Evidence map›Paper›PMID 40814001›Full record

ArticleGenome medicine2025

SCAN-ACT: adoptive T cell therapy target discovery through single-cell transcriptomics.

Stefano Testa, Aastha Pal, Ajay Subramanian, Sushama Varma, Jack Pengfei Tang, Danielle Graham, Sara Arfan, Minggui Pan, Nam Q Bui, Kristen N Ganjoo and 6 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genome medicine, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

3 citing papers in PubMed.

  1. Article
  2. Review
  3. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

16 authors.

Stefano TestaDepartment of Medicine, Stanford University, Stanford, CA, USA.
Aastha PalDepartment of Radiation Oncology, Stanford University, Stanford, CA, USA.
Ajay SubramanianDepartment of Radiation Oncology, Stanford University, Stanford, CA, USA.
Sushama VarmaDepartment of Pathology, Stanford University, Stanford, CA, USA.
Jack Pengfei TangDepartment of Pediatrics, Boston Children's Hospital, Boston, MA, USA.
Danielle GrahamDepartment of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
Sara ArfanDivision of Molecular Pathology, The Institute of Cancer Research, London, UK.
Minggui PanDivision of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA.
Nam Q BuiDivision of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA.
Kristen N GanjooDivision of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA.
Sarah DryDepartment of Pathology, University of California, Los Angeles, CA, USA.
Paul HuangDivision of Molecular Pathology, The Institute of Cancer Research, London, UK.
Matt van de RijnDepartment of Pathology, Stanford University, Stanford, CA, USA.
Wei JiangJWE Science Technology, Inc, Beijing, China.
Anusha KalbasiDepartment of Radiation Oncology, Stanford University, Stanford, CA, USA. akalbasi@stanford.edu.
Everett J ModingDepartment of Radiation Oncology, Stanford University, Stanford, CA, USA. emoding@stanford.edu.

Funding

Targeting Radiation-Induced Myeloid Cells to Promote T cell Immunity in Undifferentiated Pleomorphic SarcomaK08CA245181 · NCI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI KALBASI, ANUSHA · 2020 to 2025
$1.1M
Cancer Research Institute CRI14104NCI NIH HHS K08 CA245181NIH HHS K08CA245181
6 · The paper itself

Abstract

backgroundThe FDA approval of T cell receptor-engineered T cells (TCR-T) for synovial sarcoma demonstrates the potential for adoptive T cell therapies (ACTs) in solid tumors. However, the paucity of tumor-associated targets without expression in normal tissues remains a major bottleneck, especially in rare cancer subtypes.

methodsWe developed a comprehensive computational pipeline called SCAN-ACT that leverages single-cell RNA sequencing and multi-omics data from tumor and normal tissues to nominate and prioritize putative targets for both chimeric antigen receptor (CAR)- and TCR-T cells. For surface membrane targets, SCAN-ACT proposes monospecific targets and potential target pairs for bispecific Boolean logic-gated CAR T cells. For peptide-MHC targets, SCAN-ACT proposes intracellular peptides bound to a diverse set of human leukocyte antigens. Selected targets were validated experimentally by protein expression and for peptide-MHC binding.

resultsWe applied the SCAN-ACT pipeline to soft tissue sarcoma (STS), analyzing 986,749 single cells to identify and prioritize 395 monospecific CAR-T targets, 14,192 bispecific CAR-T targets, and 5020 peptide-MHC targets for TCR-T cells. Proposed targets and target pairs reflected the mesenchymal, neuronal, and hematopoietic ontogeny of STS. We further validated SCAN-ACT in glioblastoma revealing its versatility.

conclusionsThis work provides a robust data repository along with a web-based and user-friendly set of analysis tools to accelerate ACT development for solid tumors ( https://scanact.stanford.edu/ ).

Indexed as

Computational BiologyImmunotherapy, AdoptiveSingle-Cell Gene Expression AnalysisHumansInternetMolecular Targeted TherapyReceptors, Chimeric AntigenSarcomaT-LymphocytesUser-Computer InterfaceReceptors, Chimeric AntigenCAR-T cellsCellular therapyImmunotherapyLogic-gated CAR-TPeptide-centric CAR-TSingle-cell RNA sequencingSoft tissue sarcomaTCR-T cells

Identifiers

PMID40814001
PMCPMC12351953

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.