Publications by authors named "J A Lacava"
To thrive, cancer cells must navigate acute inflammatory signaling accompanying oncogenic transformation, such as via overexpression of repeat elements. We examined the relationship between immunostimulatory repeat expression, tumor evolution, and the tumor-immune microenvironment. Integration of multimodal data from a cohort of pancreatic ductal adenocarcinoma (PDAC) patients revealed expression of specific Alu repeats predicted to form double-stranded RNAs (dsRNAs) and trigger retinoic-acid-inducible gene I (RIG-I)-like-receptor (RLR)-associated type-I interferon (IFN) signaling.
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- Data-Independent Acquisition (DIA) enhances co-immunoprecipitation analysis by reducing quantitation variability and improving the detection of specific interactors compared to Data-Dependent Acquisition (DDA).
- A comparison of DIA and DDA across various bioinformatics workflows revealed that DIA can effectively generate spectral libraries without needing separate DDA experiments, and software struggles with indistinct signals from mock pull-downs.
- Spectronaut and DIA-NN provided the best control of coefficient of variation in protein quantification, while using DIA for both building spectral libraries and quantifying proteins leads to more consistent results and fewer missing values.
Background: Systemic lupus erythematosus (SLE) is a chronic autoimmune disease with an unpredictable course of recurrent exacerbations alternating with more stable disease. SLE is characterized by broad immune activation and autoantibodies against double-stranded DNA and numerous proteins that exist in cells as aggregates with nucleic acids, such as Ro60, MOV10, and the L1 retrotransposon-encoded ORF1p.
Results: Here we report that these 3 proteins are co-expressed and co-localized in a subset of SLE granulocytes and are concentrated in cytosolic dots that also contain DNA: RNA heteroduplexes and the DNA sensor ZBP1, but not cGAS.
Article Synopsis
- - Immunoprecipitation (IP) paired with mass spectrometry is a powerful method for mapping how proteins interact, especially when using tagged cell collections, but many protein interactions remain unexplored due to limitations in current high-throughput techniques.
- - A major challenge in IP is maintaining stable interactions when transferring samples, as this can result in losing real interactions and failing to identify them later.
- - The authors developed a high-content screening approach that investigates how different chemical conditions affect IP results, allowing for quick optimization of methods to better capture protein complexes.
Article Synopsis
- - CCDC88B is linked to chronic inflammatory diseases and impacts dendritic cell (DC) migration in mice; disrupting this gene results in defective DC movement.
- - Researchers found that the proteins ARHGEF2 and RASAL3 interact with CCDC88B and influence neuroinflammation and colitis susceptibility in mice with mutations in these proteins.
- - The CCDC88B/RASAL3/ARHGEF2 complex regulates DC migration by affecting RHOA activation, with ARHGEF2 and RASAL3 having opposing effects on cell movement.