Peter de Greef

Data - Modelling - Immunology

[Peter de Greef @pcdegreef]

Estimating TCR diversity from a sample 🧪 can be quite tricky, but integrating information from multiple samples 🧪🧪🧪 helps! We discuss challenges and opportunities in our newest preprint @BinfUtrecht

[bioRxiv @biorxivpreprint]

Towards a robust comparison of diversity between sampled TCR repertoires https://t.co/xE4AIXVsRw #bioRxiv

[Arpit Chandan Swain @SwainArpit]

#PhDproject
Long-term diversity of memory T cells:
Low, if source makes long-lived cells
High, if long-lived source makes short-lived cells that become less fit aka cellular aging
Nice discussions with @BorghansJose @CTI_UMCUtrecht, Rob de Boer @BinfUtrecht, now in @FrontImmunol

[Peter de Greef @pcdegreef]

Together, our study highlights a limited-diversity set of TCRβ sequences that closely resemble TCRα sequences as they lack a D segment. Many thanks to all authors of previous studies for making their data (publicly) available! (6/6)

[Peter de Greef @pcdegreef]

Excited to see our work published in PNAS: TCRβ rearrangements without a D segment are common, abundant, and public. https://t.co/Mn68LRYqmZ
Quick summary below 🧵 (1/6)

[Peter de Greef @pcdegreef]

Sequences without a D segment seem to be preferentially produced before birth, when the TdT enzyme is still down-regulated. Such clones are long-lived and, perhaps as a result, they are excessively shared among individuals. (5/6)

[Theoretical Biology & Bioinformatics @ UU @BinfUtrecht]

We’re looking for a new #computationalbiology #bioinformatics group leader @UniUtrecht @BINFutrecht. Apply here (deadline Oct 17 2021): https://t.co/k6JeFZbaCb. Please retweet or share with potential candidates!

[Peter de Greef @pcdegreef]

Check out in @FrontAging: we studied how antigen-specific T-cell repertoires change during aging and CMV-infection. Really enjoyed the team effort with great people from @rivm and @CTI_UMCUtrecht @BinfUtrecht

[Frontiers - Aging @FrontAging]

New Research: Age and CMV-Infection Jointly Affect the EBV-Specific CD8+ T-Cell Repertoire https://t.co/rOnzwTGLFo #Aging

[Peter de Greef @pcdegreef]

@antigenomics @biorxivpreprint Thanks @antigenomics! Excellent idea, which we did not yet, but we should definitely look at!

[Peter de Greef @pcdegreef]

Despite their likely generation very early in life, we find them in individuals of old age, and also in memory repertoires and the VDJdb, indicating that they are persistent and functional. Full story on bioRxiv: https://t.co/Ep7pcxYbEC (6/6)

[Peter de Greef @pcdegreef]

Which TCRs are more common in the (naive) repertoire than others? We find that many abundant and public TCRβs have no D-segment: https://t.co/Ep7pcxYbEC .

Where do they come from and what do they do? A short summary (1/6)

[Peter de Greef @pcdegreef]

Interestingly, cord blood samples of extremely preterm neonates contain many TCRβ rearrangements without D-segment, indicating that the TCR repertoire starts with this restricted set of β chains that look like α chains (5/6).

[Theoretical Biology & Bioinformatics @ UU @BinfUtrecht]

Deadline for a tenure track position in our group has been extended until June 15th! Educate the next generation of biologists in bioinformatics - full/part time (0.8-1.0 FTE). Please fwd to suitable friends or colleagues: https://t.co/5krac8oRXP - please RT

[Peter de Greef @pcdegreef]

@3DiMMUNE Hi David, interesting analogy! Note that this is data from naive T cells in humans, without sorting epitope-specific cells. We find evidence for naive clones (TCR α&β nucleotide sequence) of > 10^5 cells, which means a much larger range of clone sizes than found in mice

[Peter de Greef @pcdegreef]

First paper of my PhD out in @eLife : Combining experiments, bioinformatics and mathematical modelling, we find many small but also large naive T cell clones: https://t.co/3VE4JMH8q6. Many thanks to the team including @BennyChain @BinfUtrecht @jamimmunology