ArticleCellular oncology (Dordrecht, Netherlands)2024
Robust detection of clinically relevant features in single-cell RNA profiles of patient-matched fresh and formalin-fixed paraffin-embedded (FFPE) lung cancer tissue.
Article in Cellular oncology (Dordrecht, Netherlands), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
What it found
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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.
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Who cites it
11 citing papers in PubMed, 14 citations in OpenAlex.
- Single nucleus RNA profiling reveals potential therapeutic vulnerabilities in sinonasal carcinomas.NPJ precision oncology · 2026Article
- New biological insights into osteosarcoma-lessons from single cell sequencing studies.Cancer metastasis reviews · 2026Review
- Probing the Feasibility of Single-Cell Fixed RNA Sequencing from FFPE Tissue.International journal of molecular sciences · 2026Article
- Single-nucleus RNA sequencing identifies a novel tenogenic heterologous differentiation in endometrial carcinosarcomas: implications for diagnosis and tumor classification.The Journal of pathology · 2026Article
- Single-cell profiling defines the cellular landscape of the urinary bladder: a scoping review.European journal of medical research · 2026Review
- Article
- Cancer genomics and bioinformatics in Latin American countries: applications, challenges, and perspectives.Frontiers in oncology · 2025Review
- Genetic and therapeutic heterogeneity shape the baseline and longitudinal immune ecosystem of ovarian clear cell carcinoma.Journal for immunotherapy of cancer · 2024Article
- snPATHO-seq, a versatile FFPE single-nucleus RNA sequencing method to unlock pathology archives.Communications biology · 2024Article
- Single-cell and single-nucleus RNA-sequencing from paired normal-adenocarcinoma lung samples provide both common and discordant biological insights.PLoS genetics · 2024Article
- Single-Nucleus RNA-Seq: Open the Era of Great Navigation for FFPE Tissue.International journal of molecular sciences · 2023Review
Corrections and comments
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Authors and funding
9 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
purposeSingle-cell transcriptional profiling reveals cell heterogeneity and clinically relevant traits in intra-operatively collected patient-derived tissue. So far, single-cell studies have been constrained by the requirement for prospectively collected fresh or cryopreserved tissue. This limitation might be overcome by recent technical developments enabling single-cell analysis of FFPE tissue.
methodsWe benchmark single-cell profiles from patient-matched fresh, cryopreserved and archival FFPE cancer tissue.
resultsWe find that fresh tissue and FFPE routine blocks can be employed for the robust detection of clinically relevant traits on the single-cell level. Specifically, single-cell maps of fresh patient tissues and corresponding FFPE tissue blocks could be integrated into common low-dimensional representations, and cell subtype clusters showed highly correlated transcriptional strengths of signaling pathway, hallmark, and clinically useful signatures, although expression of single genes varied due to technological differences. FFPE tissue blocks revealed higher cell diversity compared to fresh tissue. In contrast, single-cell profiling of cryopreserved tissue was prone to artifacts in the clinical setting.
conclusionOur analysis highlights the potential of single-cell profiling in the analysis of retrospectively and prospectively collected archival pathology cohorts and increases the applicability in translational research.
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Registered trials
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.