was screened by GEO2R, functional annotation of DEG was gained from GO database, gene ontology (GO) enrichment analysis was performed via Kyoto Encyclopedia of Genes and Genomes (KEGG) database, and key genes were screened by Matthews correlation coefficient (MCC) based on STRING database.@*RESULTS@#There were 112 DEGs identified, including 85 up-regulated genes and 27 down-regulated genes. GO enrichment analysis showed that biological processes were mainly enriched in immune response, etc, cellular component in cell membrane, etc, and molecular function in protein binding, etc. KEGG signaling pathway analysis showed that main gene enrichment pathways were primary immunodeficiency, hematopoietic cell lineage, B cell receptor signaling pathway, Hippo signaling pathway, and asthma. Three significant modules were screened by Cytoscape software MCODE plug-in, while 10 key node genes (CD19, CD79A, CD79B, EBF1, VPREB1, IRF4, BLNK, RAG1, POU2AF1, IRF8) in protein-protein interaction (PPI) network were screened based on STRING database.@*CONCLUSION@#These screened key genes and signaling pathways are helpful to better understand molecular mechanism of MDS, and provide theoretical basis for clinical targeted therapy.

Bioinformatics Analysis of Core Genes and Key Pathways in Myelodysplastic Syndrome / 中国实验血液学杂志

OBJECTIVE@#To screen differentially expressed gene (DEG) related to myelodysplastic syndrome (MDS) based on Gene Expression Omnibus (GEO) database, and explore the core genes and pathogenesis of MDS by analyzing the biological functions and related signaling pathways of DEG.@*METHODS@#The expression profiles of GSE4619, GSE19429, GSE58831 including MDS patients and normal controls were downloaded from GEO database. The gene expression analysis tool (GEO2R) of GEO database was used to screen DEG according to | log FC (fold change) |≥1 and P<0.01. David online database was used to annotate gene ontology function (GO). Metascape online database was used to enrich and analyze differential genes in Kyoto Encyclopedia of Genes and Genomes (KEGG). The protein-protein interaction network (PPI) was constructed by using STRING database. CytoHubba and Mcode plug-ins of Cytoscape were used to analyze the key gene clusters and hub genes. R language was used to diagnose hub genes and draw the ROC curve. GSEA enrichment analysis was performed on GSE19429 according to the expression of LEF1.@*RESULTS@#A total of 74 co-DEG were identified, including 14 up-regulated genes and 60 down regulated genes. GO enrichment analysis indicated that BP of down regulated genes was mainly enriched in the transcription and regulation of RNA polymerase II promoter, negative regulation of cell proliferation, and immune response. CC of down regulated genes was mainly enriched in the nucleus, transcription factor complexes, and adhesion spots. MF was mainly enriched in protein binding, DNA binding, and β-catenin binding. KEGG pathway was enriched in primary immunodeficiency, Hippo signaling pathway, cAMP signaling pathway, transcriptional mis-regulation in cancer and hematopoietic cell lineage. BP of up-regulated genes was mainly enriched in type I interferon signaling pathway and viral response. CC was mainly enriched in cytoplasm. MF was mainly enriched in RNA binding. Ten hub genes and three important gene clusters were screened by STRING database and Cytoscape software. The functions of the three key gene clusters were closely related to immune regulation. ROC analysis showed that the hub genes had a good diagnostic significance for MDS. GSEA analysis indicated that LEF1 may affect the normal function of hematopoietic stem cells by regulating inflammatory reaction, which further revealed the pathogenesis of MDS.@*CONCLUSION@#Bioinformatics can effectively screen the core genes and key signaling pathways of MDS, which provides a new strategy for the diagnosis and treatment of MDS.

Bioinformatics analysis of nasal epithelial cell gene expression in seasonal and perennial allergic rhinitis / 中华耳鼻咽喉头颈外科杂志

Objective: Transcriptome sequencing and bioinformatics analysis were performed on the gene expression of nasal epithelial cells in patients with seasonal allergic rhinitis (AR) and perennial AR, so as to obtain the differences in the gene expression of nasal epithelial cells between seasonal AR and perennial AR. Methods: The human nasal epithelial cell line(HNEpC) was cultured in vitro, treated with 100 μg/ml mugwort or house dust mite (HDM) extracts for 24 hours. Total cell RNA was extracted, and quantitative real-time polymerase chain reaction (qPCR) was used to detect the expression of cytokines, including IL-6, IL-8, IL-33 and thymic stromal lymphopoietin (TSLP). From November 2019 to November 2020, 3 seasonal AR patients, 3 perennial AR patients, and 3 healthy controls who attended the Department of Otolaryngology Head and Neck Surgery, China-Japan Union Hospital of Jilin University were analyzed. The patients' primary nasal epithelial cells were cultured in vitro, treated with corresponding allergens for 24 hours. Total RNA was extracted for transcriptome sequencing, and the sequencing results were analyzed by bioinformatics. Results: The qPCR results showed that the cytokines IL-6, IL-8, IL-33 and TSLP of HNEpC treated with mugworts extracts and HDM extracts had the same trend of change. After the nasal epithelial cells from patients with seasonal AR and perennial AR were treated with corresponding allergens, there were differences in biological processes and signal pathways between those and control. Gene ontology (GO) enrichment analysis showed that the differentially expressed genes (DEG) in AR patients allergic to mugwort were mainly enriched in the oxidation-reduction process, the negative regulation of apoptosis process, and the cell adhesion; the DEG in AR patients allergic to HDM were mainly enriched in cell adhesion, the negative regulation of cell proliferation and the response to drug. Enrichment analysis of Kyoto Encyclopedia of Genes and Genomes (KEGG) signaling pathway showed that the DEG of AR patients allergic to mugwort were significantly enriched in arachidonic acid metabolism, p53 signaling pathway and transforming growth factor β (TGF-β) signaling pathway, while the DEG of AR patients allergic to HDM were mainly enriched in cells cycle, Fanconi anemia pathway and DNA replication. Gene Set Enrichment Analysis (GSEA) showed that the inflammatory response, TNF-α/NF-κB signaling pathway and IL-2/STAT5 signaling pathway were significantly up-regulated in AR patients allergic to mugwort, indicating the promotion of inflammatory response; and AR patients allergic to HDM had significant down-regulation of G2M, E2F, and MYC, indicating the inhibition of cell proliferation. The protein-protein interaction network showed that TNF and CDK1 were the most interacting proteins in mugwort and HDM allergic AR patients, respectively. Conclusion: Seasonal AR and perennial AR may affect the different biological processes and signal pathways of nasal epithelial cells, leading to differences in the occurrence and development of AR.

Bioinformatics screening and analysis of key differentially expressed genes characteristics in nonalcoholic fatty liver disease / 中华肝脏病杂志

Objective: To screen and analyze the key differentially expressed genes characteristics in nonalcoholic fatty liver disease (NAFLD) with bioinformatics method. Methods: NAFLD-related expression matrix GSE89632 was downloaded from the GEO database. Limma package was used to screen differentially expressed genes (DEGs) in healthy, steatosis (SS), and nonalcoholic steatohepatitis (NASH) samples. WGCNA was used to analyze the output gene module. The intersection of module genes and differential genes was used to determine the differential genes characteristic, and then GO function and KEGG signaling pathway enrichment analysis were performed. The protein-protein interaction network (PPI) was constructed using the online website STRING and Cytoscape software, and the key (Hub) genes were screened. Finally, R software was used to analyze the receiver operating characteristic curve (ROC) of the Hub gene. Results: 92 differentially expressed genes characteristic were obtained through screening, which were mainly enriched in inflammatory response-related functions of "lipopolysaccharide response and molecular response of bacterial origin", as well as cancer signaling pathways of "proteoglycan in cancer" and "T-cell leukemia virus infection-related". 10 hub genes (FOS, CXCL8, SERPINE1, CYR61, THBS1, FOSL1, CCL2, MYC, SOCS3 and ATF3) had good diagnostic value. Conclusion: The differentially expressed hub genes among the 10 NAFLD disease-related characteristics obtained with bioinformatics analysis may become a diagnostic and prognostic marker and potential therapeutic target for NAFLD. However, further basic and clinical studies are needed to validate.

Next-generation diagnostic pathology / 中华病理学杂志

With the technological progresses and applications of human genome sequencing, bioinformatics analysis and data mining, and molecular pathology and artificial intelligence-assisted pathological diagnosis, the development of clinical medicine is moving towards the era of precision diagnosis and treatment. In the context of this era, the traditional diagnostic pathology is facing unprecedented opportunities and challenges in our history and is striving towards the "next-generation diagnostic pathology" (NGDP). NGDP is based on histomorphology and clinical data, and characterized by the combination of molecular detection and bioinformatics analysis, intelligent sampling and process quality control, intelligent diagnosis and remote consultation, lesion visualization and "non-invasive" pathology as well as other innovative cutting edge interdisciplinary technologies. The NGDP reports will include the results from multi-omics and cross-scale integrated diagnosis for final diagnosis. NGDP will also be applied for predicting disease progression and outcomes, and determining optional therapeutics as well as assessing treatment responses, so that a novel "golden standard" of disease diagnosis can be established. In the near fature, it is necessary to stimulate the innovative vitality of pathology disciplines, accelerate the maturity and application for NGDP, update the theory and technical system of pathology, and perform its important applicable role in the prevention, diagnosis, treatment of diseases so that the futher development of clinical medicine will be promoted and the strategy for maintenance of being healthy in China will be served.

Bioinformatics Analysis on Key Genes and Immune Infiltration of Osteosarcoma / 中国医学科学院学报

Objective To screen the potential key genes of osteosarcoma by bioinformatics methods and analyze their immune infiltration patterns. Methods The gene expression profiles GSE16088 and GSE12865 associated with osteosarcoma were obtained from the Gene Expression Omnibus(GEO),and the differentially expressed genes(DEGs)related to osteosarcoma were screened by bioinformatics tools.Gene Ontology(GO)annotation,Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway enrichment,and analysis of immune cell infiltration were then carried out for the DEGs.The potential Hub genes of osteosarcoma were identified by protein-protein interaction network,and the expression of Hub genes in osteosarcoma and normal tissue samples was verified via the Cancer Genome Atlas(TCGA). Results A total of 108 DEGs were screened out.GO annotation and KEGG pathway enrichment revealed that the DEGs were mainly involved in integrin binding,extracellular matrix (ECM) structural components,ECM receptor interactions,and phosphatidylinositol 3-kinase/protein kinase B(PI3K/Akt)signaling pathway.Macrophages were the predominant infiltrating immune cells in osteosarcoma.Secreted phosphoprotein 1(SPP1),matrix metallopeptidase 2(MMP2),lysyl oxidase(LOX),collagen type V alpha(II)chain(COL5A2),and melanoma cell adhesion molecule(MCAM)presented differential expression between osteosarcoma and normal tissue samples(all P<0.05). Conclusions SPP1,MMP2,LOX,COL5A2,and MCAM are all up-regulated in osteosarcoma,which may serve as potential biomarkers of osteosarcoma.Macrophages are the key infiltrating immune cells in osteosarcoma,which may provide new perspectives for the treatment of osteosarcoma.

Avances de la bioinformática en Costa Rica: vista retrospectiva y perspectivas / Bioinformatics advances in Costa Rica: retrospective view and perspectives

Resumen Introducción: La disciplina científica de la bioinformática tiene el potencial de generar aplicaciones innovadoras para las sociedades humanas. Costa Rica, pequeña en tamaño y población en comparación con otros países de América Latina, ha ido adoptando la disciplina de manera progresiva. El reconocer los avances permite determinar hacia dónde puede dirigirse el país en este campo, así como su contribución a la región latinoamericana. Objetivo: En este manuscrito se reporta evidencia de la evolución de la bioinformática en Costa Rica, para identificar debilidades y fortalezas que permitan definir acciones a futuro. Métodos: Se realizaron búsquedas en bases de datos de publicaciones científicas y repositorios de secuencias, así como información de actividades de capacitación, redes, infraestructura, páginas web y fuentes de financiamiento. Resultados: Se observan avances importantes desde el 2010, incluyendo un aumento en oportunidades de entrenamiento y número de publicaciones, aportes significativos a las bases de datos de secuencias y conexiones por medio de redes. Sin embargo, ciertas áreas, como la masa crítica y la financiación requieren más desarrollo. La comunidad científica y sus patrocinadores deben promover la investigación basada en bioinformática, invertir en la formación de estudiantes de posgrado, aumentar la formación de profesionales, crear oportunidades laborales para carreras en bioinformática y promover colaboraciones internacionales a través de redes. Conclusiones: Se sugiere que para experimentar los beneficios de las aplicaciones de la bioinformática se deben fortalecer tres aspectos clave: la comunidad científica, la infraestructura de investigación y las oportunidades de financiamiento. El impacto de tal inversión sería el desarrollo de proyectos ambiciosos pero factibles y colaboraciones extendidas dentro de la región latinoamericana. Esto permitiría realizar contribuciones significativas para abordar los desafíos globales y la aplicación de nuevos enfoques de investigación, innovación y transferencia de conocimiento para el desarrollo de la economía, dentro de un marco de ética de la investigación.

Abstract Introduction: The scientific discipline of bioinformatics has the potential to generate innovative applications for human societies. Costa Rica, small in size and population compared to other Latin American countries, has been progressively adopting the discipline. Recognizing progress makes it possible to determine where the country can go in this field, as well as its contribution to the Latin American region. Objective: This manuscript reports evidence of the evolution of bioinformatics in Costa Rica, to identify weaknesses and strengths allowing future actions plans. Methods: We searched databases of scientific publications and sequence repositories, as well as information on training activities, networks, infrastructure, web pages and funding sources. Results: Important advances have been observed since 2010, such as increases in training opportunities and the number of publications, significant contributions to the sequence databases and connections through networks. However, areas such as critical mass and financing require further development. The scientific community and its sponsors should promote bioinformatics-based research, invest in graduate student training, increase professional training, create career opportunities in bioinformatics, and promote international collaborations through networks. Conclusions: It is suggested that in order to experience the benefits of bioinformatics applications, three key aspects must be strengthened: the scientific community, the research infrastructure, and funding opportunities. The impact of such investment would be the development of ambitious but feasible projects and extended collaborations within the Latin American region and abroad. This would allow significant contributions to address global challenges and the implementation of new approaches to research, innovation and knowledge transfer for the development of the economy, within an ethics of research framework.