The Immune Epitope Database!

The Immune Epitope Database (IEDB) is a freely available resource funded by NIAID. It catalogs experimental data on antibody and T cell epitopes studied in humans, non-human primates, and other animal species in the context of infectious disease, allergy, autoimmunity and transplantation. The IEDB also hosts tools to assist in the prediction and analysis of epitopes.

http://www.iedb.org/home_v3.php

We have deposited our favorite CRISPR screen plasmid @Addgene

It’s a version of LentiGuide-puro where Sudeepta Panda and Long Jiang added P2A-eGFP after PuroR, lac-mRFP in the stuffer, and a cloning site directly after the sgRNA scaffold.

The plasmid allows for both puro and eGFP selection and MOI determination. The lac-mRFP in the stuffer gives a simple visual quality control step when expanding in bacteria (red=stuffer, white=spacer successfully introduced). The cloning site allows for introducing e.g. UMIs.

https://addgene.org/137730/

Multilayered VBC score predicts sgRNAs that efficiently generate loss-of-function alleles

Beautiful paper from the Elling  and Zuber  Labs on a novel score to predict sgRNA efficiency. Also including a website for sgRNA design based on the VBC score: https://www.vbc-score.org/ . Brought to my attention by shared first author Julian Jude.

Paper: https://pubmed.ncbi.nlm.nih.gov/32514112/

Commentary: https://www.viennabiocenter.org/about/news/new-prediction-tool-sharpens-the-crispr-scissors/

Collection of popular scientific texts/observations I have written in the past (in Swedish).

2020 about the Nobel Prize in Chemistry for CRISPR (https://nyheter.ki.se/ki-forskare-kommenterar-2020-ars-nobelpris-i-kemi-jattekul-antligen):

2018 for the membership magazine Legatus Mensae (“A strong Immune System”):

2005 for the student magazine “Bukpressen”:

Our review “Designing custom CRISPR libraries for hypothesis-driven drug target discovery” is online!

Here we describe the bioinformatic tools we use designing and analyzing hypothesis-driven CRISPR Screens.

Great work by talented PhD student Vaishnavi Iyer, and everyone else involved!

–> https://www.sciencedirect.com/science/article/pii/S2001037020303627?via%3Dihub

Interesting study by Orange et al – PRIME Cells Predicting Rheumatoid Arthritis Flares

N Engl. J. Med. 2020 Jul 16;383(3):218-228. doi: 10.1056/NEJMoa2004114. PMID: 32668112

RNA Identification of PRIME Cells Predicting Rheumatoid Arthritis Flares

Dana E OrangeVicky YaoKirsty SawickaJohn FakMayu O FrankSalina ParveenNathalie E BlachereCaryn HaleFan ZhangSoumya RaychaudhuriOlga G TroyanskayaRobert B Darnell

 

Abstract

Background: Rheumatoid arthritis, like many inflammatory diseases, is characterized by episodes of quiescence and exacerbation (flares). The molecular events leading to flares are unknown.

Methods: We established a clinical and technical protocol for repeated home collection of blood in patients with rheumatoid arthritis to allow for longitudinal RNA sequencing (RNA-seq). Specimens were obtained from 364 time points during eight flares over a period of 4 years in our index patient, as well as from 235 time points during flares in three additional patients. We identified transcripts that were differentially expressed before flares and compared these with data from synovial single-cell RNA-seq. Flow cytometry and sorted-blood-cell RNA-seq in additional patients were used to validate the findings.

Results: Consistent changes were observed in blood transcriptional profiles 1 to 2 weeks before a rheumatoid arthritis flare. B-cell activation was followed by expansion of circulating CD45-CD31-PDPN+ preinflammatory mesenchymal, or PRIME, cells in the blood from patients with rheumatoid arthritis; these cells shared features of inflammatory synovial fibroblasts. Levels of circulating PRIME cells decreased during flares in all 4 patients, and flow cytometry and sorted-cell RNA-seq confirmed the presence of PRIME cells in 19 additional patients with rheumatoid arthritis.

Conclusions: Longitudinal genomic analysis of rheumatoid arthritis flares revealed PRIME cells in the blood during the period before a flare and suggested a model in which these cells become activated by B cells in the weeks before a flare and subsequently migrate out of the blood into the synovium. (Funded by the National Institutes of Health and others.).