RESUMO

Therapeutic cancer vaccines have been considered in recent decades as important immunotherapeutic strategies capable of leading to tumor regression. In the development of these vaccines, the identification of neoepitopes plays a critical role, and different computational methods have been proposed and employed to direct and accelerate this process. In this context, this review identified and systematically analyzed the most recent studies published in the literature on the computational prediction of epitopes for the development of therapeutic vaccines, outlining critical steps, along with the associated program's strengths and limitations. A scoping review was conducted following the PRISMA extension (PRISMA-ScR). Searches were performed in databases (Scopus, PubMed, Web of Science, Science Direct) using the keywords: neoepitope, epitope, vaccine, prediction, algorithm, cancer, and tumor. Forty-nine articles published from 2012 to 2024 were synthesized and analyzed. Most of the identified studies focus on the prediction of epitopes with an affinity for MHC I molecules in solid tumors, such as lung carcinoma. Predicting epitopes with class II MHC affinity has been relatively underexplored. Besides neoepitope prediction from high-throughput sequencing data, additional steps were identified, such as the prioritization of neoepitopes and validation. Mutect2 is the most used tool for variant calling, while NetMHCpan is favored for neoepitope prediction. Artificial/convolutional neural networks are the preferred methods for neoepitope prediction. For prioritizing immunogenic epitopes, the random forest algorithm is the most used for classification. The performance values related to the computational models for the prediction and prioritization of neoepitopes are high; however, a large part of the studies still use microbiome databases for training. The in vitro/in vivo validations of the predicted neoepitopes were verified in 55% of the analyzed studies. Clinical trials that led to successful tumor remission were identified, highlighting that this immunotherapeutic approach can benefit these patients. Integrating high-throughput sequencing, sophisticated bioinformatics tools, and rigorous validation methods through in vitro/in vivo assays as well as clinical trials, the tumor neoepitope-based vaccine approach holds promise for developing personalized therapeutic vaccines that target specific tumor cancers.

RESUMO

BACKGROUND: Postmenopausal osteoporosis is a multifactorial disease. Genetic factors play an essential role in contributing to bone mineral density (BMD) variability, which ranges from 60 to 85%. Alendronate is used as the first line of pharmacological treatment for osteoporosis; however, some patients do not respond adequately to therapy with alendronate. AIM: The aim of this work was to investigate the influence of combinations of potential risk alleles (genetic profiles) associated with response to anti-osteoporotic treatment in postmenopausal women with primary osteoporosis. METHODS: A total of 82 postmenopausal women with primary osteoporosis receiving alendronate (70 mg administered orally per week) for one year were observed. The bone mineral density (BMD; g/cm2) of the femoral neck and lumbar spine was measured. According to BMD change, patients were divided into two groups: responders and non-responders to alendronate therapy. Polymorphic variants in CYP19, ESR1, IL-6, PTHR1, TGFß, OPG and RANKL genes were determined and profiles were generated from the combination of risk alleles. RESULTS: A total of 56 subjects were responders to alendronate and 26 subjects were non-responders. Carriers of the G-C-G-C profile (constructed from rs700518, rs1800795, rs2073618 and rs3102735) were predisposed to response to alendronate treatment (p = 0.001). CONCLUSIONS: Our findings highlight the importance of the identified profiles for the pharmacogenetics of alendronate therapy in osteoporosis.

Assuntos

Conservadores da Densidade Óssea , Osteoporose , Humanos , Feminino , Alendronato/uso terapêutico , Conservadores da Densidade Óssea/efeitos adversos , Estudos Retrospectivos , Pós-Menopausa/genética , Osteoporose/tratamento farmacológico , Vértebras Lombares

RESUMO

The Barretos Cancer Hospital Animal Facility (BCHAF) is a unique facility in Brazil exclusively dedicated to working with animal models for cancer research. In this article, we briefly present our modern facility and the main experiments performed, focusing on mutant strains of mice (PTCH-knockout and ApcMin mice), xenograft models, and patient-derived xenografts (PDXs). Our results show the progress and challenges in establishing these models and the need for having an appropriate representation of our cancer population to better understand tumor biology and to identify cancer biomarkers, which could be putatively targeted, allowing for personalized therapy.

RESUMO

BACKGROUND: Colorectal cancer is one of the most frequent neoplasms worldwide, and the majority of patients are diagnosed in advanced stages. Metastatic colorectal cancer (mCRC) harbors several mutations with different prognostic and predictive values; KRAS, NRAS, and BRAF mutations are the best known. Indeed, RAS and BRAF molecular status are associated with a different response to monoclonal antibodies (Anti-epidermal growth factor receptor and anti-vascular endothelial growth factor receptor agents), which are usually added to chemotherapy in first-line, and thus allow to select the optimal therapy for patients with mCRC. Furthermore, sidedness is an important predictive and prognostic factor in mCRC, which is explained by the different molecular profile of left and right-sided tumors. Recently, microsatellite instability-high has emerged as a predictive factor of response and survival from immune checkpoint inhibitors in mCRC. Finally, several other alterations have been described in lower frequencies, such as human epidermal growth factor receptor-2 overexpression/amplification, PIK3CA pathway alterations, phosphatase and tension homolog loss, and hepatocyte growth factor/mesenchymal-epithelial transition factor pathway dysregulation, with several targeted therapies already demonstrating activity or being tested in currently ongoing clinical trials. AIM: To review the importance of studying the predictive and prognostic roles of the molecular profile of mCRC, the changes occurred in recent years and how they would potentially change in the near future, to guide physicians in treatment decisions. RELEVANCE FOR PATIENTS: Today, several different therapeutic options can be offered to patients in the first-line setting of mCRC. Therapies at present approved or under investigation in clinical trials will be thoroughly reviewed, with special emphasis on the molecular rationale behind them. Understanding the molecular status, resistance mechanisms and potential new druggable targets may allow physicians to choose the best therapeutic option in the first-line mCRC.

RESUMO

Alzheimer's disease (AD) is a chronic brain disorder characterized by progressive intellectual decline and memory and neuronal loss, caused mainly by extracellular deposition of amyloid-ß (Aß) and intracellular accumulation of hyperphosphorylated tau protein, primarily in areas implicated in memory and learning as prefrontal cortex and hippocampus. There are two forms of AD, a late-onset form that affects people over 65 years old, and the early-onset form, which is hereditable and affect people at early ages ~45 years. To date, there is no cure for the disease; consequently, it is essential to develop new tools for the study of processes implicated in the disease. Currently, in vitro AD three-dimensional (3D) models using induced pluripotent stem cells (iPSC)-derived neurons have broadened the horizon for in vitro disease modeling and gained interest for mechanistic studies and preclinical drug discovery due to their potential advantages in providing a better physiologically relevant information and more predictive data for in vivo tests. Therefore, this study aimed to establish a 3D cell culture model of AD in vitro using iPSCs carrying the A246E mutation. We generated human iPSCs from fibroblasts from a patient with AD harboring the A246E mutation in the PSEN1 gene. Cell reprogramming was performed using lentiviral vectors with Yamanaka's factors (OSKM: Oct4, Sox2, Klf4, and c-Myc). The resulting iPSCs expressed pluripotency genes (such as Nanog and Oct4), alkaline phosphatase activity, and pluripotency stem cell marker expression, such as OCT4, SOX2, TRA-1-60, and SSEA4. iPSCs exhibited the ability to differentiate into neuronal lineage in a 3D environment through dual SMAD inhibition as confirmed by Nestin, MAP2, and Tuj1 neural marker expression. These iPSC-derived neurons harbored Aß oligomers confirmed by Western Blot (WB) and immunostaining. With human iPSC-derived neurons able to produce Aß oligomers, we established a novel human hydrogel-based 3D cell culture model that recapitulates Aß aggregation without the need for mutation induction or synthetic Aß exposure. This model will allow the study of processes implicated in disease spread throughout the brain, the screening of molecules or compounds with therapeutic potential, and the development of personalized therapeutic strategies.

RESUMO

INTRODUCTION: Recently, new oncology therapies were developed using a biomarker for patient selection. In the era of cancer genomics, this paradigm is expected to increase. Most cytotoxic chemotherapies and other oncological treatments were historically approved without a biomarker. However, this strategy seems to be less efficient. We reviewed the biomarker-based strategy and its impact in cancer drug development. AREAS COVERED: Oncology drugs approval rates are low and most of the drugs that failed to be approved were in late stages of development. In addition to that, attrition rates are high. The use of biomarkers in drug development has shown higher response rates, longer progression-free survival rates and even higher overall survival rates. Hence, the biomarker-based strategy seems to be associated with more successful drug programs, including a shorter timeline and higher likelihood of success. EXPERT OPINION: Even though the development of biomarker-driven strategies is promising, there are some challenges surrounding this field of study, such as reducing the cost of drug development, enhancing the technique of biomarkers identification (aiming more specific biomarkers and considering tumor heterogeneity) and exploring the role of next-generation sequencing tests in drug development. Also, collaboration between clinicians, scientists and regulatory agencies is fundamental.

Assuntos

Antineoplásicos/uso terapêutico , Biomarcadores Tumorais , Desenvolvimento de Medicamentos/métodos , Terapia de Alvo Molecular , Neoplasias/tratamento farmacológico , Medicina de Precisão/métodos , Antineoplásicos/economia , Antineoplásicos/farmacologia , Inteligência Artificial , Biomarcadores Tumorais/análise , Biomarcadores Tumorais/antagonistas & inibidores , Biomarcadores Tumorais/genética , Ensaios Clínicos como Assunto/métodos , Análise Mutacional de DNA , Aprovação de Drogas , Desenvolvimento de Medicamentos/tendências , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Inibidores de Checkpoint Imunológico/uso terapêutico , Colaboração Intersetorial , Metanálise como Assunto , Técnicas de Diagnóstico Molecular , Terapia de Alvo Molecular/economia , Terapia de Alvo Molecular/métodos , Neoplasias/química , Neoplasias/genética , Seleção de Pacientes , Fatores de Tempo , Estados Unidos , United States Food and Drug Administration

RESUMO

Cancer is the second-leading cause of death in the world, accounting for one out of six deaths. Consequently, there is an urgent need for new and more effective therapeutic options as well as drug screening methods. Immortal, "stable" cancer cell lines have been employed since the past century to assess drug response but face several disadvantages. They often accumulate new genetic aberrations due to long-term culture and lack the indisputable heterogeneity of solid tumors, therefore, compromising the recapitulation of molecular features from parental tumors. Primary cancer cells have emerged as an attractive alternative to commercial cell lines since they can preserve such properties more closely. Here, we provide an overview of the basic concepts underlying generation and characterization of primary cell cultures from tumor samples. We emphasize the advantages and disadvantages of using these types of cancer cell cultures, and we make a comparison with other types of cultures used for personalized therapy. Finally, we consider the use of primary cancer cell cultures in personalized therapy as a means to improve drug response prediction and therapeutic outcomes.

Assuntos

Técnicas de Cultura de Células , Neoplasias/terapia , Medicina de Precisão/métodos , Humanos , Neoplasias/patologia , Células Tumorais Cultivadas

RESUMO

ABSTRACT Cancer is the second-leading cause of death in the world, accounting for one out of six deaths. Consequently, there is an urgent need for new and more effective therapeutic options as well as drug screening methods. Immortal, “stable” cancer cell lines have been employed since the past century to assess drug response but face several disadvantages. They often accumulate new genetic aberrations due to long-term culture and lack the indisputable heterogeneity of solid tumors, therefore, compromising the recapitulation of molecular features from parental tumors. Primary cancer cells have emerged as an attractive alternative to commercial cell lines since they can preserve such properties more closely. Here, we provide an overview of the basic concepts underlying generation and characterization of primary cell cultures from tumor samples. We emphasize the advantages and disadvantages of using these types of cancer cell cultures, and we make a comparison with other types of cultures used for personalized therapy. Finally, we consider the use of primary cancer cell cultures in personalized therapy as a means to improve drug response prediction and therapeutic outcomes.

Assuntos

Humanos , Técnicas de Cultura de Células , Medicina de Precisão/métodos , Neoplasias/terapia , Células Tumorais Cultivadas , Neoplasias/patologia

RESUMO

Cancer is a complex group of diseases where different signaling pathways have been found to be deregulated, mainly related to cell proliferation, angiogenesis, metastasis, evasion of apoptosis and insensitivity to anti-growth sings among others. Diet plays a fundamental role in the treatment of the oncological patients, we must be aware that food can interact with certain types of cancer therapy. On the other hand, cancer therapies sometimes affect the patient's sense of smell, taste, appetite, gastric capacity or nutrient absorption, which often results in malnutrition due to the lack of essential nutriments. In this chapter we will review the effect of different metabolic disorders in cancer and mechanisms of action of some phytochemicals found in different foods like resveratrol, EGCG, curcumin and lycopene.

Assuntos

Neoplasias , Fenômenos Fisiológicos da Nutrição , Medicina de Precisão , Apoptose , Proliferação de Células , Humanos , Neoplasias/fisiopatologia , Neoplasias/terapia , Compostos Fitoquímicos/metabolismo , Medicina de Precisão/tendências

RESUMO

OBJECTIVE: To review the state-of-the-art in relation to the current information on squamous cell lung cancer (SCLC). We describe the genetic anomalies reported, their effect, and finally the most promising therapeutic agents. MATERIALS AND METHODS: We reviewed published articles in peer-reviewed journals as well as current treatment guidelines from local and international resources. RESULTS: SCLC represents a smaller proportion of the global burden of disease for lung cancer compared to its more frequent presentation, the adenocarcinoma. However, more than 400 000 cases are reported annually, a substantial population for whom therapeutic options are scarce and with limited efficacy. Several groups have been given the task of elucidating the mechanisms that lead to the development of SCLC, including molecular anomalies that can be used as targets for drug design. CONCLUSIONS: There are potential therapeutic targets for SCLC, which must be studied in clinical trials for validation.

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OBJETIVO: Revisar el estado del arte en relación con la información actual sobre el cáncer de pulmón de células escamosas (CPCE) y describir las anomalías genéticas reportadas, su efecto y los agentes terapéuticos más prometedores. MATERIAL Y MÉTODOS: Se realizó una revisión de artículos publicados en revistas indizadas, así como las guías de tratamiento publicadas por instancias locales e internacionales. RESULTADOS: El CPCE representa una proporción menor de la carga mundial de la enfermedad por cáncer pulmonar en comparación con su presentación más frecuente, el adenocarcinoma. Sin embargo, más de 400 000 casos son reportados anualmente, una población sustancial para quienes las opciones terapéuticas son escasas y con una eficacia limitada. Diversos grupos se han dado a la tarea de elucidar los mecanismos que conllevan al desarrollo del CPCE, incluyendo anomalías moleculares que puedan servir como blancos para el diseño de fármacos. CONCLUSIONES: Existen blancos terapéuticos potenciales para el CPCE que deben ser estudiados en ensayos clínicos para ser validados.

Assuntos

Carcinoma de Células Escamosas/genética , Carcinoma de Células Escamosas/terapia , Neoplasias Pulmonares/genética , Neoplasias Pulmonares/terapia , Medicina de Precisão , Genômica , Humanos

RESUMO

Boron neutron capture therapy (BNCT) is a targeted therapy, which consists of preferential accumulation of boron carriers in tumor followed by neutron irradiation. Each oral cancer patient has different risks of developing one or more carcinomas and/or oral mucositis induced after treatment. Our group proposed the hamster oral cancer model to study the efficacy of BNCT and associated mucositis. Translational studies are essential to the advancement of novel boron delivery agents and targeted strategies. Herein, we review our work in the hamster model in which we studied BNCT induced mucositis using three different cancerization protocols, mimicking three different clinical scenarios. The BNCT-induced mucositis increases with the aggressiveness of the carcinogenesis protocol employed, suggesting that the study of different oral cancer patient scenarios would help to develop personalized therapies.

Assuntos

Terapia por Captura de Nêutron de Boro/efeitos adversos , Neoplasias Bucais/radioterapia , Mucosite/diagnóstico , Neoplasias Experimentais/radioterapia , Lesões por Radiação/diagnóstico , 9,10-Dimetil-1,2-benzantraceno/toxicidade , Animais , Terapia por Captura de Nêutron de Boro/métodos , Carcinógenos/toxicidade , Cricetinae , Relação Dose-Resposta à Radiação , Humanos , Neoplasias Bucais/induzido quimicamente , Neoplasias Bucais/complicações , Mucosite/etiologia , Mucosite/prevenção & controle , Neoplasias Experimentais/induzido quimicamente , Lesões por Radiação/etiologia , Lesões por Radiação/prevenção & controle , Dosagem Radioterapêutica , Índice de Gravidade de Doença

RESUMO

Abstract: Objective: To review the state-of-the-art in relation to the current information on squamous cell lung cancer (SCLC). We describe the genetic anomalies reported, their effect, and finally the most promising therapeutic agents. Materials and methods: We reviewed published articles in peer-reviewed journals as well as current treatment guidelines from local and international resources. Results: SCLC represents a smaller proportion of the global burden of disease for lung cancer compared to its more frequent presentation, the adenocarcinoma. However, more than 400 000 cases are reported annually, a substantial population for whom therapeutic options are scarce and with limited efficacy. Several groups have been given the task of elucidating the mechanisms that lead to the development of SCLC, including molecular anomalies that can be used as targets for drug design. Conclusion: There are potential therapeutic targets for SCLC, which must be studied in clinical trials for validation.

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Resumen: Objetivo: Revisar el estado del arte en relación con la información actual sobre el cáncer de pulmón de células escamosas (CPCE) y describir las anomalías genéticas reportadas, su efecto y los agentes terapéuticos más prometedores. Material y métodos: Se realizó una revisión de artículos publicados en revistas indizadas, así como las guías de tratamiento publicadas por instancias locales e internacionales. Resultados: El CPCE representa una proporción menor de la carga mundial de la enfermedad por cáncer pulmonar en comparación con su presentación más frecuente, el adenocarcinoma. Sin embargo, más de 400 000 casos son reportados anualmente, una población sustancial para quienes las opciones terapéuticas son escasas y con una eficacia limitada. Diversos grupos se han dado a la tarea de elucidar los mecanismos que conllevan al desarrollo del CPCE, incluyendo anomalías moleculares que puedan servir como blancos para el diseño de fármacos. Conclusiones: Existen blancos terapéuticos potenciales para el CPCE que deben ser estudiados en ensayos clínicos para ser validados.

Assuntos

Humanos , Carcinoma de Células Escamosas/genética , Carcinoma de Células Escamosas/terapia , Medicina de Precisão , Neoplasias Pulmonares/genética , Neoplasias Pulmonares/terapia , Genômica

RESUMO

BACKGROUND: Triple therapy efficacy against Helicobacter pylori is low worldwide, and thus, alternatives must be sought to improve eradication. The aim of the present study was to determine CYP2C19 genetic polymorphism effect on H pylori eradication. METHODS: A randomized, single-blinded clinical trial including 133 participants was carried out. H pylori infection was confirmed by histologic and microbiologic test. Antibiotic susceptibility to amoxicillin and clarithromycin was performed. CYP2C19 polymorphisms *1, *2, and *3 were analyzed by real-time PCR (Roche ®), and nested PCR for CYP2C19*17 polymorphisms. Participants were randomized into two groups for different H pylori therapies, one with standard omeprazole doses and another with omeprazole doses depending on CYP2C19 polymorphism. H pylori eradication was verified by stool antigen tests (Meridian ®). RESULTS: The most common CYP2C19 polymorphism was *1/*1 in 54.9% of the participants followed by *17/*17 in 21.1%. Triple therapy efficacy with standard omeprazole doses versus personalized therapy based on CYP2C19 polymorphism by ITT analysis was 84% (95% CI: 0.73-0.91) vs 92.2% (95% CI: 0.82-0.97) (P = 0. 14), respectively. The efficacy by PP analysis was 92.1% (95% CI: 0.82-0.97) vs 100% (95% CI: 0.92-0.01) (P = 0.027), respectively. CONCLUSIONS: The most frequent polymorphism was extensive PPI metabolizers (62.4%). Effectiveness of guided therapies by susceptibility test was good, yet they can be further improved by customized therapy based on CYP genotype. Therefore, high PPI (80 mg/d) doses are recommended for H pylori eradication therapies in Colombia. ClinicalTrials.gov ID: NCT03650543.

Assuntos

Antibacterianos/administração & dosagem , Citocromo P-450 CYP2C19/genética , Infecções por Helicobacter/tratamento farmacológico , Helicobacter pylori/efeitos dos fármacos , Polimorfismo Genético/genética , Amoxicilina/administração & dosagem , Claritromicina/administração & dosagem , Quimioterapia Combinada , Genótipo , Infecções por Helicobacter/microbiologia , Helicobacter pylori/genética , Humanos , Omeprazol/administração & dosagem , Medicina de Precisão

RESUMO

Gynecologic cancers are among the leading causes of death worldwide, ovarian cancer being the one with the highest mortality rate. Olaparib is a targeted therapy used in patients presenting mutations in BRCA1 and BRCA2 genes. The aim of this study was to describe BRCA1 and BRCA2 gene variants in Mexican patients with ovarian cancer. Sequencing of BRCA1 and BRCA2 genes from tumors of 50 Mexican patients with ovarian cancer was made in a retrospective, non-randomized, and exploratory study. We found genetic variants in 48 of 50 cases. A total of 76 polymorphic variants were found in BRCA1, of which 50 (66%) had not been previously reported. Furthermore, 104 polymorphic variants were found in BRCA2, of which 63 (60%) had not been reported previously. Of these polymorphisms, 5/76 (6.6%) and 4/104 (3.8%) were classified as pathogenic in BRCA1 and BRCA2, respectively. We have described the genetic variants in BRCA1 and BRCA2 of tumors from Northeast Mexican patients with sporadic ovarian cancers. Our results showed that the use of genetic testing helps recognize patients that carry pathogenic variants which could be beneficial for personalized medicine treatments.

RESUMO

Genomics must be combined with proteomics and metabolomics to rationalize a therapeutic strategy that considers gene expression, protein expression and metabolic profiles in the target organ to gain insight into other pathways implicated in the same or contributory tissues. Multidisciplinary strategies such as this provide an interactive process by which findings are translated into novel therapies.