{rfName}
A

Indexed in

License and use

Citations

185

Altmetrics

Analysis of institutional authors

Rubio-Pérez CAuthor
Share
Publications
>
Article

A single-cell tumor immune atlas for precision oncology.

Publicated to:Genome Research. 31 (10): 1913-1926 - 2021-10-01 31(10), DOI: 10.1101/gr.273300.120

Authors: Nieto P; Elosua-Bayes M; Trincado JL; Marchese D; Massoni-Badosa R; Salvany M; Henriques A; Nieto J; Aguilar-Fernández S; Mereu E; Moutinho C; Ruiz S; Lorden P; Chin VT; Kaczorowski D; Chan CL; Gallagher R; Chou A; Planas-Rigol E; Rubio-Perez C; Gut I; Piulats JM; Seoane J; Powell JE; Batlle E; Heyn H

Affiliations

Cancer Diagnosis and Pathology Group, Kolling Institute of Medical Research, Royal North Shore Hospital, St. Leonards NSW 2065, Australia.; NSW Health Pathology, Department of Anatomical Pathology, Royal North Shore Hospital, Sydney NSW 2065, Australia.; - Author
CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain. - Author
CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain.; Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain. - Author
Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Darlinghurst NSW 2010, Sydney, Australia. - Author
Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Darlinghurst NSW 2010, Sydney, Australia.; St. Vincent's Hospital Clinical School, University of New South Wales, Sydney, Australia, and St. Vincent's Hospital Sydney, Dar - Author
Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Darlinghurst NSW 2010, Sydney, Australia.; UNSW Cellular Genomics Futures Institute, University of New South Wales, Sydney NSW 2052, Australia. - Author
Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, 08028 Barcelona, Spain. - Author
Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, 08028 Barcelona, Spain.; Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain.; CIBERONC, 08908 Barcelona, Spain. - Author
Medical Oncology Department, Institut Català d'Oncologia - ICO; Clinical Research in Solid Tumors Group - CREST, Bellvitge Biomedical Research Institute IDIBELL-OncoBell; CIBERONC; 08908 L'Hospitalet de Llobregat, Barcelona, Spain. - Author
St. Vincent's Hospital Sydney, Darlinghurst NSW 2010, Australia.; University of Notre Dame, Chippendale NSW 2007, Sydney, Australia. - Author
Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, 08035 Barcelona, Spain. - Author
Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, 08035 Barcelona, Spain.; Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain.; Universitat Autònoma de Barcelona (UAB), 08193 Barcelona, Spain.; C - Author
See more

Abstract

The tumor immune microenvironment is a main contributor to cancer progression and a promising therapeutic target for oncology. However, immune microenvironments vary profoundly between patients, and biomarkers for prognosis and treatment response lack precision. A comprehensive compendium of tumor immune cells is required to pinpoint predictive cellular states and their spatial localization. We generated a single-cell tumor immune atlas, jointly analyzing published data sets of >500,000 cells from 217 patients and 13 cancer types, providing the basis for a patient stratification based on immune cell compositions. Projecting immune cells from external tumors onto the atlas facilitated an automated cell annotation system. To enable in situ mapping of immune populations for digital pathology, we applied SPOTlight, combining single-cell and spatial transcriptomics data and identifying colocalization patterns of immune, stromal, and cancer cells in tumor sections. We expect the tumor immune cell atlas, together with our versatile toolbox for precision oncology, to advance currently applied stratification approaches for prognosis and immunotherapy.

Keywords
Biomarkers, tumorHumansImmunotherapyNeoplasmsPrecision medicinePrognosisTumor microenvironment

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal Genome Research due to its progression and the good impact it has achieved in recent years, according to the agency WoS (JCR), it has become a reference in its field. In the year of publication of the work, 2021, it was in position 11/175, thus managing to position itself as a Q1 (Primer Cuartil), in the category Genetics & Heredity. Notably, the journal is positioned above the 90th percentile.

From a relative perspective, and based on the normalized impact indicator calculated from the Field Citation Ratio (FCR) of the Dimensions source, it yields a value of: 31.17, which indicates that, compared to works in the same discipline and in the same year of publication, it ranks as a work cited above average. (source consulted: Dimensions May 2025)

Specifically, and according to different indexing agencies, this work has accumulated citations as of 2025-05-19, the following number of citations:

  • Scopus: 87
  • Europe PMC: 98
  • OpenCitations: 96
Impact and social visibility

From the perspective of influence or social adoption, and based on metrics associated with mentions and interactions provided by agencies specializing in calculating the so-called "Alternative or Social Metrics," we can highlight as of 2025-05-19:

  • The use, from an academic perspective evidenced by the Altmetric agency indicator referring to aggregations made by the personal bibliographic manager Mendeley, gives us a total of: 298.
  • The use of this contribution in bookmarks, code forks, additions to favorite lists for recurrent reading, as well as general views, indicates that someone is using the publication as a basis for their current work. This may be a notable indicator of future more formal and academic citations. This claim is supported by the result of the "Capture" indicator, which yields a total of: 298 (PlumX).

With a more dissemination-oriented intent and targeting more general audiences, we can observe other more global scores such as:

  • The Total Score from Altmetric: 101.6.
  • The number of mentions on the social network Facebook: 1 (Altmetric).
  • The number of mentions on the social network X (formerly Twitter): 120 (Altmetric).

It is essential to present evidence supporting full alignment with institutional principles and guidelines on Open Science and the Conservation and Dissemination of Intellectual Heritage. A clear example of this is:

  • The work has been submitted to a journal whose editorial policy allows open Open Access publication.
Leadership analysis of institutional authors

This work has been carried out with international collaboration, specifically with researchers from: Australia.