amitava banerjee
LightNews LightNews
banner
amitava-immuno.bsky.social
amitava banerjee
@amitava-immuno.bsky.social
710 followers 2.4K following 21 posts
@cshlnews.bsky.social postdoc with @hannahvmeyer.bsky.social and Saket Navlakha • How your T cells know it's you • Develops immuno tools named after Gotham characters: github.com/meyer-lab-cshl/BATMAN 🦇 • they/he 🏳️‍🌈🏳️‍⚧️
Posts Replies Media Videos
amitava-immuno.bsky.social
Anyone?🙏
Text: "Negative Data (all caps, bold font) for TCR-pMHC predictions" in bold orange font with red shadow on blue background, generated using https://homes.luddy.indiana.edu/ccshan/for/for.html
November 9, 2025 at 2:29 PM
amitava-immuno.bsky.social
Autoimmunity vs cross-reactive protection against evolving pathogens by immune systems

1. www.nature.com/articles/s41...
2. oncohemakey.com/assessing-t-...
3. pmc.ncbi.nlm.nih.gov/articles/PMC...
Illustration of the expression-controlled trade-off between the benefit of protection range and the cost of autoimmunity in anti-phage defense systems. Model integrating the relationship between T cell function, TCR affinity, and positive/negative regulators modulating cell responsiveness. A panel of CD8 T lymphocytes engineered to express antitumoral TCRs with incremental affinities toward the HLA-A2/NY-ESO-1 epitope (x-axis) was assessed for functional capacity (y-axis). An optimal window of TCR-pMHC affinity can be detected in the upper natural range (K D from 5 to 1 μM), corresponding to the range where most peripheral nonself-/virus-specific T cells can be detected. We recently described how positive regulators of T cell function including CD28 and TNFR cofactors are enriched in T cells lying within the optimal affinity window and how the inhibitory receptor PD-1 and SHP-1 phosphatase are involved in restricting T cell activation and responsiveness in TCR-engineered CD8 T cells of very high supraphysiological affinities. On-target toxicity is known to follow the functional and activatory signatures of CD8 T cells, while off-target responsiveness and toxicity are described to increase along TCR-pMHC affinity, within the supranatural affinity range. With differing binding affinities of the T cell receptor (TCR) repertoires of Treg and Tconv cells to self- and non-self-antigens, the Treg-Tconv cellular circuit can mount an effective anti-pathogen immune response without causing excessive immunopathology. Infection by a foreign pathogen, accompanied by innate immune activation and presentation of foreign antigens, promotes an effector Tconv response which is needed for pathogen clearance. However, if pathogen clearance by effector Tconv cells results in excessive self-tissue damage, the self-antigens generated and presented to Tregs can strengthen Treg-mediated immunosuppression, helping to reign in the effector Tconv response and tissue damage. The circuit is capable of striking a delicate balance between Tconv and Treg responses, allowing for effective pathogen clearance while restraining immunopathology.
July 28, 2025 at 1:08 PM
amitava-immuno.bsky.social
Gotta say the cshl.edu website looks extra cool today
Cold Spring Harbor Laboratory website screenshot showing ribbons in blue, and a cartoon of bats emerging from a cave with a bright red round object looking like a virus in the back. Title reads "BATMAN brings TCR therapy out of the shadows". Subtitle reads "A new AI model developed by CSHL quantitative biologists could help improve immunotherapy treatments not only for cancer but all human illness."
July 25, 2025 at 9:25 PM
amitava-immuno.bsky.social
First postdoc paper with @hannahvmeyer.bsky.social on #TCR cross-reactivity database & modeling out now in Cell Systems: doi.org/10.1016/j.ce...

BATCAVE database + Paper codes: github.com/meyer-lab-cs...

BATMAN + Tutorial Notebooks: github.com/meyer-lab-cs...

#ImmunoSky #T-cells #CancerImmunology
Alt Text: Infographic summarizing a study on T cell receptor (TCR) activation by mutant epitopes. The graphic is divided into three sections: Database (top panel): Describes a dataset with over 22,000 TCR-pMHC pairs, involving more than 150 activated TCRs and 25 mutagenized epitopes, covering both MHC class I and II, aggregated from 20+ years of experiments. A heatmap of epitope mutations and TCR structures is illustrated. Model (middle panel): Shows the BATMAN model for predicting TCR activation. The model combines an amino acid mutation similarity matrix with a learned mutation position weight profile and an MHC binding factor, outputting a prediction of TCR activation. Predictions (bottom panel): Highlights two applications — predicting tissue targets of cancer-specific TCRs and T cell responses to mutant viral antigens — accompanied by illustrative icons of organs, T cells, and viruses.
July 25, 2025 at 2:59 PM
amitava-immuno.bsky.social
Nice day to start the CSHL #cshlsysimm @cshlmeetings.bsky.social Meeting
Holding an abstract book for "Systems Immunology" conference, blossoms in the background
April 22, 2025 at 11:03 PM