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A multilevel pan-cancer map links gene mutations to cancer hallmarks.

ABSTRACT: A central challenge in cancer research is to create models that bridge the gap between the molecular level on which interventions can be designed and the cellular and tissue levels on which the disease phenotypes are manifested. This study was undertaken to construct such a model from functional annotations and explore its use when integrated with large-scale cancer genomics data.We created a map that connects genes to cancer hallmarks via signaling pathways. We projected gene mutation and focal copy number data from various cancer types onto this map. We performed statistical analyses to uncover mutually exclusive and co-occurring oncogenic aberrations within this topology.Our analysis showed that although the genetic fingerprint of tumor types could be very different, there were less variations at the level of hallmarks, consistent with the idea that different genetic alterations have similar functional outcomes. Additionally, we showed how the multilevel map could help to clarify the role of infrequently mutated genes, and we demonstrated that mutually exclusive gene mutations were more prevalent in pathways, whereas many co-occurring gene mutations were associated with hallmark characteristics.Overlaying this map with gene mutation and focal copy number data from various cancer types makes it possible to investigate the similarities and differences between tumor samples systematically at the levels of not only genes but also pathways and hallmarks.

SUBMITTER: Knijnenburg TA

PROVIDER: S-EPMC4593384 | biostudies-literature | 2015 Sep

REPOSITORIES: biostudies-literature

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A multilevel pan-cancer map links gene mutations to cancer hallmarks.

Knijnenburg Theo A TA Bismeijer Tycho T Wessels Lodewyk F A LF Shmulevich Ilya I

Chinese journal of cancer 20150914 10

<h4>Background</h4>A central challenge in cancer research is to create models that bridge the gap between the molecular level on which interventions can be designed and the cellular and tissue levels on which the disease phenotypes are manifested. This study was undertaken to construct such a model from functional annotations and explore its use when integrated with large-scale cancer genomics data.<h4>Methods</h4>We created a map that connects genes to cancer hallmarks via signaling pathways. W ...[more]

PMID: 26369414

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Project description:Heat shock proteins play crucial roles in various biochemical processes, encompassing protein folding and translocation. HSP90B1, a conserved member of the heat shock protein family, growing evidences have demonstrated that it might be closely associated with cancer development. In the present study, we employed multi-omics analyses and cohort validations to explore the dynamic expression of HSP90B1 in pan-cancer and comprehensively evaluate HSP90B1 as a novel biomarker that hold promise for precision cancer diagnostics and therapeutics. The results suggest HSP90B1 was highly expressed in various kinds of tumors, often correlating with a poor prognosis. Notably, methylation of HSP90B1 emerged as a protective factor in several cancer types. In immune infiltration analysis, the expression of HSP90B1 in most tumors showed a negative association with CD8 + T cells. HSP90B1 expression was positively correlated with microsatellite instability and tumor mutational burden. HSP90B1 expression was also discovered to be positively correlated with tumor metabolism, cell cycle-related pathways and the expression of immune checkpoint genes. The expression of HSP90B1 was mainly negatively correlated with immunostimulatory genes and positively correlated with immunosuppressive genes, as well as strongly correlated with chemokines and their receptor genes. In addition, the HSP90B1 inhibitor PU-WS13 demonstrated significant efficacy in suppressing cancer cell proliferation in both leukemic and solid tumor cells, and remarkably reduced the expression of the cancer cell surface immune checkpoint PD-L1. The single-cell RNA sequencing analysis further highlighted that HSP90B1 was significantly higher in tumor cells compared to surrounding cells, revealing a potential target therapeutic window. Taken together, HSP90B1 emerges as a promising avenue for breakthroughs in cancer diagnosis, prognosis and therapy. This study provides a rationale for HSP90B1 targeted cancer diagnosis and therapy in future.

Dataset Information

A multilevel pan-cancer map links gene mutations to cancer hallmarks.

Publications

A multilevel pan-cancer map links gene mutations to cancer hallmarks.

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