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1.
Eur J Cancer ; 149: 193-210, 2021 05.
Artigo em Inglês | MEDLINE | ID: mdl-33866228

RESUMO

The rising interest for precise characterization of the tumour immune contexture has recently brought forward the high potential of RNA sequencing (RNA-seq) in identifying molecular mechanisms engaged in the response to immunotherapy. In this review, we provide an overview of the major principles of single-cell and conventional (bulk) RNA-seq applied to onco-immunology. We describe standard preprocessing and statistical analyses of data obtained from such techniques and highlight some computational challenges relative to the sequencing of individual cells. We notably provide examples of gene expression analyses such as differential expression analysis, dimensionality reduction, clustering and enrichment analysis. Additionally, we used public data sets to exemplify how deconvolution algorithms can identify and quantify multiple immune subpopulations from either bulk or single-cell RNA-seq. We give examples of machine and deep learning models used to predict patient outcomes and treatment effect from high-dimensional data. Finally, we balance the strengths and weaknesses of single-cell and bulk RNA-seq regarding their applications in the clinic.


Assuntos
Biomarcadores Tumorais/genética , Perfilação da Expressão Gênica , Neoplasias/genética , Neoplasias/imunologia , RNA Neoplásico/genética , RNA-Seq , Análise de Célula Única , Transcriptoma , Microambiente Tumoral/imunologia , Inteligência Artificial , Tomada de Decisão Clínica , Humanos , Neoplasias/tratamento farmacológico , Neoplasias/patologia , Medicina de Precisão , Valor Preditivo dos Testes , Prognóstico
2.
Immunity ; 52(6): 910-941, 2020 06 16.
Artigo em Inglês | MEDLINE | ID: mdl-32505227

RESUMO

The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has affected millions of people worldwide, igniting an unprecedented effort from the scientific community to understand the biological underpinning of COVID19 pathophysiology. In this Review, we summarize the current state of knowledge of innate and adaptive immune responses elicited by SARS-CoV-2 infection and the immunological pathways that likely contribute to disease severity and death. We also discuss the rationale and clinical outcome of current therapeutic strategies as well as prospective clinical trials to prevent or treat SARS-CoV-2 infection.


Assuntos
Betacoronavirus/fisiologia , Infecções por Coronavirus/imunologia , Pneumonia Viral/imunologia , Animais , COVID-19 , Infecções por Coronavirus/diagnóstico , Infecções por Coronavirus/patologia , Infecções por Coronavirus/terapia , Suscetibilidade a Doenças , Humanos , Imunidade Inata , Memória Imunológica , Inflamação/imunologia , Inflamação/virologia , Linfócitos/imunologia , Células Mieloides/imunologia , Pandemias , Pneumonia Viral/diagnóstico , Pneumonia Viral/patologia , Pneumonia Viral/terapia , SARS-CoV-2
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