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Patient-derived organoids model treatment response of metastatic gastrointestinal cancers

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Science  23 Feb 2018:
Vol. 359, Issue 6378, pp. 920-926
DOI: 10.1126/science.aao2774
  • Fig. 1 Histopathological, molecular, and functional characterization of patient-derived organoids (PDOs).

    (A) Phase-contrast image of a mCRC PDO culture (top) and hematoxylin and eosin staining comparing organoids to their matching patient biopsy (bottom). (B) Intestinal and diffuse growth patterns are retained in mGOC PDOs. (C) ERBB2 amplification and overexpression in mGOC PDOs and parental tissue biopsy (CISH, chromogenic in situ hybridization; IHC, immunohistochemistry). (D) Heatmap showing the most frequently mutated and/or copy number–altered genes in PDOs (left) and Venn diagram demonstrating 96% mutational overlap between PDOs and parental tissue biopsies (right). (E) Target engagement in genotype–drug phenotype combinations: pathway analysis downstream of ERBB2 in ERBB2-amplified and nonamplified PDOs treated with lapatinib (24 hours) (right), BRAF inhibition (24 hours) (center), and AKT inhibition (4 hours) (left). wt, wild type. (F) Concentration-dependent effect of the dual PI3K/mTOR inhibitor GDC-0980 in three PDOs from patient R-009, all carrying an acquired PIK3CA mutation (H1047R). PDOs established from a liver metastasis biopsied at disease progression (R-009 PD-A) that also harbored PIK3CA amplification showed concentration-dependent response to GDC-0980. PIK3CA-mutant but nonamplified PDOs established before regorafenib treatment (R-009 BL) or from a different liver metastasis biopsied at disease progression (R-009 PD-B) did not respond to GDC-0980. Viability data shown are means ± SEM of indicated independent experiments. (G) Correlation (Fisher’s exact test) between presence of RB1 amplification in PDOs (D) and response to the CDK4/CDK6 inhibitor palbociclib in the reported drug screen (fig. S9A). BL, baseline; SD, stable disease; PD, posttreatment/progressive disease.

  • Fig. 2 PDO-based ex vivo co-clinical trials in mGOC and mCRC.

    (A) PDOs were generated from sequential biopsies of a liver metastasis (red circles in the bottom panel) of mGOC patient F-014 that showed initial response to paclitaxel (F-014 BL) and subsequently progressed (F-014 PD). Violet bars indicate overall tumor volume [according to RECIST (Response Evaluation Criteria in Solid Tumors) 1.1], and red bars indicate volume of the target metastasis used to generate PDOs. (B) Cell viability upon paclitaxel treatment was compared in BL and PD PDOs from patient F-014 and PDOs from patients that exhibited primary (F-015) or acquired (F-012) resistance to paclitaxel in the clinic. Viability data shown are means ± SEM of indicated independent experiments. (C) Cell cycle analysis upon paclitaxel treatment in the F-014 BL PDO compared with the F-014 PD PDO. DMSO, dimethyl sulfoxide. (D) Concentration-dependent DNA damage was observed in the F-014 BL PDO in response to paclitaxel but not in PDOs from the same patient established at PD. (E) PDOs were established from BL (C-003 and C-004) and PD (C-001 and C-002) biopsies from patients treated with the anti-EGFR monoclonal antibody cetuximab. PDOs were treated with cetuximab in vitro; data shown are means ± SD from independent experiments performed in triplicate. (F) Molecular analysis of BL and PD PDOs, matching biopsy (tumor), and primary bowel cancer (archival); arrows indicate the presence of clonal or subclonal mutations in BRAF or KRAS, respectively, in two patients. VAF, variant allele frequency; FFPE, formalin-fixed paraffin-embedded.

  • Fig. 3 PDO-based co-clinical trials mimic primary and acquired resistance to regorafenib in mice.

    (A) mCRC patients on regorafenib treatment underwent biopsies at BL, SD, or PD. An early reduction (15 days) in functional imaging (DCE-MRI) parameters correlated with changes in microvasculature assessed by CD31 staining and clinical benefit from regorafenib (right). Arrowheads indicate CRC metastases; Ktrans, volume transfer constant. (B) Changes in microvasculature in response to regorafenib were assessed in PDO-xenografts in mice by quantification of tumor-associated CD31-positive vessels. Data show PDO-xenografts from a primary resistant patient (R-009) and a long-term responder (R-005) to regorafenib. Means ± SD from the indicated number of mice (n) in a representative experiment are shown; significance was determined using Student’s unpaired t test. (C) Reduction in fractional blood volume (fBV) in regorafenib-treated mice carrying long-term regorafenib responder (R-005) PDO-xenografts. A total of 10 animals were analyzed (five in each arm); shown are the means ± SD of an individual experiment. Day 0 fBV values could not be obtained for two animals owing to respiratory movement. Significance was determined using Student’s paired t test for fBV and unpaired t test for CD31 and necrosis. (D) Schematic representation of the animal experiment using PDOs from patient R-011, established pre- and posttreatment with regorafenib. Mice carrying liver orthotopic R-011 pretreatment (BL) and posttreatment (PD) PDO-xenografts were randomized to control and treatment arms and treated with vehicle or regorafenib for 10 days. After treatment, each arm was further randomized to a cohort culled for histopathological analysis and a survival cohort, which was monitored over time. (E) CD31 immunostaining in the parental patient BL, SD, and PD biopsies, demonstrating an initial reduction in tumor microvasculature in response to regorafenib. Shown are means ± SD calculated by scoring 10 high-power-field tumor areas. (F) Representative images (top) and analysis (bottom) of CD31 immunostaining in the BL and PD R-011 PDO-xenografts. Shown are means ± SD calculated by scoring at least 10 high-power-field tumor areas per animal in an individual experiment; n, number of animals analyzed in each group. Significance was determined using Student’s unpaired t test. (G) Kaplan-Mayer curves for regorafenib- or vehicle-treated mice bearing BL and PD PDO-xenografts from patient R-011 from an individual experiment (n, number of mice analyzed). Significance was determined using the Mantel-Cox log-rank test.

  • Fig. 4 PDOs recapitulate intra- and interpatient heterogeneity in response to TAS-102.

    (A) PDOs were established from a patient (R-019) with mixed response to TAS-102. Whereas the segment 2 metastasis rapidly progressed, the segment 5 metastasis remained stable upon TAS-102 treatment (white arrowheads in the CT scan indicate metastases; bars represent pre- and posttreatment measurements of the indicated metastases). (B) Ex vivo concentration-response curves in BL and PD multiregion PDOs from patient R-019 (with mixed response to TAS-102). (C) TK1 IHC expression in TAS-102–refractory (segment 2) and –sensitive (segment 5) PDOs. (D) Cell viability (left) and TK1 mRNA expression (right) in PDOs from TAS-102–responsive and –refractory patients. In (B) and (D), N indicates the number of independent experiments, and viability values are expressed as means ± SEM.

Supplementary Materials

  • Patient-derived organoids model treatment response of metastatic gastrointestinal cancers

    Georgios Vlachogiannis, Somaieh Hedayat, Alexandra Vatsiou, Yann Jamin, Javier Fernández-Mateos, Khurum Khan, Andrea Lampis, Katherine Eason, Ian Huntingford, Rosemary Burke, Mihaela Rata, Dow-Mu Koh, Nina Tunariu, David Collins, Sanna Hulkki-Wilson, Chanthirika Ragulan, Inmaculada Spiteri, Sing Yu Moorcraft, Ian Chau, Sheela Rao, David Watkins, Nicos Fotiadis, Maria Bali, Mahnaz Darvish-Damavandi, Hazel Lote, Zakaria Eltahir, Elizabeth C. Smyth, Ruwaida Begum, Paul A. Clarke, Jens C. Hahne, Mitchell Dowsett, Johann de Bono, Paul Workman, Anguraj Sadanandam, Matteo Fassan, Owen J. Sansom, Suzanne Eccles, Naureen Starling, Chiara Braconi, Andrea Sottoriva, Simon P. Robinson, David Cunningham, Nicola Valeri

    Materials/Methods, Supplementary Text, Tables, Figures, and/or References

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    • Materials and Methods
    • Supplementary Text
    • Figs. S1 to S13
    • References
    Tables S1 and S3 to S8
    Table S2

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