Stromal Genes Add Prognostic Information to Proliferation and Histoclinical Markers: A Basis for the Next Generation of Breast Cancer Gene Signatures

BACKGROUND: First-generation gene signatures that identify breast cancer patients at risk of recurrence are confined to estrogen-positive cases and are driven by genes involved in the cell cycle and proliferation. Previously we induced sets of stromal genes that are prognostic for both estrogen-positive and estrogen-negative samples. Creating risk-management tools that incorporate these stromal signatures, along with existing proliferation-based signatures and established clinicopathological measures such as lymph node status and tumor size, should better identify women at greatest risk for metastasis and death. METHODOLOGY/PRINCIPAL FINDINGS: To investigate the strength and independence of the stromal and proliferation factors in estrogen-positive and estrogen-negative patients we constructed multivariate Cox proportional hazards models along with tree-based partitions of cancer cases for four breast cancer cohorts. Two sets of stromal genes, one consisting of DCN and FBLN1, and the other containing LAMA2, add substantial prognostic value to the proliferation signal and to clinical measures. For estrogen receptor-positive patients, the stromal-decorin set adds prognostic value independent of proliferation for three of the four datasets. For estrogen receptor-negative patients, the stromal-laminin set significantly adds prognostic value in two datasets, and marginally in a third. The stromal sets are most prognostic for the unselected population studies and may depend on the age distribution of the cohorts. CONCLUSION: The addition of stromal genes would measurably improve the performance of proliferation-based first-generation gene signatures, especially for older women. Incorporating indicators of the state of stromal cell types would mark a conceptual shift from epithelial-centric risk assessment to assessment based on the multiple cell types in the cancer-altered tissue

Protein interaction network of alternatively spliced isoforms from brain links genetic risk factors for autism

Increased risk for autism spectrum disorders (ASD) is attributed to hundreds of genetic loci. The convergence of ASD variants have been investigated using various approaches, including protein interactions extracted from the published literature. However, these datasets are frequently incomplete, carry biases and are limited to interactions of a single splicing isoform, which may not be expressed in the disease-relevant tissue. Here we introduce a new interactome mapping approach by experimentally identifying interactions between brain-expressed alternatively spliced variants of ASD risk factors. The Autism Spliceform Interaction Network reveals that almost half of the detected interactions and about 30% of the newly identified interacting partners represent contribution from splicing variants, emphasizing the importance of isoform networks. Isoform interactions greatly contribute to establishing direct physical connections between proteins from the de novo autism CNVs. Our findings demonstrate the critical role of spliceform networks for translating genetic knowledge into a better understanding of human diseases

Energetic control of redox-active polymers toward safe organic Bioelectronic materials

Avoiding faradaic side reactions during the operation of electrochemical devices is important to enhance the device stability, to achieve low power consumption, and to prevent the formation of reactive side‐products. This is particularly important for bioelectronic devices, which are designed to operate in biological systems. While redox‐active materials based on conducting and semiconducting polymers represent an exciting class of materials for bioelectronic devices, they are susceptible to electrochemical side‐reactions with molecular oxygen during device operation. Here, electrochemical side reactions with molecular oxygen are shown to occur during organic electrochemical transistor (OECT) operation using high‐performance, state‐of‐the‐art OECT materials. Depending on the choice of the active material, such reactions yield hydrogen peroxide (H2O2), a reactive side‐product, which may be harmful to the local biological environment and may also accelerate device degradation. A design strategy is reported for the development of redox‐active organic semiconductors based on donor–acceptor copolymers that prevents the formation of H2O2 during device operation. This study elucidates the previously overlooked side‐reactions between redox‐active conjugated polymers and molecular oxygen in electrochemical devices for bioelectronics, which is critical for the operation of electrolyte‐gated devices in application‐relevant environments