Pancreatic adenocarcinoma human organoids share structural and genetic features with primary tumors

Abstract

Patient-derived pancreatic ductal adenocarcinoma (PDAC) organoid systems show great promise for understanding the biological underpinnings of disease and advancing therapeutic precision medicine. Despite the increased use of organoids, the fidelity of molecular features, genetic heterogeneity, and drug response to the tumor of origin remain important unanswered questions limiting their utility. To address this gap in knowledge, we created primary tumor- and PDX-derived organoids, and 2D cultures for in-depth genomic and histopathological comparisons to the primary tumor. Histopathological features and PDAC representative protein markers showed strong concordance. DNA and RNA sequencing of single organoids revealed patient-specific genomic and transcriptomic consistency. Single-cell RNAseq demonstrated that organoids are primarily a clonal population. In drug response assays, organoids displayed patient-specific sensitivities. Additionally, we examined the in vivo PDX response to FOLFIRINOX and Gemcitabine/Abraxane treatments, which was recapitulated in vitro by organoids. The patient-specific molecular and histopathological fidelity of organoids indicate that they can be used to understand the etiology of the patient’s tumor and the differential response to therapies and suggests utility for predicting drug responses.

Automated microfluidic platform for dynamic and combinatorial drug screening of tumor organoids

“…Patient 2 was the most sensitive to the 72-h gemcitabine and temporally-delivered gemcitabine + 5-FU. This is consistent with previously published organoid sensitivity data 8 using traditional plate-based testing methods. In the clinic, patient 2 received adjuvant rounds of gemcitabine followed by FOLFIRINOX with dose reduction before ultimately being transferred into hospice.…”

“…feeding were optimized using the high-throughput features of the system to ensure a suitable environment where the cells could proliferate and ultimately grow into 3D glandular structures. The cellular phenotypes of PDAC organoids grown on our platform were then compared to traditional plate-based experiments and other known tumor tissue characteristics for these same organoids in previously published work 8 (Fig. 2b).…”

“…The formation of multilumen structures with a high degree of cytologic atypia seen in patient 1 in contrast to the well-differentiated cysts in patient 4 were consistent between platforms. The contrasting patient morphologies are a reflection of the organoids ability to reflect the individualized characteristics of the tumor they are derived from, which is retained between the platforms 8 . To accommodate the entire 3D structure, we took multiple Z image slices or stacks to fully image the entire volume of each organoid (Fig.…”

“…Patient-derived organoids have several advantages as personalized tumor models. Primary cancer tumor cells cultured as 2D monolayers do not reflect the heterogeneity of the primary tumor due to selection in culture, tissue-specific architecture, and mechanical stresses, while tumor organoids can overcome these deficiencies [6][7][8] . Patient-derived cancer tumor organoids can be established in a shorter period and are much more economical than costly patient-derived xenograft (PDX) models, which requires a large tissue sample, up to 6 months to establish tumor growth, and retains complications from infiltrating murine stromal cells 9,10 .…”