Spatially Resolvedin vivoCRISPR Screen Sequencing via Perturb-DBiT Article Swipe
Alev Baysoy
,
Xiaolong Tian
,
Feifei Zhang
,
Paul Renauer
,
Zhiliang Bai
,
Hao Shi
,
Haikuo Li
,
Bo Tao
,
Mingyu Yang
,
Archibald Enninful
,
Fu Gao
,
Guangchuan Wang
,
Wanqiu Zhang
,
Thao Tran
,
Nathan Heath Patterson
,
Shuozhen Bao
,
Chuanpeng Dong
,
Xin Shan
,
Mei Zhong
,
Sherri L. Rankin
,
Cliff Guy
,
Yan Wang
,
Jon P. Connelly
,
Shondra M. Pruett‐Miller
,
Hongbo Chi
,
Sidi Chen
,
Rong Fan
·
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.1101/2024.11.18.624106
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.1101/2024.11.18.624106
SUMMARY Perturb-seq enabled the profiling of transcriptional effects of genetic perturbations in single cells but lacks the ability to examine the impact on tissue environments. We present Perturb-DBiT for simultaneous co- sequencing of spatial transcriptome and guide RNAs (gRNAs) on the same tissue section for in vivo CRISPR screen with genome-scale gRNA libraries, offering a comprehensive understanding of how genetic modifications affect cellular behavior and tissue architecture. This platform supports a variety of delivery vectors, gRNA library sizes, and tissue preparations, along with two distinct gRNA capture methods, making it adaptable to a wide range of experimental setups. In applying Perturb-DBiT, we conducted un-biased knockouts of tens of genes or at genome-wide scale across three cancer models. We mapped all gRNAs in individual colonies and corresponding transcriptomes in a human cancer metastatic colonization model, revealing clonal dynamics and cooperation. We also examined the effect of genetic perturbation on the tumor immune microenvironment in an immune-competent syngeneic model, uncovering differential and synergistic perturbations in promoting immune infiltration or suppression in tumors. Perturb-DBiT allows for simultaneously evaluating the impact of each knockout on tumor initiation, development, metastasis, histopathology, and immune landscape. Ultimately, it not only broadens the scope of genetic inquiry, but also lays the groundwork for developing targeted therapeutic strategies.
Related Topics
Metadata
- Type
- preprint
- Language
- en
- Landing Page
- https://doi.org/10.1101/2024.11.18.624106
- https://www.biorxiv.org/content/biorxiv/early/2024/11/19/2024.11.18.624106.full.pdf
- OA Status
- green
- Cited By
- 37
- References
- 116
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4404511829
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4404511829Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1101/2024.11.18.624106Digital Object Identifier
- Title
-
Spatially Resolvedin vivoCRISPR Screen Sequencing via Perturb-DBiTWork title
- Type
-
preprintOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2024Year of publication
- Publication date
-
2024-11-19Full publication date if available
- Authors
-
Alev Baysoy, Xiaolong Tian, Feifei Zhang, Paul Renauer, Zhiliang Bai, Hao Shi, Haikuo Li, Bo Tao, Mingyu Yang, Archibald Enninful, Fu Gao, Guangchuan Wang, Wanqiu Zhang, Thao Tran, Nathan Heath Patterson, Shuozhen Bao, Chuanpeng Dong, Xin Shan, Mei Zhong, Sherri L. Rankin, Cliff Guy, Yan Wang, Jon P. Connelly, Shondra M. Pruett‐Miller, Hongbo Chi, Sidi Chen, Rong FanList of authors in order
- Landing page
-
https://doi.org/10.1101/2024.11.18.624106Publisher landing page
- PDF URL
-
https://www.biorxiv.org/content/biorxiv/early/2024/11/19/2024.11.18.624106.full.pdfDirect link to full text PDF
- Open access
-
YesWhether a free full text is available
- OA status
-
greenOpen access status per OpenAlex
- OA URL
-
https://www.biorxiv.org/content/biorxiv/early/2024/11/19/2024.11.18.624106.full.pdfDirect OA link when available
- Concepts
-
CRISPR, Computational biology, In vivo, Biology, Computer science, Genetics, GeneTop concepts (fields/topics) attached by OpenAlex
- Cited by
-
37Total citation count in OpenAlex
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2025: 37Per-year citation counts (last 5 years)
- References (count)
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116Number of works referenced by this work
- Related works (count)
-
10Other works algorithmically related by OpenAlex
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