GRB10 sustains AR activity by interacting with PP2A in prostate cancer cells

Polymorphic tandem repeats influence cell type-specific gene expression across the human immune landscape

Tandem repeats (TRs) - highly polymorphic, repetitive sequences dispersed across the human genome - are crucial regulators of gene expression and diverse biological processes, but have remained underexplored relative to other classes of genetic variation due to historical challenges in their accurate calling and analysis. Here, we leverage whole genome and single-cell RNA sequencing from over 5.4 million blood-derived cells from 1,925 individuals to explore the impact of variation in over 1.7 million polymorphic TR loci on blood cell type-specific gene expression. We identify over 62,000 single-cell expression quantitative trait TR loci (sc-eTRs), 16.6% of which are specific to one of 28 distinct immune cell types. Further fine-mapping uncovers 4,283 sc-eTRs as candidate causal drivers of gene expression in 13.6% of genes tested genome-wide. We show through colocalization that TRs are likely mediators of genetic associations with immune-mediated and hematological traits in over 700 genes, and further identify novel TRs warranting investigation in rare disease cohorts. TRs are critical, yet long-overlooked, contributors to cell type-specific gene expression, with implications for understanding rare disease pathogenesis and the genetic architecture of complex traits.

GraphLoc: a graph neural network model for predicting protein subcellular localization from immunohistochemistry images

Motivation

Recognition of protein subcellular distribution patterns and identification of location biomarker proteins in cancer tissues are important for understanding protein functions and related diseases. Immunohistochemical (IHC) images enable visualizing the distribution of proteins at the tissue level, providing an important resource for the protein localization studies. In the past decades, several image-based protein subcellular location prediction methods have been developed, but the prediction accuracies still have much space to improve due to the complexity of protein patterns resulting from multi-label proteins and variation of location patterns across cell types or states.

Results

Here, we propose a multi-label multi-instance model based on deep graph convolutional neural networks, GraphLoc, to recognize protein subcellular location patterns. GraphLoc builds a graph of multiple IHC images for one protein, learns protein-level representations by graph convolutions, and predicts multi-label information by a dynamic threshold method. Our results show that GraphLoc is a promising model for image-based protein subcellular location prediction with model interpretability. Furthermore, we apply GraphLoc to the identification of candidate location biomarkers and potential members for protein networks. A large portion of the predicted results have supporting evidence from the existing literatures and the new candidates also provide guidance for further experimental screening.

Availability

The dataset and code are available at: www.csbio.sjtu.edu.cn/bioinf/GraphLoc.

Supplementary information

Supplementary data are available at Bioinformatics online.

Post-Translational Modifications That Drive Prostate Cancer Progression

While a protein primary structure is determined by genetic code, its specific functional form is mostly achieved in a dynamic interplay that includes actions of many enzymes involved in post-translational modifications. This versatile repertoire is widely used by cells to direct their response to external stimuli, regulate transcription and protein localization and to keep proteostasis. Herein, post-translational modifications with evident potency to drive prostate cancer are explored. A comprehensive list of proteome-wide and single protein post-translational modifications and their involvement in phenotypic outcomes is presented. Specifically, the data on phosphorylation, glycosylation, ubiquitination, SUMOylation, acetylation, and lipidation in prostate cancer and the enzymes involved are collected. This type of knowledge is especially valuable in cases when cancer cells do not differ in the expression or mutational status of a protein, but its differential activity is regulated on the level of post-translational modifications. Since their driving roles in prostate cancer, post-translational modifications are widely studied in attempts to advance prostate cancer treatment. Current strategies that exploit the potential of post-translational modifications in prostate cancer therapy are presented.