Evidence map›Paper›PMID 36604765›Full record

ArticleJournal of experimental & clinical cancer research : CR2023

"Proteotranscriptomic analysis of advanced colorectal cancer patient derived organoids for drug sensitivity prediction".

Federica Papaccio, Blanca García-Mico, Francisco Gimeno-Valiente, Manuel Cabeza-Segura, Valentina Gambardella, María Fernanda Gutiérrez-Bravo, Clara Alfaro-Cervelló, Carolina Martinez-Ciarpaglini, Pilar Rentero-Garrido, Sheila Zúñiga-Trejos and 10 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Journal of experimental & clinical cancer research : CR, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.

0numbers the graph read from it
0cells of the map it votes in
50citing papers in PubMed
21.3field-weighted citation impact, top 1% of its field
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

50 citing papers in PubMed, 85 citations in OpenAlex.

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  7. From mono- to multi-cellularFrontiers in cell and developmental biology · 2026
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  10. Multiscale Construction, Evaluation, and Application of Organoids.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025
    Review
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  13. Integrative RNA-seq analysis reveals immune-related hub genesInternational journal of reproductive biomedicine · 2025
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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

20 authors at 4 institutions in 4 countries.

Federica PapaccioDepartment of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, Via S. Allende, 84081, Baronissi, Italy. fpapaccio@unisa.it.
Blanca García-MicoDepartment of Medical Oncology, Hospital Clínico Universitario de Valencia, INCLIVA Biomedical Research Institute, University of Valencia, Avda. Blasco Ibañez 17, 46010, Valencia, Spain.
Francisco Gimeno-ValienteUniversity College London Cancer Institute, Cancer Evolution and Genome Instability Laboratory, London, UK.
Manuel Cabeza-SeguraDepartment of Medical Oncology, Hospital Clínico Universitario de Valencia, INCLIVA Biomedical Research Institute, University of Valencia, Avda. Blasco Ibañez 17, 46010, Valencia, Spain.
Valentina GambardellaDepartment of Medical Oncology, Hospital Clínico Universitario de Valencia, INCLIVA Biomedical Research Institute, University of Valencia, Avda. Blasco Ibañez 17, 46010, Valencia, Spain.
María Fernanda Gutiérrez-BravoDepartment of Medical Oncology, Hospital Clínico Universitario de Valencia, INCLIVA Biomedical Research Institute, University of Valencia, Avda. Blasco Ibañez 17, 46010, Valencia, Spain.
Clara Alfaro-CervellóDepartment of Pathology, Hospital Clínico Universitario, INCLIVA Biomedical Research Institute, University of Valencia, Avda. Blasco Ibañez 17, 46010, Valencia, Spain.
Carolina Martinez-CiarpagliniCentro de Investigación Biomédica en Red (CIBERONC), Instituto de Salud Carlos III, 28029, Madrid, Spain.
Pilar Rentero-GarridoPrecision Medicine Unit, INCLIVA Biomedical Research Institute, University of Valencia, Avda. Blasco Ibañez 17, 46010, Valencia, Spain.
Sheila Zúñiga-TrejosBioinformatic and Biostatistic Unit, INCLIVA Biomedical Research Institute, University of Valencia, Avda. Blasco Ibañez 17, 46010, Valencia, Spain.
Juan Antonio Carbonell-AsinsBioinformatic and Biostatistic Unit, INCLIVA Biomedical Research Institute, University of Valencia, Avda. Blasco Ibañez 17, 46010, Valencia, Spain.
Tania FleitasDepartment of Medical Oncology, Hospital Clínico Universitario de Valencia, INCLIVA Biomedical Research Institute, University of Valencia, Avda. Blasco Ibañez 17, 46010, Valencia, Spain.
Susana RosellóDepartment of Medical Oncology, Hospital Clínico Universitario de Valencia, INCLIVA Biomedical Research Institute, University of Valencia, Avda. Blasco Ibañez 17, 46010, Valencia, Spain.
Marisol HuertaDepartment of Medical Oncology, Hospital Clínico Universitario de Valencia, INCLIVA Biomedical Research Institute, University of Valencia, Avda. Blasco Ibañez 17, 46010, Valencia, Spain.
Manuel M Sánchez Del PinoUniversity Institute of Biotechnology and Biomedicine (BIOTECMED), University of Valencia, 46100, Burjassot, Spain.
Luís SabaterLiver, Biliary and Pancreatic Unit, Department of Surgery, Hospital Clínico Universitario of Valencia, University of Valencia, INCLIVA Biomedical Research Institute, University of Valencia, Avda. Blasco Ibañez 17, 46010, Valencia, Spain.
Desamparados RodaDepartment of Medical Oncology, Hospital Clínico Universitario de Valencia, INCLIVA Biomedical Research Institute, University of Valencia, Avda. Blasco Ibañez 17, 46010, Valencia, Spain.
Noelia TarazonaDepartment of Medical Oncology, Hospital Clínico Universitario de Valencia, INCLIVA Biomedical Research Institute, University of Valencia, Avda. Blasco Ibañez 17, 46010, Valencia, Spain.
Andrés CervantesDepartment of Medical Oncology, Hospital Clínico Universitario de Valencia, INCLIVA Biomedical Research Institute, University of Valencia, Avda. Blasco Ibañez 17, 46010, Valencia, Spain. andres.cervantes@uv.es.ORCID http://orcid.org/0000-0003-3806-3691
Josefa CastilloDepartment of Medical Oncology, Hospital Clínico Universitario de Valencia, INCLIVA Biomedical Research Institute, University of Valencia, Avda. Blasco Ibañez 17, 46010, Valencia, Spain. pepa.castillo@uv.es.
Universitat de València · ESInstituto de Salud Carlos III · ESLondon Cancer · GBUniversity of Salerno · IT

Funding

Conselleria d'Educació, Investigació, Cultura i Esport GRISOLIAP/2017/161European Society for Medical Oncology ESMO Translational Research Fellowship 2018-2020Fundación Científica Asociación Española Contra el Cáncer predoctoral grantGeneralitat Valenciana APOSTD/2021/168Generalitat Valenciana PROMETEU/2019/065Instituto de Salud Carlos III 2018 grantInstituto de Salud Carlos III Joan Rodés contract JR16/00040Instituto de Salud Carlos III Joan Rodés contract JR17/00026Instituto de Salud Carlos III Joan Rodés contract JR20/00005Instituto de Salud Carlos III Joan Rodés contract JR21/00042Instituto de Salud Carlos III PI18/01508Instituto de Salud Carlos III PI18/01909Instituto de Salud Carlos III PI21/00689Instituto de Salud Carlos III PI21/0693Ministerio de Ciencia e Innovación PID2020-119111GB-I00Universitat de València and INCLIVA VLC Bioclinic grant 2021/257
6 · The paper itself

Abstract

backgroundPatient-derived organoids (PDOs) from advanced colorectal cancer (CRC) patients could be a key platform to predict drug response and discover new biomarkers. We aimed to integrate PDO drug response with multi-omics characterization beyond genomics.

methodsWe generated 29 PDO lines from 22 advanced CRC patients and provided a morphologic, genomic, and transcriptomic characterization. We performed drug sensitivity assays with a panel of both standard and non-standard agents in five long-term cultures, and integrated drug response with a baseline proteomic and transcriptomic characterization by SWATH-MS and RNA-seq analysis, respectively.

resultsPDOs were successfully generated from heavily pre-treated patients, including a paired model of advanced MSI high CRC deriving from pre- and post-chemotherapy liver metastasis. Our PDOs faithfully reproduced genomic and phenotypic features of original tissue. Drug panel testing identified differential response among PDOs, particularly to oxaliplatin and palbociclib. Proteotranscriptomic analyses revealed that oxaliplatin non-responder PDOs present enrichment of the t-RNA aminoacylation process and showed a shift towards oxidative phosphorylation pathway dependence, while an exceptional response to palbociclib was detected in a PDO with activation of MYC and enrichment of chaperonin T-complex protein Ring Complex (TRiC), involved in proteome integrity. Proteotranscriptomic data fusion confirmed these results within a highly integrated network of functional processes involved in differential response to drugs.

conclusionsOur strategy of integrating PDOs drug sensitivity with SWATH-mass spectrometry and RNA-seq allowed us to identify different baseline proteins and gene expression profiles with the potential to predict treatment response/resistance and to help in the development of effective and personalized cancer therapeutics.

Indexed as

Antineoplastic AgentsColorectal NeoplasmsHumansOrganoidsOxaliplatinProteomicsAntineoplastic AgentsOxaliplatinColorectal cancerDrug resistanceOrganoidsPrecision medicineProteotranscriptomics integrative functional network analysisQuantitative proteomicsTranscriptomics

Identifiers

PMID36604765
PMCPMC9817273
OpenAlexW4313648324

What OpenQuestion holds

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LicenceCC BY
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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.