Applications of systems biology in cancer immunotherapy: from target discovery to biomarkers of clinical outcome

Figures & data

Figure 1. Biospecimens, molecules and omics platforms that can be used in the context of cancer immunotherapy studies.

Each platform can have a multitude of applications, some of which are described in the text.

Adapted with modifications from [39].

Figure 2. A conceptual integrated framework for the discovery of antigens from omics studies in cancer patients, database mining and algorithmic predictions of immunogenicity.

A number of platforms can be applied to study both tumor and peripheral samples. Since the omics platforms can have a high false discovery rate, integration of data across orthogonal platforms can enable rapid discovery of antigens that have a higher probability of validation in subsequent preclinical testing.

Figure 3. Examples of omics platforms being used to assess post-treatment therapeutic responses against the tumor, such as the extent of lymphocyte infiltration, tumor destruction and epitope spread against ‘secondary’ antigens (or epitopes).

mRNA profiling may be used to assess the extent of tumor infiltration of lymphocytes. Protein or peptide microarrays can be used to assess the diversity of antibody (B cell) responses and next-generation sequencing (T-cell receptor sequencing) can be used to assess the diversity of T cell clones. Specific examples are provided in the text.

Chaussabel D, Pascual V, Banchereau J. Assessing the human immune system through blood transcriptomics. BMC Biol. 8, 84 (2010).

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