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Sagar Bapat

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@bapat_lab

News from Dr. Sagar Bapat's lab @UCSF, focusing on how nutrition and other lifestyle factors modify immune function in health and chronic disease.
bapatlab.org Joined July 2020
378 Following 445 Followers 78 Posts

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Sagar Bapat Verified account @bapat_lab
Our @Nature paper is out!

It's been known for a while that long-term dietary habits can affect how our immune system behaves. But what about much briefer changes in diet?

In mice, we found that even a few days of dietary change (think cheat days...or perhaps salad Sundays) at the onset of inflammation can profoundly alter disease severity and establish lasting inflammatory memory in tissues, even after the diet changes back.

nature.com/articles/s4158…

This work was led by two extraordinarily dedicated and inexhaustible members of our lab: former graduate student @OwenJ457 and former technician John Tayeri. It was also an exercise in collaborative science as many labs @UCSF and @Stanford came together to bring this over the finish line - special thanks to @gardnerlabUCSF, @Molofsky_lab, @alexis_combes, @Treg_Mike. Deeply grateful to everyone who contributed!
www.nature.com Diet at disease onset determines tissue inflammatory memory Nature - Dietary state during a narrow temporal window can durably reprogram disease trajectory.
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Sagar Bapat Verified account @bapat_lab
Very cool work from @neal_amin and the Sculpta team. The idea of covalently barcoding RNA before any enzymatic library prep step is both conceptually elegant and potentially very powerful. Exciting first application here with highly multiplexed, isoform resolved drug screening.
Neal Amin Verified account @neal_amin Sep 24
Today, Sculpta releases the first demonstration of bioorthogonal barcoding ("bobcoding"), the process by which we:

1) covalently attach oligonucleotide barcodes to RNA at multiple internal positions with two-step chemistry, and 2) perform a multiplexed reverse transcription reaction to generate barcoded cDNA libraries with >99% barcoding accuracy.

To the best of our knowledge, it is the first time ever that either of these steps have ever been performed by anyone. No one has ever broken the barrier of multiplexing prior to any enzymatic step in library preparation, driving simplicity and higher data quality. Instead of other methods that add 0 or 1 barcode, we add one barcode every ~300bp, adding redundancy and fidelity to RNA measurements.

In our first application described in our pre-print below, we used bobcodes to create the first RNA isoform-resolved drug screening platform. It beats Novartis' DRUG-seq platform by:

- generating full length transcript capture of RNA isoforms, instead of just 3' end counting
- capturing 25-fold more RNA splicing events
- reducing barcode swapping by 10-fold
- using 18 fewer PCR cycles (~250,000 less amplification)
- reducing sample-to-sample variability in gene expression measurements
- eliminating costly and cumbersome library fragmentation/tagmentation steps completely
- reducing workflow complexity and number of steps
- reducing overall protocol duration by ~25%

Though our chemical barcoding method improved transcriptomic data quality while also being simpler and faster than all existing methods, the implications of this work go well beyond this particular use case:

The gate to greater applications of AI in transcriptomics is not a lack of compute. Nor is it a lack of data volume. The elephant in the room has always been our limited ability to faithfully and accurately measure cellular RNAs.

Sculpta now has line of sight to build what we call the first ground truth transcriptomics platform [for single cell, spatial and more] for the future of biological research, drug development and AI-enabled discoveries for the betterment of human health and longevity.

[PS Until the kind folks at bioRxiv get through the apparent backlog of AI slop submissions, Sculpta will host the pre-print PDF on our website. You can sign up for product offerings and other updates at this link too]

sculpta.bio/preprint
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Sagar Bapat Verified account @bapat_lab
Excited to see this beautiful work from @jccarnevale, Qi Liu, and the whole collaborative team! This is a major technical and conceptual advance for engineering human T cells to improve cellular therapies. Congrats to everyone involved!
Julia Carnevale Verified account @jccarnevale Aug 13
Incredibly excited to share the first major paper from my lab @carnevale_lab led by postdoc Qi Liu @GladstoneInst @UCSF executing the first ever genome-wide in vivo screens for genetic modifications to enhance human T cell therapies for solid tumors. Now in @Nature: nature.com/articles/s4158…
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Sagar Bapat Verified account @bapat_lab
Congrats Theo and @Roth_Lab!
Arc Institute Verified account @arcinstitute Feb 27
Congratulations to Arc Innovation Investigator Theo Roth (@Roth_Lab) on receiving a 2026 @MichelsonMedRF Next Generation Grant.

Theo's team is using combinatorial genetic engineering to create immune cell states not found in nature.

michelsonmedicalresearch.org/news/michelson…
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Sagar Bapat Verified account @bapat_lab
Excited to be a part of Project FEAST to better understand how food and diet can modify and enhance anti-tumor immunity!
Long Lab @longlabstanford Jul 23, 2025
Grateful to Joan and Sandy Weill for their visionary gift, bringing the best from @Stanford @UCSF together to transform cancer care. And excited for our Project FEAST team tackle critically unanswered questions at the intersection of cancer, nutrition, obesity, and GLP-1 drugs.
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