Spatially Resolved Panoramic in vivo CRISPR Screen via Perturb-DBiT Article Swipe
Rong Fan
,
Alev Baysoy
,
Xiaolong Tian
,
Feifei Zhang
,
Paul Renauer
,
Zhiliang Bai
,
Hao Shi
,
Dingyao Zhang
,
Haikuo Li
,
Bo Tao
,
Mingyu Yang
,
Archibald Enninful
,
Fu Gao
,
Guangchuan Wang
,
Wanqiu Zhang
,
Thao Tran
,
Nathan Heath Patterson
,
Jie Sheng
,
Shuozhen Bao
,
Chuanpeng Dong
,
Xin Shan
,
Binfan Chen
,
Mei Zhong
,
Sherri L. Rankin
,
Cliff Guy
,
Yan Wang
,
Jon P. Connelly
,
Shondra M. Pruett‐Miller
,
Daifeng Wang
,
Mina L. Xu
,
Mark Gerstein
,
Hongbo Chi
,
Sidi Chen
·
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.21203/rs.3.rs-6481967/v1
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.21203/rs.3.rs-6481967/v1
Spatially resolved in vivo CRISPR screening integrates gene editing with spatial transcriptomics to examine how genetic perturbations alter gene expression within native tissue environments. However, current methods are limited to small perturbation panels and the detection of a narrow subset of protein-coding RNAs. We present Perturb-DBiT, a distinct and versatile approach for the simultaneous co-sequencing of spatial total RNA whole-transcriptome and single-guide RNAs (sgRNAs), base-by-base, on the same tissue section. This method enables unbiased discovery of how genetic perturbations influence RNA regulation, cellular dynamics, and tissue architecture in situ. Applying Perturb-DBiT to a human cancer metastatic colonization model, we mapped large panels of sgRNAs across tumor colonies in consecutive tissue sections alongside their corresponding total RNA transcriptomes. This revealed novel insights into how perturbations affect long non-coding RNA (lncRNA) co-variation, microRNA–mRNA interactions, and global and distinct tRNA alterations in amino acid metabolism linked to tumor migration and growth. By integrating transcriptional pseudotime trajectories, we further uncovered the impact of perturbations on clonal dynamics and cooperation. In an immune-competent syngeneic mouse model, Perturb-DBiT enabled investigation of genetic perturbations within the tumor immune microenvironment, revealing distinct and synergistic effects on immune infiltration and suppression. Perturb-DBiT provides a spatially resolved comprehensive view of how genetic knockouts influence diverse molecular and cellular responses including small and large RNA regulation, tumor proliferation, migration, metastasis, and immune interactions, offering a panoramic perspective on perturbation responses in complex tissues.
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Metadata
- Type
- preprint
- Language
- en
- Landing Page
- https://doi.org/10.21203/rs.3.rs-6481967/v1
- https://www.researchsquare.com/article/rs-6481967/latest.pdf
- OA Status
- gold
- Cited By
- 14
- References
- 61
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4410186021
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4410186021Canonical identifier for this work in OpenAlex
- DOI
-
https://doi.org/10.21203/rs.3.rs-6481967/v1Digital Object Identifier
- Title
-
Spatially Resolved Panoramic in vivo CRISPR Screen via Perturb-DBiTWork title
- Type
-
preprintOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2025Year of publication
- Publication date
-
2025-05-08Full publication date if available
- Authors
-
Rong Fan, Alev Baysoy, Xiaolong Tian, Feifei Zhang, Paul Renauer, Zhiliang Bai, Hao Shi, Dingyao Zhang, Haikuo Li, Bo Tao, Mingyu Yang, Archibald Enninful, Fu Gao, Guangchuan Wang, Wanqiu Zhang, Thao Tran, Nathan Heath Patterson, Jie Sheng, Shuozhen Bao, Chuanpeng Dong, Xin Shan, Binfan Chen, Mei Zhong, Sherri L. Rankin, Cliff Guy, Yan Wang, Jon P. Connelly, Shondra M. Pruett‐Miller, Daifeng Wang, Mina L. Xu, Mark Gerstein, Hongbo Chi, Sidi ChenList of authors in order
- Landing page
-
https://doi.org/10.21203/rs.3.rs-6481967/v1Publisher landing page
- PDF URL
-
https://www.researchsquare.com/article/rs-6481967/latest.pdfDirect link to full text PDF
- Open access
-
YesWhether a free full text is available
- OA status
-
goldOpen access status per OpenAlex
- OA URL
-
https://www.researchsquare.com/article/rs-6481967/latest.pdfDirect OA link when available
- Concepts
-
CRISPR, Computer science, Biology, Genetics, GeneTop concepts (fields/topics) attached by OpenAlex
- Cited by
-
14Total citation count in OpenAlex
- Citations by year (recent)
-
2025: 14Per-year citation counts (last 5 years)
- References (count)
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61Number of works referenced by this work
- Related works (count)
-
10Other works algorithmically related by OpenAlex
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| publication_date | 2025-05-08 |
| publication_year | 2025 |
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