Os subtipos moleculares de câncer versus o arsenal da indústria. qual deles determina o tratamento do câncer gástrico? / The molecular cancer subtypes versus the industry arsenal. which one drives gastric cancer treatment?

ABSTRACT Molecular medicine opened new horizons in understanding disease mechanisms and discovering target interventions. The wider availability of DNA and RNA sequencing, immunohistochemical analysis, proteomics, and other molecular tests changed how physicians manage diseases. The gastric cancer molecular classification proposed by The Cancer Genome Atlas Program divides gastric adenocarcinomas into four subtypes. However, the available targets and/or immunotherapies approved for clinical use seem to be dissociated from these molecular subtypes. Until a more reliable interpretation of the stupendous amount of data provided by the molecular classifications is presented, the clinical guidelines will rely on available actionable targets and approved therapies to guide clinicians in conducting cancer management in the era of molecular therapies.

RESUMO A medicina molecular abriu novos horizontes na compreensão dos mecanismos das doenças e na descoberta de intervenções alvo. A maior disponibilidade de sequenciação de DNA e RNA, análise imuno-histoquímica, proteômica e outros testes moleculares mudou a forma como os médicos conduzem as doenças. A classificação molecular do câncer gástrico proposta pelo Atlas do Genoma do Câncer divide os adenocarcinomas gástricos em quatro subtipos. No entanto, os alvos disponíveis e/ou imunoterapias aprovadas para uso clínico parecem estar dissociados desses subtipos moleculares. Até que seja apresentada uma interpretação mais confiável da estupenda quantidade de dados fornecidos pelas classificações moleculares, as diretrizes clínicas irão se basear nos alvos acionáveis disponíveis e nas terapias aprovadas para orientar os médicos na condução da gestão do câncer na era das terapias moleculares.

Understanding COVID-19 progression with longitudinal peripheral blood mononuclear cell proteomics: Changes in the cellular proteome over time.

The clinical presentation of COVID-19 is highly variable, and understanding the underlying biological processes is crucial. This study utilized a proteomic analysis to investigate dysregulated processes in the peripheral blood mononuclear cells of patients with COVID-19 compared to healthy volunteers. Samples were collected at different stages of the disease, including hospital admission, after 7 days of hospitalization, and 30 days after discharge. Metabolic pathway alterations and increased abundance of neutrophil-related proteins were observed in patients. Patients progressing to critical illness had significantly low-abundance proteins in the pentose phosphate and glycolysis pathways compared with those presenting clinical recovery. Important biological processes, such as fatty acid concentration and glucose metabolism disorder, remained altered even after 30 days of hospital discharge. Temporal proteomic changes revealed distinct pathways in critically ill and non-critically ill patients. Our study emphasizes the significance of longitudinal cellular proteomic studies in identifying disease progression-related pathways and persistent protein changes post-hospitalization.

A Potent N-(piperidin-4-yl)-1H-pyrrole-2-carboxamide Inhibitor of Adenylyl Cyclase of G. lamblia: Biological Evaluation and Molecular Modelling Studies.

In this work, we report a derivative of N-(piperidin-4-yl)-1H-pyrrole-2-carboxamide as a new inhibitor for adenylyl cyclase of Giardia lamblia which was obtained from a study using structural data of the nucleotidyl cyclase 1 (gNC1) of this parasite. For such a study, we developed a model for this specific enzyme by using homology techniques, which is the first model reported for gNC1 of G. lamblia. Our studies show that the new inhibitor has a competitive mechanism of action against this enzyme. 2-Hydroxyestradiol was used as the reference compound for comparative studies. Results in this work are important from two points of view. on the one hand, an experimentally corroborated model for gNC1 of G. lamblia obtained by molecular modelling is presented; on the other hand, the new inhibitor obtained is an undoubtedly excellent starting structure for the development of new metabolic inhibitors for G. lamblia.

Identifying new potential genetic biomarkers for HELLP syndrome using massive parallel sequencing.

BACKGROUND: Preeclampsia (PE) is a frequently occurring multisystemic disease affecting ~5% of pregnancies. PE patients may develop HELLP syndrome (haemolysis, elevated liver enzymes, and low platelet), a mother and foetus life-threatening condition. Research into HELLP's genetic origin has been relatively unsuccessful, mainly because normal placental function and blood pressure regulation involve the fine-regulation of hundreds of genes. OBJECTIVE: To identify new genes and mutations constituting potential biomarkers for HELLP syndrome. STUDY DESIGN: The present case-control study involved whole-exome sequencing of 79 unrelated HELLP women. Candidate variants were screened in a control population constituted by 176 individuals. Stringent bioinformatics filters were used for selecting potentially etiological sequence variants in a subset of 487 genes. We used robust in silico mutation modelling for predicting the potential effect on protein structure. RESULTS: We identified numerous sequence variants in genes related to angiogenesis/coagulation/blood pressure regulation, cell differentiation/communication/adhesion, cell cycle and transcriptional gene regulation, extracellular matrix biology, lipid metabolism and immunological response. Five sequence variants generated premature stop codons in genes playing an essential role in placental physiology (STOX1, PDGFD, IGF2, MMP1 and DNAH11). Six variants (ERAP1- p.Ile915Thr, ERAP2- p.Leu837Ser, COMT-p.His192Gln, CSAD-p.Pro418Ser, CDH1- p.Ala298Thr and CCR2-p.Met249Lys) led to destabilisation of protein structure as they had significant energy and residue interaction-related changes. We identified at least two mutations in 57% of patients, arguing in favour of a polygenic origin for the HELLP syndrome. CONCLUSION: Our results provide novel evidence regarding PE/HELLP's genetic origin, leading to new biomarkers, having potential clinical usefulness, being proposed.

The Brazilian Initiative on Precision Medicine (BIPMed): fostering genomic data-sharing of underrepresented populations.

The development of precision medicine strategies requires prior knowledge of the genetic background of the target population. However, despite the availability of data from admixed Americans within large reference population databases, we cannot use these data as a surrogate for that of the Brazilian population. This lack of transferability is mainly due to differences between ancestry proportions of Brazilian and other admixed American populations. To address the issue, a coalition of research centres created the Brazilian Initiative on Precision Medicine (BIPMed). In this study, we aim to characterise two datasets obtained from 358 individuals from the BIPMed using two different platforms: whole-exome sequencing (WES) and a single nucleotide polymorphism (SNP) array. We estimated allele frequencies and variant pathogenicity values from the two datasets and compared our results using the BIPMed dataset with other public databases. Here, we show that the BIPMed WES dataset contains variants not included in dbSNP, including 6480 variants that have alternative allele frequencies (AAFs) >1%. Furthermore, after merging BIPMed WES and SNP array data, we identified 809,589 variants (47.5%) not present within the 1000 Genomes dataset. Our results demonstrate that, through the incorporation of Brazilian individuals into public genomic databases, BIPMed not only was able to provide valuable knowledge needed for the implementation of precision medicine but may also enhance our understanding of human genome variability and the relationship between genetic variation and disease predisposition.

Exploring the Molecular Aetiology of Preeclampsia by Massive Parallel Sequencing of DNA.

PURPOSE OF REVIEW: This manuscript aims to review (for the first time) studies describing NGS sequencing of preeclampsia (PE) women's DNA. RECENT FINDINGS: Describing markers for the early detection of PE is an essential task because, although associated molecular dysfunction begins early on during pregnancy, the disease's clinical signs usually appear late in pregnancy. Although several biochemical biomarkers have been proposed, their use in clinical environments is still limited, thereby encouraging research into PE's genetic origin. Hundreds of genes involved in numerous implantation- and placentation-related biological processes may be coherent candidates for PE aetiology. Next-generation sequencing (NGS) offers new technical possibilities for PE studying, as it enables large genomic regions to be analysed at affordable cost. This technique has facilitated the description of genes contributing to the molecular origin of a significant amount of monogenic and complex diseases. Regarding PE, NGS of DNA has been used in familial and isolated cases, thereby enabling new genes potentially related to the phenotype to be proposed. For a better understanding of NGS, technical aspects, applications and limitations are presented initially. Thereafter, NGS studies of DNA in familial and non-familial cases are described, including pitfalls and positive findings. The information given here should enable scientists and clinicians to analyse and design new studies permitting the identification of novel clinically useful molecular PE markers.

Genetic signature related to heme-hemoglobin metabolism pathway in sepsis secondary to pneumonia.

Sepsis is defined as a life-threatening organ dysfunction caused by a dysregulated inflammatory response to pathogens. Bioinformatics and transcriptomics studies contribute to get a better understanding of the pathogenesis of sepsis. These studies revealed differentially expressed genes (DEGs) in sepsis involved in several pathways. Here we investigated the gene expression profiles of blood leukocytes using three microarray datasets of sepsis secondary to pneumonia, focusing on the heme/hemoglobin metabolism pathway. We demonstrate that the heme/hemoglobin metabolism pathway was found to be enriched in these three cohorts with four common genes (ALAS2, AHSP, HBD, and CA1). Several studies show that these four genes are involved in the cytoprotection of non-erythrocyte cells in response to different stress conditions. The upregulation of heme/hemoglobin metabolism in sepsis might be a protective response of white cells to the hostile environment present in septic patients (follow-up samples).

Molecular alterations associated with prostate cancer.

INTRODUCTION: The amount of information and knowledge about pathways and genetic alterations regarding prostate cancer, including the tools available for its study has been recently increasing. Additionally, a variety of molecular signaling pathways control cell proliferation, however, this incompletely understood process is disturbed in cancer cells. MATERIALS AND METHODS: A literature review was made using the MEDLINE, Embase and LILACS databases searching for the following keywords: prostate neoplasms, prostate cancer, molecular medicine, genomics, pathways, and cell cycle. RESULTS: Different biological mechanisms have been associated with the development of prostate cancer, such as alterations in tumor suppressor genes, oncogenes (TP53, RB1, among others) and CDKIs; DNA methylation; chromosomal alterations and rearrangements; changes in PTEN and PI3K / mTOR; global defects in apoptosis; alterations in the androgen receptor (AR); and epigenetic mechanisms. CONCLUSIONS: Good clinical practice and a practical approach have to be based on basic knowledge, thus, in this article, the main genetic alterations, mutations and pathways involved in prostate cancer development were reviewed.

Personalized medicine and the clinical laboratory / Medicina personalizada e o laboratório clínico

Personalized medicine is the use of biomarkers, most of them molecular markers, for detection of specific genetic traits to guide various approaches for preventing and treating different conditions. The identification of several genes related to heredity, oncology and infectious diseases lead to the detection of genetic polymorphisms that are involved not only in different clinical progression of these diseases but also in variations in treatment response. Currently, it is possible to detect these polymorphisms using several methodologies: detection of single nucleotide polymorphisms using polymerase chain reaction methods; nucleic acid microarray detection; and nucleic acid sequencing with automatized DNA sequencers using Sanger-derived methods and new generation sequencing. Personalized medicine assays are directed towards detecting genetic variations that alter interactions of drugs with targets or the metabolic pathways of drugs (upstream and downstream) and can be utilized for the selection of drug formulations and detect different immunogenicities of the drug. Personalized medicine applications have already been described in different areas of Medicine and allow specific treatment approaches to be applied to each patient and pathology according to the results of these assays. The application of such a protocol demands an increasing interaction between the clinical laboratory and the clinical staff. For its implementation, a coordinated team composed of basic researchers and physicians highly specialized in their areas supported by a highly specialized team of clinical analysts particularly trained in molecular biology assays is necessary.

Medicina personalizada é o uso de biomarcadores, em sua maioria marcadores moleculares, para a detecção de traços genéticos específicos, a fim de orientar diversas abordagens para a prevenção e o tratamento de diferentes doenças. A identificação de vários genes relacionados a doenças hereditárias, oncológicas e infecciosas permite a detecção de polimorfismos genéticos que estão envolvidos em diferentes evoluções clínicas dessas doenças, bem como com variações na resposta ao tratamento. Atualmente, já é possível detectar esses polimorfismos utilizando diversas metodologias: a detecção de polimorfismos de nucleotídeo único pela reação de polimerização em cadeia; a detecção de microarranjos de ácidos nucleicos; e o sequenciamento de ácidos nucleicos com sequenciadores de DNA automatizados usando métodos derivados de sequenciamento Sanger ou de nova geração. Os ensaios de medicina personalizada são dirigidos para detectar variações genéticas que alteram interações de fármacos com alvos ou vias metabólicas de fármacos (anabólicas e catabólicas), podendo ser utilizados para a seleção de formulações farmacêuticas e para detectar diferentes imunogenicidades da droga. As aplicações de medicina personalizada já foram descritas em várias áreas da Medicina e permitem que abordagens de tratamento específicas sejam aplicadas para cada paciente e para cada doença, de acordo com os resultados dos ensaios utilizados. A aplicação de um protocolo desse tipo exige uma relação intensa entre o laboratório e o corpo clínico. Para sua execução, é necessária uma equipe coordenada, composta por investigadores de pesquisa básica e médicos altamente especializados em suas áreas, apoiada por um time bastante especializado de analistas clínicos treinados em testes de biologia molecular.

A review of bioinformatics training applied to research in molecular medicine, agriculture and biodiversity in Costa Rica and Central America.

Today, Bioinformatics has become a scientific discipline with great relevance for the Molecular Biosciences and for the Omics sciences in general. Although developed countries have progressed with large strides in Bioinformatics education and research, in other regions, such as Central America, the advances have occurred in a gradual way and with little support from the Academia, either at the undergraduate or graduate level. To address this problem, the University of Costa Rica's Medical School, a regional leader in Bioinformatics in Central America, has been conducting a series of Bioinformatics workshops, seminars and courses, leading to the creation of the region's first Bioinformatics Master's Degree. The recent creation of the Central American Bioinformatics Network (BioCANET), associated to the deployment of a supporting computational infrastructure (HPC Cluster) devoted to provide computing support for Molecular Biology in the region, is providing a foundational stone for the development of Bioinformatics in the area. Central American bioinformaticians have participated in the creation of as well as co-founded the Iberoamerican Bioinformatics Society (SOIBIO). In this article, we review the most recent activities in education and research in Bioinformatics from several regional institutions. These activities have resulted in further advances for Molecular Medicine, Agriculture and Biodiversity research in Costa Rica and the rest of the Central American countries. Finally, we provide summary information on the first Central America Bioinformatics International Congress, as well as the creation of the first Bioinformatics company (Indromics Bioinformatics), spin-off the Academy in Central America and the Caribbean.

Investigación preclínica por microPET en la UNAM / Pre-clinical research at UNAM using microPET

La tomografía por emisión de positrones (PET) es una técnica de imágenes de medicina nuclear ya establecida en México, fundamental en el diagnóstico y seguimiento clínico de enfermedades oncológicas, neurológicas y cardiológicas. Esta modalidad de imagenología molecular está basada en la administración de cantidades muy pequeñas de fármacos marcados con emisores de positrones y en la subsecuente detección de radiación con el fin de obtener imágenes tomográficas que reflejan la distribución del radiofármaco en el paciente. El desarrollo de nuevos radiofármacos para PET requiere de un método para verificar que éstos siguen las rutas metabólicas de interés, que su vida media biológica es suficiente para la realización de un estudio, que no tienen efectos adversos y que es viable para estudios en pacientes. El desarrollo de equipos de microtomografía por emisión de positrones (microPET), dedicados a estudiar animales de laboratorio, ha permitido realizar estas pruebas antes de su aplicación clínica. Además, el microPET es una herramienta de gran utilidad en la investigación preclínica de diversas enfermedades, en el desarrollo de tratamientos innovadores que permite el seguimiento no invasivo en modelos animales. En la Unidad PET/CT-Ciclotrón de la Facultad de Medicina de la UNAM, se cuenta desde hace unos años con un equipo microPET para investigación. En este trabajo se muestran algunos resultados de los estudios que se realizan con mayor frecuencia con el microPET utilizando los radiofármacos de mayor uso en el medio clínico y se muestra la utilidad que puede tener en diversos proyectos de investigación.

Positron emission tomography (PET) is a nuclear medicine imaging technique well established in Mexico, essential for the clinical diagnosis and follow-up of oncological, neurological and cardiac pathologies. This molecular imaging modality is based on the administration of small amounts of drugs labeled with a positron emitting radionuclides and the subsequent radiation detection to obtain tomographic images which reflect the distribution of the radiopharmaceutical in the patient. The development of new radiopharmaceuticals for PET requires a method to verify that they follow the expected metabolic pathways, that they have a long-enough biological half-life for imaging studies, that they have no side effects and that it is viable for use in patients. The development of positron emission microtomography (microPET) systems to be used in small laboratory animale has allowed researchers to perform these tests on radiopharmaceuticals before being used in the clinic. In addition, microPET is a useful tool in preclinical research of different diseases in the development of innovating non-invasive treatments allowing to follow up animal models. At the PET/CT-Ciclotron Unit, Facultad de Medicina, UNAM, a microPET system has been available in the last few years for research purposes. In this work, examples of frequent imaging studies performed with the microPET and in-the-clinic commonly-used radiopharmaceuticals, as well the use it may have in different research projects are shown here.

Molecular medicine: a path towards a personalized medicine / Medicina molecular: um passo em direção à medicina personalizada

Psychiatric disorders are among the most common human illnesses; still, the molecular and cellular mechanisms underlying their complex pathophysiology remain to be fully elucidated. Over the past 10 years, our group has been investigating the molecular abnormalities in major signaling pathways involved in psychiatric disorders. Recent evidences obtained by the Instituto Nacional de Ciência e Tecnologia de Medicina Molecular (National Institute of Science and Technology - Molecular Medicine, INCT-MM) and others using behavioral analysis of animal models provided valuable insights into the underlying molecular alterations responsible for many complex neuropsychiatric disorders, suggesting that "defects" in critical intracellular signaling pathways have an important role in regulating neurodevelopment, as well as in pathophysiology and treatment efficacy. Resources from the INCT have allowed us to start doing research in the field of molecular imaging. Molecular imaging is a research discipline that visualizes, characterizes, and quantifies the biologic processes taking place at cellular and molecular levels in humans and other living systems through the results of image within the reality of the physiological environment. In order to recognize targets, molecular imaging applies specific instruments (e.g., PET) that enable visualization and quantification in space and in real-time of signals from molecular imaging agents. The objective of molecular medicine is to individualize treatment and improve patient care. Thus, molecular imaging is an additional tool to achieve our ultimate goal.

Os transtornos psiquiátricos estão entre as doenças humanas mais comuns. Os mecanismos celulares e moleculares subjacentes à sua complexa fisiopatologia ainda não estão totalmente esclarecidos. Nosso grupo está envolvido na investigação de anormalidades moleculares nas principais vias de sinalização das doenças psiquiátricas nos últimos 10 anos. Evidências recentemente obtidas pelo Instituto Nacional de Ciência e Tecnologia de Medicina Molecular (INCT-MM), utilizando análise comportamental de modelos animais, forneceram informações valiosas sobre as alterações moleculares subjacentes responsáveis por muitos distúrbios neuropsiquiátricos complexos, sugerindo que os "defeitos" nas vias de sinalização intracelular têm um papel importante na regulação do neurodesenvolvimento, bem como na fisiopatologia e eficácia do tratamento. Recursos do INCT nos permitiram iniciar pesquisas na área de imagem molecular. A imagem molecular é uma disciplina de investigação que visualiza, caracteriza e quantifica processos biológicos que ocorrem em níveis celular e molecular em seres humanos, e em outros sistemas vivos, através dos resultados de imagem dentro da realidade do ambiente fisiológico. A fim de reconhecer alvos, a imagem molecular aplica instrumentos específicos (PET, por exemplo) que permitem a visualização e quantificação em espaço e tempo real dos sinais dos agentes de imagem molecular, fornecendo medições de processos a nível molecular e celular. O objetivo da medicina molecular é individualizar o tratamento e melhorar a assistência ao paciente. Desse modo, a imagem molecular consiste em mais uma ferramenta para atingirmos nosso objetivo final.