Lingting Shi
@lingting-shi.bsky.social
T32 GEIC Postdoctoral research scientist co-mentored by @elhamazizi and @joselmcfaline @Cancer_dynamics, Ph.D. @columbiaBME, NSF Graduate Research Fellow (2019-2022)
💫Fantastic experience diving into CRISPR technology, hearing inspiring clinical stories, and connecting with incredible people! It was also a refreshing getaway from NYC — great meals, beautiful views🌄, and even better company. Truly an inspiring experience.
August 19, 2025 at 4:47 AM
💫Fantastic experience diving into CRISPR technology, hearing inspiring clinical stories, and connecting with incredible people! It was also a refreshing getaway from NYC — great meals, beautiful views🌄, and even better company. Truly an inspiring experience.
In this project, I’m using single-cell pooled CRISPR 🧬screening in glioblastoma 🧠to look for new ways to overcome immune evasion. It’s very different from my work on multimodal immune profiling in human GVHD, but both share the same theme: exploring how T cells interact in disease.
August 19, 2025 at 4:47 AM
In this project, I’m using single-cell pooled CRISPR 🧬screening in glioblastoma 🧠to look for new ways to overcome immune evasion. It’s very different from my work on multimodal immune profiling in human GVHD, but both share the same theme: exploring how T cells interact in disease.
Shoutout to co-first authors Ajna Uzuni and Ximi Wang, and to Michael Pressler, the papers would not be the same withou you all. Thanks also to the McFaline-Figueroa Lab for their support. Check out our preprint for a deeper dive into the findings!
May 29, 2025 at 6:27 PM
Shoutout to co-first authors Ajna Uzuni and Ximi Wang, and to Michael Pressler, the papers would not be the same withou you all. Thanks also to the McFaline-Figueroa Lab for their support. Check out our preprint for a deeper dive into the findings!
12/🧬 Huge thanks to everyone involved in this project—your contributions were invaluable in uncovering key biological insights. I'm especially grateful to my mentor @elhamazizi.bsky.social for her guidance, and to my collaborator Dr. Ran Reshef at CUIMC.
May 29, 2025 at 5:21 PM
12/🧬 Huge thanks to everyone involved in this project—your contributions were invaluable in uncovering key biological insights. I'm especially grateful to my mentor @elhamazizi.bsky.social for her guidance, and to my collaborator Dr. Ran Reshef at CUIMC.
11/ 🧬
📖 Full paper: www.biorxiv.org/content/10.1...
🛠 Tools: DecompTCR, StarfyshHD, and DecipherTCR now available on GitHub.
🔬 Built for GVHD, applicable to cancer, IBD, and other immune diseases.
Would love to hear from others working on T cell dynamics or GVHD—what are you seeing?
📖 Full paper: www.biorxiv.org/content/10.1...
🛠 Tools: DecompTCR, StarfyshHD, and DecipherTCR now available on GitHub.
🔬 Built for GVHD, applicable to cancer, IBD, and other immune diseases.
Would love to hear from others working on T cell dynamics or GVHD—what are you seeing?
Spatiotemporal Single-Cell Analysis Reveals T Cell Clonal Dynamics and Phenotypic Plasticity in Human Graft-versus-Host Disease
Allogeneic hematopoietic cell transplantation (alloHCT) is curative for various hematologic diseases but often leads to acute graft-versus-host disease (GVHD), a potentially life-threatening complicat...
www.biorxiv.org
May 29, 2025 at 5:15 PM
11/ 🧬
📖 Full paper: www.biorxiv.org/content/10.1...
🛠 Tools: DecompTCR, StarfyshHD, and DecipherTCR now available on GitHub.
🔬 Built for GVHD, applicable to cancer, IBD, and other immune diseases.
Would love to hear from others working on T cell dynamics or GVHD—what are you seeing?
📖 Full paper: www.biorxiv.org/content/10.1...
🛠 Tools: DecompTCR, StarfyshHD, and DecipherTCR now available on GitHub.
🔬 Built for GVHD, applicable to cancer, IBD, and other immune diseases.
Would love to hear from others working on T cell dynamics or GVHD—what are you seeing?
10/ 🧬
🧩 Implication:
The expansion and phenotypic shift of cytotoxic T cells in severe GVHD may offer a potential target for new therapies.
This study also offers a transformative paradigm for studying complex immune responses in human using integrated temporal and spatial single-cell approaches.
🧩 Implication:
The expansion and phenotypic shift of cytotoxic T cells in severe GVHD may offer a potential target for new therapies.
This study also offers a transformative paradigm for studying complex immune responses in human using integrated temporal and spatial single-cell approaches.
May 29, 2025 at 5:13 PM
10/ 🧬
🧩 Implication:
The expansion and phenotypic shift of cytotoxic T cells in severe GVHD may offer a potential target for new therapies.
This study also offers a transformative paradigm for studying complex immune responses in human using integrated temporal and spatial single-cell approaches.
🧩 Implication:
The expansion and phenotypic shift of cytotoxic T cells in severe GVHD may offer a potential target for new therapies.
This study also offers a transformative paradigm for studying complex immune responses in human using integrated temporal and spatial single-cell approaches.
9/ 🧬
💥 Bonus: We also see Tregs and unconventional T cells reprogrammed into pro-inflammatory states. It’s immune dysregulation across multiple fronts.
💥 Bonus: We also see Tregs and unconventional T cells reprogrammed into pro-inflammatory states. It’s immune dysregulation across multiple fronts.
May 29, 2025 at 5:11 PM
9/ 🧬
💥 Bonus: We also see Tregs and unconventional T cells reprogrammed into pro-inflammatory states. It’s immune dysregulation across multiple fronts.
💥 Bonus: We also see Tregs and unconventional T cells reprogrammed into pro-inflammatory states. It’s immune dysregulation across multiple fronts.
8/🧬
🌍 We used the first, to our knowledge, Visium HD dataset from human gut tissue in GVHD—2µm resolution—to show that CD8⁺ effector T cells cluster near intestinal stem cells in Severe GVHD and are enriched in crypt loss region, suggesting these effector cells drive tissue damage.
🌍 We used the first, to our knowledge, Visium HD dataset from human gut tissue in GVHD—2µm resolution—to show that CD8⁺ effector T cells cluster near intestinal stem cells in Severe GVHD and are enriched in crypt loss region, suggesting these effector cells drive tissue damage.
May 29, 2025 at 5:10 PM
8/🧬
🌍 We used the first, to our knowledge, Visium HD dataset from human gut tissue in GVHD—2µm resolution—to show that CD8⁺ effector T cells cluster near intestinal stem cells in Severe GVHD and are enriched in crypt loss region, suggesting these effector cells drive tissue damage.
🌍 We used the first, to our knowledge, Visium HD dataset from human gut tissue in GVHD—2µm resolution—to show that CD8⁺ effector T cells cluster near intestinal stem cells in Severe GVHD and are enriched in crypt loss region, suggesting these effector cells drive tissue damage.
7/🧬
🧠 Key finding:
👀 Here’s the Decipher map showing clonal trajectories across tissue compartments. We discovered that cytototix CD8⁺ T cell clones are clonally expanded, change state as they move between gut layers, and acquire resident memory (Hobit⁺ Trm) phenotypes.
🧠 Key finding:
👀 Here’s the Decipher map showing clonal trajectories across tissue compartments. We discovered that cytototix CD8⁺ T cell clones are clonally expanded, change state as they move between gut layers, and acquire resident memory (Hobit⁺ Trm) phenotypes.
May 29, 2025 at 5:03 PM
7/🧬
🧠 Key finding:
👀 Here’s the Decipher map showing clonal trajectories across tissue compartments. We discovered that cytototix CD8⁺ T cell clones are clonally expanded, change state as they move between gut layers, and acquire resident memory (Hobit⁺ Trm) phenotypes.
🧠 Key finding:
👀 Here’s the Decipher map showing clonal trajectories across tissue compartments. We discovered that cytototix CD8⁺ T cell clones are clonally expanded, change state as they move between gut layers, and acquire resident memory (Hobit⁺ Trm) phenotypes.
6/🧬
📈 DecompTCR uncovers which clones persist, expand, and associate with GVHD severity.
📈 DecompTCR uncovers which clones persist, expand, and associate with GVHD severity.
May 29, 2025 at 5:01 PM
6/🧬
📈 DecompTCR uncovers which clones persist, expand, and associate with GVHD severity.
📈 DecompTCR uncovers which clones persist, expand, and associate with GVHD severity.
5/ 🧬
🧪 We developed StarfyshHD, a spatial transcriptomics analysis tool tailored for Visium HD data to integrate multiple samples, map fine-grained cell states, and identify spatial hubs (unique composition of cell types).
🧪 We developed StarfyshHD, a spatial transcriptomics analysis tool tailored for Visium HD data to integrate multiple samples, map fine-grained cell states, and identify spatial hubs (unique composition of cell types).
May 29, 2025 at 4:59 PM
5/ 🧬
🧪 We developed StarfyshHD, a spatial transcriptomics analysis tool tailored for Visium HD data to integrate multiple samples, map fine-grained cell states, and identify spatial hubs (unique composition of cell types).
🧪 We developed StarfyshHD, a spatial transcriptomics analysis tool tailored for Visium HD data to integrate multiple samples, map fine-grained cell states, and identify spatial hubs (unique composition of cell types).
3/🧬 We built #DecompTCR, a new model to resolve T cell clonal dynamics over time.
May 29, 2025 at 4:55 PM
3/🧬 We built #DecompTCR, a new model to resolve T cell clonal dynamics over time.
2/🧬
🎯 Why it matters:
GVHD is a leading cause of mortality post-transplant. We show that its pathology is driven not just by T cell infiltration, but by clonal expansion and dynamic phenotypic shifts in the gut.
🎯 Why it matters:
GVHD is a leading cause of mortality post-transplant. We show that its pathology is driven not just by T cell infiltration, but by clonal expansion and dynamic phenotypic shifts in the gut.
May 29, 2025 at 4:49 PM
2/🧬
🎯 Why it matters:
GVHD is a leading cause of mortality post-transplant. We show that its pathology is driven not just by T cell infiltration, but by clonal expansion and dynamic phenotypic shifts in the gut.
🎯 Why it matters:
GVHD is a leading cause of mortality post-transplant. We show that its pathology is driven not just by T cell infiltration, but by clonal expansion and dynamic phenotypic shifts in the gut.
1/🧬 This is the first 🧭🧬 spatiotemporal single-cell atlas of human GVHD.
We combined 🧪 Mixed Lymphocyte Reaction, 🧬 TCR tracking, 🔬 single-cell RNA-seq, and 🗺️ spatial transcriptomics to map how donor T cells evolve 🔁, move 🧗♂️, and damage tissue 💥 after transplant.
We combined 🧪 Mixed Lymphocyte Reaction, 🧬 TCR tracking, 🔬 single-cell RNA-seq, and 🗺️ spatial transcriptomics to map how donor T cells evolve 🔁, move 🧗♂️, and damage tissue 💥 after transplant.
May 29, 2025 at 4:48 PM
1/🧬 This is the first 🧭🧬 spatiotemporal single-cell atlas of human GVHD.
We combined 🧪 Mixed Lymphocyte Reaction, 🧬 TCR tracking, 🔬 single-cell RNA-seq, and 🗺️ spatial transcriptomics to map how donor T cells evolve 🔁, move 🧗♂️, and damage tissue 💥 after transplant.
We combined 🧪 Mixed Lymphocyte Reaction, 🧬 TCR tracking, 🔬 single-cell RNA-seq, and 🗺️ spatial transcriptomics to map how donor T cells evolve 🔁, move 🧗♂️, and damage tissue 💥 after transplant.