Siino, V. | Search bioRxiv

bioRxiv2020

OmicLoupe: Facilitating biological discovery by interactive exploration of multiple omic datasets and statistical comparisons

Visual exploration of gene product behavior across multiple omic datasets can pinpoint technical limitations in data and reveal biological trends. The OmicLoupe software was developed to facilitate such exploration and provides more than 15 interactive cross-dataset visualizations for omic data. It expands visualizations to multiple datasets for quality control, statistical comparisons and overlap and correlation analyses, while allowing for rapid inspection and downloading of selected features. The usage of OmicLoupe is demonstrated in three diverse studies, including an analysis of SARS-CoV-2 infection across omic layers, based on previously published proteomics and transcriptomics studies. OmicLoupe is available at quantitativeproteomics.org/omicloupe

bioinformatics↗

bioRxiv2020

Protein synthesis is suppressed in sporadic and familial Parkinson's Disease by LRRK2

Gain of function LRRK2-G2019S is the most common mutation associated with both familial and sporadic Parkinsons disease. It is expected therefore that understanding the cellular function of LRRK2 will provide much needed insight on the pathological mechanism of sporadic Parkinsons, which is the most common form. Here we show that constitutive LRRK2 activity represses nascent protein synthesis in rodent neurons. Specifically, enzymatic inhibition of LRRK2, gene silencing or gene knockout of Lrrk2 increase translation. In the rotenone model of Parkinsons, LRRK2 activity increases, leading to repression of translation and dopaminergic neuron atrophy both of which are prevented by LRRK2 inhibition. This is accompanied by altered phosphorylation of eIF2-S52({uparrow}), eIF2s2-S2({downarrow}) and eEF2-T57({uparrow}) in striatum/substantia nigra in a direction that signifies inhibition of protein synthesis. Significantly, LRRK2 is activated and translation is 40% reduced in Parkinsons patient fibroblasts (G2019S and sporadic) and LRRK2 inhibition restores normal translation. In contrast, translation is unchanged in cells from multiple system atrophy patients, implying disease specificity. These findings suggest that LRRK2-dependent repression of translation may be a proximal function of LRRK2 in Parkinsons pathology.

neuroscience↗