Skip to main content
Premium Trial:

Request an Annual Quote

PNAS Papers on CLInt-seq, Secretome Mouse Model, Mouse Inflammation

A team from the University of California, Los Angeles, presents a droplet-based messenger RNA (mRNA) sequencing strategy aimed at profiling the antigen-specific T cell receptor (TCR) sequences that arise as alpha and beta chains of the TCR heterodimer recombine somatically to recognize specific antigens. The "mRNA sequencing via cross-linker regulated intracellular phenotype," or CLInt-seq, strategy was developed for finding even low-frequency TCR representatives in a high-throughput manner with droplet-based sequencing on fixed or intracellular-stained cells, the researchers say. "We present a technique that allows for TCR sequencing based on intracellular signaling molecules, such as cytokines and transcription factors," they write. "The core concept is highly generalizable and should be applicable to global gene expression analysis where intracellular marker-based cell isolation is required."

Researchers at the University of Pittsburgh and the National Heart, Lung, and Blood Institute outline the rationale behind a so-called "secretome mouse" model designed for following tissue-specific protein and peptide secretion in an in vivo setting. The team describes its ER-BioID-HA mouse model — developed using a promiscuous proximity biotinylation enzyme known as BioID2 — "an epitope tagged version of BioID that constitutively localizes to the lumen of the endoplasmic reticulum." Using this secretome mouse model, for example, the researchers focused on the proteins pumped out by endothelial cells or by skeletal muscle tissue after exercise, though they suggest that the same sort of genetic platform may ultimately prove useful for "delineating a wide range of in vivo physiology and for the rational development of disease-relevant biomarkers."

Investigators in China and the US use CRISPR-Cas9-based genome screening, protein depletion, protein interaction, and other experiments to explore "ankyrin repeat and suppressor of cytokine signaling box containing 1" (ASB1) protein contributions to inflammation and immunity in a mouse model. Their results suggest that mice exposed to the bacterial pathogens such as Salmonella typhimurium, bacterial lipopolysaccharides (LPS), cytokines, or colitis-causing compounds may be protected from septic shock, pronounced intestinal inflammation, severe colitis, and other negative effects when the gene coding for ASB1 is dialed down, reflecting apparent interactions between ASB1 and other proteins that mediate inflammation and related signaling pathways. "Given the crucial role of ASB proteins in inflammatory signaling pathways," the authors say, "our study offers insights into the immune regulation in pathogen infection and inflammatory disorders with therapeutic implications."

The Scan

Study Points to Tuberculosis Protection by Gaucher Disease Mutation

A mutation linked to Gaucher disease in the Ashkenazi Jewish population appears to boost Mycobacterium tuberculosis resistance in a zebrafish model of the lysosomal storage condition, a new PNAS study finds.

SpliceVault Portal Provides Look at RNA Splicing Changes Linked to Genetic Variants

The portal, described in Nature Genetics, houses variant-related messenger RNA splicing insights drawn from RNA sequencing data in nearly 335,700 samples — a set known as the 300K-RNA resource.

Automated Sequencing Pipeline Appears to Allow Rapid SARS-CoV-2 Lineage Detection in Nevada Study

Researchers in the Journal of Molecular Diagnostics describe and assess a Clear Labs Dx automated workflow, sequencing, and bioinformatic analysis method for quickly identifying SARS-CoV-2 lineages.

UK Team Presents Genetic, Epigenetic Sequencing Method

Using enzymatic DNA preparation steps, researchers in Nature Biotechnology develop a strategy for sequencing DNA, along with 5-methylcytosine and 5-hydroxymethylcytosine, on existing sequencers.