Pancreatic ductal adenocarcinoma (PDAC) is a dismaldisease with a fast evolution and unpredictable treatmentresponse. Nowadays, FOLFIRINOX and gemcitabine are the preferred treatments with a response rateof 33% and 11%, respectively. This poor patient responsehas been associated with an inefficient/non-personalizedtreatment allocation. Consequently, developing a rapidand efficient preclinical tool to test tumor drug sensitivityfor each patient is hugely needed. Biopsy patient-derivedorganoid (PDO) appears to be a promising tool for devel-oping individualized treatments for patients with PDAC.Several PDO-based platforms are in development world-wide as a guide to optimize therapy by directing tailored treatments.Fil: Fraunhoffer Navarro, Nicolas Alejandro. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Centro de Estudios Farmacológicos y Botánicos. Universidad de Buenos Aires. Facultad de Medicina. Centro de Estudios Farmacológicos y Botánicos; Argentina. Aix-Marseille University; FranciaFil: Abuelafia, Analía Meilerman. Aix-Marseille University; FranciaFil: Dusetti, Nelson. Aix-Marseille University; FranciaFil: Iovanna, Juan Lucio. Aix-Marseille University; Franci

Abuelafia, Analía Meilerman

Dusetti, Nelson

Fraunhoffer Navarro, Nicolas Alejandro

Iovanna, Juan Lucio

Cancer Communications

English

PubMed

CONICET Digital

Received: 19 February 2022 Revised: 27 April 2022 Accepted: 4 July 2022DOI: 10.1002/cac2.12335LETTER TO TH E EDITORLimitation and challenges in using pancreaticcancer-derived organoids as a preclinical toolDear Editor,Pancreatic ductal adenocarcinoma (PDAC) is a dismaldisease with a fast evolution and unpredictable treatmentresponse. Nowadays, FOLFIRINOX [1] and gemcitabine[2] are the preferred treatments with a response rateof 33% and 11%, respectively. This poor patient responsehas been associated with an inefficient/non-personalizedtreatment allocation. Consequently, developing a rapidand efficient preclinical tool to test tumor drug sensitivityfor each patient is hugely needed. Biopsy patient-derivedorganoid (PDO) appears to be a promising tool for devel-oping individualized treatments for patients with PDAC.Several PDO-based platforms are in development world-wide as a guide to optimize therapy by directing tailoredtreatments. A critical point to consider PDO as promisingis that it must represent the great clinical heterogene-ity of PDAC as much as possible. Moreover, PDO hasdisplayed histological features that mimic the PDAC phe-notype. These characteristics make PDO an interestingoption to obtaining reliable chemo-response profiles at areasonable timeframe for most PDAC patients. However,although PDO has potential advantages as a preclinicaltool, several concerns related to their phenotype stabilityin culture have recently arisen. Specifically, PDO culturemedia contain several growth factors and small-moleculeinhibitors, which induce phenotypic modifications fromthe original tumor that could be easily evaluated at thetranscriptome level. This is a central point consideringthat PDAC drug sensitivity highly depends on the tran-scriptomic phenotype [3–6]. Therefore, is PDO a faithfulmodel that reproduces in vitro the huge phenotypicalAbbreviations: 5-FU, 5-fluorouracil; CDA, cytidine deaminase;HC-PAMG, High contributive genes from the PDAC molecular gradient;ICA, Independent component analysis; IGF1, Insulin-like growth factor1; LGR5, Leucine-Rich Repeat Containing G Protein-Coupled Receptor5; LGR6, Leucine-Rich Repeat Containing G Protein-Coupled Receptor6; PDAC, Pancreatic ductal adenocarcinoma; PDC, Patient-derived cellcultures; PDO, Patient-derived organoids; RSPO1, R-Spondin 1; WNT3A,Wingless-Type MMTV Integration Site Family, Member 3A; WNT7B,Wingless-Type MMTV Integration Site Family, Member 7B.This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License, which permits use and distribution in any medium,provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.© 2022 The Authors. Cancer Communications published by John Wiley & Sons Australia, Ltd. on behalf of Sun Yat-sen University Cancer Center.heterogeneity observed in PDAC? Here, we analyzed thetranscriptome of several PDAC preclinical models in asso-ciation with the chemo-response profile for gemcitabine,5-fluorouracil (5-FU), oxaliplatin and irinotecan. Further-more, we characterized the pathways associated withPDO-specific phenotype.Transcriptome dispersion was computed for PDO,patient-derived cell culture (PDC), patient-derivedxenograft (PDX), and PDAC tumors using inter-sampleEuclidean distance on the gene sets that define PurIST [5],the Chan-Seng-Yue classifier [7], and the high contributivegenes from the PDAC molecular gradient (HC-PAMG)[6]. These three well-known stratification patterns arestrongly associated with PDAC prognosis and drugresponse phenotype. PDO displayed the lowest transcrip-tomic dispersion compared with PDC, PDX, and PDACtumors in all the tested gene sets (Figure 1A). Moreover,we observed that the low transcriptome variability ofPDO was accompanied with an extreme enrichment ina classical phenotype (Figure 1B). On the contrary, PDCshowed a strong displacement toward basal-like/basalA, whereas PDX was the most diverse and proximal toPDAC tumor displaying all the subtypes described by theChan-Seng-Yue classifier (Figure 1B).To further investigate the association between the tran-scriptome variability and the drug response profile amongthese preclinical models, 43 PDOs, 54 PDCs, and 18 PDXswere evaluated for gemcitabine, 5-FU, oxaliplatin, andirinotecan (Supplementary Figure S1A). A strong associa-tion between the degree of transcriptome dispersion andresponse profile was observed. PDO showed the lowestrange of chemo-response measured by the area under thecurve (AUC) for the four anti-cancer drugs, followed byPDC and PDX (Figure 1C). These observations were con-firmed in a paired scheme where PDX was the preclinicalmodel with the broadest response (Figure 1D).Next, we analyzed the potential PDO phenotype drivers.Independent component analysis (ICA) was performedusing PDAC molecular gradient calculated with HC-PAMG as a reference parameter. The ICA4 component1028 wileyonlinelibrary.com/journal/cac2 Cancer Communications. 2022;42:1028–1031.LETTER TO THE EDITOR 1029F IGURE 1 Analysis of transcriptome heterogeneity and chemo-response profiles of preclinical models for PDAC. (A) Thetranscriptomic dispersion of PDO, PDC, PDX, and PDAC tumors was estimated through inter-sample euclidean distance using the three genesets that define PurIST, Chan-Seng-Yue classifier, and HC-PAMG. The B-F ANOVA test following Dunnett’s multiple-comparison test wasapplied. (B) For each preclinical model and PDAC tumors, stratification was performed using the PurIST, Chan-Seng-Yue classifier, andHC-PAMG. (C) The area under the curve was estimated to compare the chemo-response variability of 43 PDOs, 54 PDCs, and 18 PDXs forgemcitabine, 5-fluorouracil, oxaliplatin, and irinotecan. AUC inter-preclinical model variance was tested using the F test. (D) Thechemo-response variability was also estimated in a paired setting between the three preclinical models. Boxplot data are represented as themedian ±max/min; *P < 0.05, **P < 0.01, ***P < 0.001, and ****P < 0.0001. Abbreviations: PDAC, pancreatic ductal adenocarcinoma; PDC,patient-derived cell culture; PDO, patient-derived organoid; PDX, patient-derived xenograft; HC-PAMG, high contributive genes from thePDAC molecular gradient; B-T, Brown-Forsythe; a.u., arbitrary unitsshowed the highest correlationwithHC-PAMG (r= 0.57, P= 0.002, Supplementary Figure S1B). Pathway enrichmentanalysis on the ICA4 component revealed that Wnt signal-ing was a strong promoter of the PDO phenotype (Supple-mentary Figure S1C). Moreover, we identified that PDOhad significantly higher WNT7B, LGR5, and LGR6 levelsthan PDC, PDX, and PDAC tumors (Supplementary FigureS1D). These observations were confirmed by differentialexpression analysis between PDO and PDAC tumors (Sup-plementary Figure S1E, Supplementary Table S1), wherewe detected activation of the Wnt signaling pathway andcell cycle in PDO compared to PDAC tumors (Supplemen-tary Table S1). Additionally, we analyzed the expression ofbiomarkers associated with gemcitabine response, such ascytidine deaminase (CDA) [4] and insulin-like growth fac-tor 1 (IGF1) [8]. CDA displayed a strong association withthe gemcitabine response profile for the preclinical mod-els and PDAC tumors, whereas IGF1 did not associate withgemcitabine response (Supplementary Figure S1F).The findings provided by the current analysis vali-date the association between the transcriptomic variabilityand drug response in the PDAC preclinical models andhighlight the limitations associated with the model set-tings. Specifically, we demonstrated that PDO displayed areduced transcriptomic variability compared to PDC andPDX. This limited heterogeneity is reflected in the nar-row chemo-response profile for the most common PDACanti-cancer drugs. In addition, our results suggest a strongrole of theWnt/R-spondin signaling as a driver of the PDOphenotype, which could be triggered by PDO culture con-ditions. These observations are aligned with recent studiesthat demonstrated a PDO-specific profile is highly diver- 25233548, 2022, 10, Downloaded from https://onlinelibrary.wiley.com/doi/10.1002/cac2.12335 by Cochrane France, Wiley Online Library on [11/06/2023]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License1030 LETTER TO THE EDITORgent from the source PDAC biopsy [9]. A potential strategyto overcome the observed limitations of PDO is to mod-ify the culture medium to capture PDAC heterogeneity,similar to the strategy proposed for breast cancer [10].In conclusion, although the PDO is a promising tool forstudying PDAC biology, we must consider the current lim-itations of this model for its use in a clinical setting, suchas determining treatment protocol. Moreover, the lack ofrecapitulation of PDAC heterogeneity associated with areduced response spectrum for the anti-cancer drugs indi-cates that further optimization is needed. Therefore, theculture conditions need to be improved to avoid a pheno-typic polarization mediated by the over-activation of theWnt/R-spondin pathways.DECLARATIONSACKNOWLEDGMENTSThis work was supported by National Institute of Cancer(Grants number 2019-37, 2018-078 and 2018-079), AmidexFoundation and National Institute of Health and MedicalResearch.CONFL ICTS OF INTERESTThe authors declare no potential conflicts of interestAUTH ORS ’ CONTRIBUT IONSNAF and AMA: acquisition of data; analysis and inter-pretation of data; drafting of the manuscript; statisticalanalysis;ND: study concept and design; analysis and interpre-tation of data; critical revision of the manuscript forimportant intellectual content; obtained funding; studysupervision;JI: study concept and design; analysis and interpretationof data; drafting of the manuscript; critical revision of themanuscript for important intellectual content; obtainedfunding; study supervision.ETH ICS APPROVAL AND CONSENT TOPART IC IPATEThe study was approved by the local ethics committee(Comité de protection des personnes Sud MéditerranéeI) following patient informed consent collection. ThePaCaOmics study was registered at www.clinicaltrials.govwith registration number NCT01692873. PDAC sampleswere collected between January 2012 and December 2015.All experimental procedures on animals were approved bythe Comité d’éthique de Marseille numéro 14 (C2EA-14).CONSENT FOR PUBL ICAT IONNot applicable.DATA AVAILAB IL ITY STATEMENTICGC-PACA-AU Seq expression dataset was downloadedfrom the International Cancer Genome Consortium(ICGC) data portal (https://dcc.icgc.org/). TCGA-PAADwas downloaded using The Cancer Genome Atlas (TCGA)biolinks R package. PDX dataset is available from Array-Express (https://www.ebi.ac.uk/arrayexpress/) under theaccession number E-MTAB-5039.Nicolas A. Fraunhoffer1,2Analía Meilerman Abuelafia1Nelson Dusetti1Juan Iovanna11Cancer Research Center of Marseille, Inserm,Paoli-Calmettes Institut, Aix-Marseille University, Scientificand Technological Park of Luminy, Marseille 13288, France2Buenos Aires University, Center for Pharmacological andBotanical Studies, Faculty of Medicine, National Councilfor Scientific and Technical Research, Buenos AiresC1121ABG, ArgentinaCorrespondenceJuan Iovanna, Cancer Research Center of Marseille,Inserm, Paoli-Calmettes Institut, Aix-MarseilleUniversity, Scientific and Technological Park of Luminy,Marseille, 13288, France.Email: juan.iovanna@inserm.frORCIDNelsonDusetti https://orcid.org/0000-0002-6161-8483Juan Iovanna https://orcid.org/0000-0003-1822-2237REFERENCES1. Conroy T, Hammel P, Hebbar M, Ben Abdelghani M, Wei AC,Raoul JL, et al. FOLFIRINOX or Gemcitabine as Adjuvant Ther-apy for Pancreatic Cancer. N Engl J Med. 2018;379(25):2395–406.2. Burris HA, Moore MJ, Andersen J, Green MR, Rothenberg ML,Modiano MR, et al. Improvements in survival and clinical ben-efit with gemcitabine as first- line therapy for patients withadvanced pancreas cancer: A randomized trial. J Clin Oncol.1997;15(6):2403–13.3. Aung KL, Fischer SE, Denroche RE, Jang GH, Dodd A,Creighton S, et al. Genomics-driven precision medicine foradvanced pancreatic cancer: Early results from the COMPASStrial. Clin Cancer Res. 2018;24(6):1344–54.4. Nicolle R, Gayet O, Duconseil P, Vanbrugghe C, Roques J,Bigonnet M, et al. A transcriptomic signature to predict adju-vant gemcitabine sensitivity in pancreatic adenocarcinoma.AnnOncol. 2021;32(2):250–60.5. Rashid NU, Peng XL, Jin C, Moffitt RA, Volmar KE, BeltBA, et al. Purity Independent Subtyping of Tumors (PurIST),A Clinically Robust, Single-sample Classifier for Tumor Sub-typing in Pancreatic Cancer. Clin Cancer Res. 2020;26(1):82–92. 25233548, 2022, 10, Downloaded from https://onlinelibrary.wiley.com/doi/10.1002/cac2.12335 by Cochrane France, Wiley Online Library on [11/06/2023]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons LicenseLETTER TO THE EDITOR 10316. Nicolle R, Blum Y, Duconseil P, Vanbrugghe C, Brandone N,Poizat F, et al. Establishment of a pancreatic adenocarcinomamolecular gradient (PAMG) that predicts the clinical outcomeof pancreatic cancer. EBioMedicine. 2020;57(102858).7. Chan-Seng-Yue M, Kim JC, Wilson GW, Ng K, Figueroa EF,O’Kane GM, et al. Transcription phenotypes of pancreatic can-cer are driven by genomic events during tumor evolution. NatGenet. 2020;52(2):231–40.8. Turaga RC, Sharma M, Mishra F, Krasinskas A, Yuan Y, YangJJ, et al. Modulation of Cancer-Associated Fibrotic Stromaby An Integrin αvβ3 Targeting Protein for Pancreatic Can-cer Treatment. Cell Mol Gastroenterol Hepatol. 2021;11(1):161-79. Available from: https://doi.org/10.1016/j.jcmgh.2020.08.0049. Raghavan S, Winter PS, Navia AW, Williams HL, DenAdel A,Lowder KE, et al. Microenvironment drives cell state, plasticity,and drug response in pancreatic cancer. Cell. 2021;184(25):6119–6137.e26.10. Guillen KP, Fujita M, Butterfield AJ, Scherer SD, Bailey MH,Chu Z, et al. A human breast cancer-derived xenograft andorganoid platform for drug discovery and precision oncology.Nat Cancer. 2022;3:232–50.SUPPORT ING INFORMATIONAdditional supporting information can be found onlinein the Supporting Information section at the end of thisarticle. 25233548, 2022, 10, Downloaded from https://onlinelibrary.wiley.com/doi/10.1002/cac2.12335 by Cochrane France, Wiley Online Library on [11/06/2023]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License

Limitation and challenges in using pancreatic cancer-derived organoids as a preclinical tool

Nicolas A. Fraunhoffer

Analía Meilerman Abuelafia

Nelson Dusetti

Juan Iovanna

Crossref

Limitation and challenges in using pancreatic cancer‐derived organoids as a preclinical tool

LAReferencia - Red Federada de Repositorios Institucionales de Publicaciones Científicas Latinoamericanas

Fraunhoffer, Nicolas A.

Iovanna, Juan

PubMed Central

https://ri.conicet.gov.ar/bitstream/11336/213097/2/CONICET_Digital_Nro.469565ac-339e-4e96-89e7-f62b73b92790_B.pdf

Limitation and challenges in using pancreatic cancer-derived organoids as a preclinical tool

Abstract

Similar works

Full text

Available Versions

CONICET Digital

Crossref

LAReferencia - Red Federada de Repositorios Institucionales de Publicaciones Científicas Latinoamericanas

PubMed Central