Julia Carnevale, Assistant Professor at the Gladstone-UCSF Institute of Genomic Immunology, shared on X:
“Incredibly excited to share the first major paper from my lab Carnevale Lab led by postdoc Qi Liu Gladstone Institutes 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.
By using A375 tumors engineered to express anti-CD3 scFv, we were able to recover many millions of T cells per tumor, allowing genome-wide screening coverage for the first time in relatively few mice.
Polyclonal T cells infiltrated these in vivo tumors in massive numbers and in what appeared to be an exhausted state – perfect for screens to find modifications that enhance tumor accumulation and anti-tumor function.
In vivo GW knockout screens for T cell abundance identified G protein coupled receptor regulators as modulators of solid-tumor enrichment, and we defined a role for the P2RY8 signaling pathway in restricting human T cell trafficking into tumors.
Because P2RY8 is not conserved in mice, this result would have been missed in a purely murine screen, underscoring a key strength of our platform – its ability to reveal functions of human specific genes in human T cells within the physiologic context of tumor bearing mice.
Because P2RY8 is not conserved in mice, this result would have been missed in a purely murine screen, underscoring a key strength of our platform – its ability to reveal functions of human specific genes in human T cells within the physiologic context of tumor bearing mice.
Although P2RY8 pathway disruption increased T cell accumulation, infiltrating cells remained susceptible to exhaustion and dysfunction. So we performed a complementary screen to ID mutations that selected for T cells that both infiltrated tumors and produced high levels of IFN-γ.
The IFN-γ screen again highlighted GPCR genes as crucial regulators of T cells in tumors, including a new GPCR hit – GNAS.
GNAS encodes the stimulatory subunit of the heterotrimeric G protein complex that couples with GPCRs, integrating signaling downstream of suppressive cues often found in the TME.
Ablation of GNAS confers a notable advantage to T cells in the presence of such suppressive signals.
We evaluated the ability of GNAS KO CAR/TCR T cells to control tumors in an array of solid tumor models and found that GNAS KO endowed therapeutic T cells with broad resistance to diverse tumor-derived inhibitory cues, enabling robust tumor control across tumor or antigen targets.
Importantly, because we can recover so many cells from each tumor, we can screen by sorting on functional markers of T cell states, which requires significantly more cells than abundance screens.
Finally, we demonstrated further enhanced tumor control through the powerful combinatorial knockout of P2RY8, which enhances T cell trafficking, and GNAS, which promotes effector function within the suppressive tumor microenvironment.
This finding highlights the power of targeting complementary axes of T cell biology and underscores the utility of our screening platform in supporting parallel, functional readouts
This was a Herculean effort led by Qi Liu but could not have been achieved without our many collaborators!”
Title: In vivo genome-wide CRISPR screens of human T cells in solid tumours
Authors: Qi Liu, Peixin Amy Chen, Esha Urs, Shimin Zhang, Maya M. Arce, Charlotte H. Wang, Jun Yan, Vinh Q. Nguyen, Zhongmei Li, Jin Seo, Nupura Kale, Fanglue Peng, Yikai Luo, Laine Goudy, Taylor N. LaFlam, Haixia Zhong, Chandrima Modak, Emma Dann,
Jae Hyung Jung, Amanda Kirane, Allison Betof Warner, Boi Bryant Quach, Zinaida Good, Brian R. Shy, Eric Shifrut, Sagar P. Bapat, Greg M. Allen, Justin Eyquem, Katherine Fuh, Stacie E. Dodgson, Jason G. Cyster, Alexander Marson, Julia Carnevale
