Tumor immune microenvironment and immunotherapy
Guest Editors: Zlatko Trajanoski and Noel de Miranda
Genome Medicine is pleased to present a special issue on ‘Tumor immune microenvironment and immunotherapy’, guest edited by Zlatko Trajanoski of Medical University of Innsbruck and Noel de Miranda of Leiden University Medical Center. Cancer treatment has been revolutionized by recent unraveling and targeting of the interaction between tumors and the host immune system. This special issue captures recent insights using genomic approaches toward characterizing the immune system in the tumor microenvironment, immunotherapeutic targeting, as well as functional – and dysfunctional – anti-tumor immune responses, highlighting the clinical applications of these advances.This collection of articles has not been sponsored and articles have undergone the journal’s standard peer-review process. The Guest Editors declare that they have no competing interests. Guest Editors serve an advisory role to guide the scope of the special issue and commissioned content; final editorial decisions lie with the Editor.
Burden of tumor mutations, neoepitopes, and other variants are weak predictors of cancer immunotherapy response and overall survival
Tumor mutational burden (TMB; the quantity of aberrant nucleotide sequences a given tumor may harbor) has been associated with response to immune checkpoint inhibitor therapy and is gaining broad acceptance as...Genome Medicine 2020 12:33Single-cell transcriptome analysis reveals TOX as a promoting factor for T cell exhaustion and a predictor for anti-PD-1 responses in human cancer
T cells exhibit heterogeneous functional states in the tumor microenvironment. Immune checkpoint inhibitors (ICIs) can reinvigorate only the stem cell-like progenitor exhausted T cells, which suggests that inh...Genome Medicine 2020 12:22Large-scale public data reuse to model immunotherapy response and resistance
Despite growing numbers of immune checkpoint blockade (ICB) trials with available omics data, it remains challenging to evaluate the robustness of ICB response and immune evasion mechanisms comprehensively. To...Genome Medicine 2020 12:21Neoantigen-specific immunity in low mutation burden colorectal cancers of the consensus molecular subtype 4
The efficacy of checkpoint blockade immunotherapies in colorectal cancer is currently restricted to a minority of patients diagnosed with mismatch repair-deficient tumors having high mutation burden. However, ...Genome Medicine 2019 11:87Immune receptor repertoires in pediatric and adult acute myeloid leukemia
Acute myeloid leukemia (AML), caused by the abnormal proliferation of immature myeloid cells in the blood or bone marrow, is one of the most common hematologic malignancies. Currently, the interactions between...Genome Medicine 2019 11:73pTuneos: prioritizing tumor neoantigens from next-generation sequencing data
Cancer neoantigens are expressed only in cancer cells and presented on the tumor cell surface in complex with major histocompatibility complex (MHC) class I proteins for recognition by cytotoxic T cells. Accur...Genome Medicine 2019 11:67Best practices for bioinformatic characterization of neoantigens for clinical utility
Neoantigens are newly formed peptides created from somatic mutations that are capable of inducing tumor-specific T cell recognition. Recently, researchers and clinicians have leveraged next generation sequenci...Genome Medicine 2019 11:56- Genome Medicine 2019 11:51
The good, the bad, and the ugly: hyperprogression in cancer patients following immune checkpoint therapy
Immune checkpoint blockade therapy can elicit robust and durable responses in a variety of cancer types. While many patients do not respond, recent reports highlight a distinct group of patients whose tumors u...Genome Medicine 2019 11:43Evolving neoantigen profiles in colorectal cancers with DNA repair defects
Neoantigens that arise as a consequence of tumor-specific mutations can be recognized by T lymphocytes leading to effective immune surveillance. In colorectal cancer (CRC) and other tumor types, a high number ...Genome Medicine 2019 11:42Radiation therapy and anti-tumor immunity: exposing immunogenic mutations to the immune system
The expression of antigens that are recognized by self-reactive T cells is essential for immune-mediated tumor rejection by immune checkpoint blockade (ICB) therapy. Growing evidence suggests that mutation-ass...Genome Medicine 2019 11:40Mechanisms of immune-related adverse events associated with immune checkpoint blockade: using germline genetics to develop a personalized approach
Personalized care of cancer patients undergoing treatment with immune checkpoint inhibitors will require approaches that can predict their susceptibility to immune-related adverse events. Understanding the rol...Genome Medicine 2019 11:39Molecular and pharmacological modulators of the tumor immune contexture revealed by deconvolution of RNA-seq data
We introduce quanTIseq, a method to quantify the fractions of ten immune cell types from bulk RNA-sequencing data. quanTIseq was extensively validated in blood and tumor samples using simulated, flow cytometry...Genome Medicine 2019 11:34The Correction to this article has been published in Genome Medicine 2019 11:50Discovery and characterization of actionable tumor antigens
The nature of the tumor antigens that are detectable by T cells remains unclear. In melanoma, T cells were shown to react against major histocompatibility complex (MHC)-associated peptides (MAPs) that are deri...Genome Medicine 2019 11:29The Research to this article has been published in Genome Medicine 2019 11:28Multi-omics discovery of exome-derived neoantigens in hepatocellular carcinoma
Although mutated HLA ligands are considered ideal cancer-specific immunotherapy targets, evidence for their presentation is lacking in hepatocellular carcinomas (HCCs). Employing a unique multi-omics approach ...Genome Medicine 2019 11:28The Comment to this article has been published in Genome Medicine 2019 11:29
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