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Models that recapitulate the complexity of human tumors are urgently needed to develop more effective cancer therapies. We report a bank of human patient-derived xenografts (PDXs) and matched organoid cultures from tumors that represent the greatest unmet need: endocrine-resistant, treatment-refractory and metastatic breast cancers. We leverage matched PDXs and PDX-derived organoids (PDxO) for drug screening that is feasible and cost-effective with in vivo validation. Moreover, we demonstrate the feasibility of using these models for precision oncology in real time with clinical care in a case of triple-negative breast cancer (TNBC) with early metastatic recurrence. Our results uncovered a Food and Drug Administration (FDA)-approved drug with high efficacy against the models. Treatment with this therapy resulted in a complete response for the individual and a progression-free survival (PFS) period more than three times longer than their previous therapies. This work provides valuable methods and resources for functional precision medicine and drug development for human breast cancer.

Development of candidate cancer treatments is a resource-intensive process, with the research community continuing to investigate options beyond static genomic characterization. Toward this goal, we have established the genomic landscapes of 536 patient-derived xenograft (PDX) models across 25 cancer types, together with mutation, copy number, fusion, transcriptomic profiles, and NCI-MATCH arms. Compared with human tumors, PDXs typically have higher purity and fit to investigate dynamic driver events and molecular properties via multiple time points from same case PDXs. Here, we report on dynamic genomic landscapes and pharmacogenomic associations, including associations between activating oncogenic events and drugs, correlations between whole-genome duplications and subclone events, and the potential PDX models for NCI-MATCH trials. Lastly, we provide a web portal having comprehensive pan-cancer PDX genomic profiles and source code to facilitate identification of more druggable events and further insights into PDXs’ recapitulation of human tumors., Patient-derived xenograft models (PDX) have been extensively used to study the molecular and clinical features of cancers. Here the authors present a cohort of 536 PDX models from 25 cancers, as well as their genomic and evolutionary profiles and their suitability for clinical trials.

Patient-derived xenografts (PDXs) model human intra-tumoral heterogeneity in the context of the intact tissue of immunocompromised mice. Histological imaging via hematoxylin and eosin (H&E) staining is performed on PDX samples for routine assessment and, in principle, captures the complex interplay between tumor and stromal cells. Deep learning (DL)-based analysis of large human H&E image repositories has extracted inter-cellular and morphological signals correlated with disease phenotype and therapeutic response. Here, we present an extensive, pan-cancer repository of nearly 1,000 PDX and paired human progenitor H&E images. These images, curated from the PDXNet consortium, are associated with genomic and transcriptomic data, clinical metadata, pathological assessment of cell composition, and, in several cases, detailed pathological annotation of tumor, stroma, and necrotic regions. We demonstrate that DL can be applied to these images to classify tumor regions with an accuracy of 0.87. Further, we show that DL can predict xenograft-transplant lymphoproliferative disorder, the unintended outgrowth of human lymphocytes at the transplantation site, with an accuracy of 0.97. This repository enables PDX-specific investigations of cancer biology through histopathological analysis and contributes important model system data that expand on existing human histology repositories. We expect the PDXNet Image Repository to be valuable for controlled digital pathology analysis, both for the evaluation of technical issues such as stain normalization and for development of novel computational methods based on spatial behaviors within cancer tissues. Citation Format: Brian S. White, Xing Yi Woo, Soner Koc, Todd Sheridan, Steven B. Neuhauser, Shidan Wang, Yvonne A. Evrard, John David Landua, R Jay Mashl, Sherri R. Davies, Bingliang Fang, Maria Gabriela Raso, Kurt W. Evans, Matthew H. Bailey, Yeqing Chen, Min Xiao, Jill Rubinstein, Ali Foroughi pour, Lacey Elizabeth Dobrolecki, Maihi Fujita, Junya Fujimoto, Guanghua Xiao, Ryan C. Fields, Jacqueline L. Mudd, Xiaowei Xu, Melinda G. Hollingshead, Shahanawaz Jiwani, PDXNet consortium, Tiffany A. Wallace, Jeffrey A. Moscow, James H. Doroshow, Nicholas Mitsiades, Salma Kaochar, Chong-xian Pan, Moon S. Chen, Luis G. Carvajal-Carmona, Alana L. Welm, Bryan E. Welm, Ramaswamy Govindan, Shunqiang Li, Michael A. Davies, Jack A. Roth, Funda Meric-Bernstam, Yang Xie, Meenhard Herlyn, Li Ding, Michael T. Lewis, Carol J. Bolt, Dennis A. Dean, Jeffrey H. Chuang. A pan-cancer PDX histology image repository with genomic and pathological annotations for deep learning analysis. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5407.

Background Metastatic breast cancer (MBC) is incurable, with a 5-year survival rate of 28%. In the USA, more than 42,000 patients die from MBC every year. The most common type of breast cancer is estrogen receptor-positive (ER+), and more patients die from ER+ breast cancer than from any other subtype. ER+ tumors can be successfully treated with hormone therapy, but many tumors acquire endocrine resistance, at which point treatment options are limited. There is an urgent need for model systems that better represent human ER+ MBC in vivo, where tumors can metastasize. Patient-derived xenografts (PDX) made from MBC spontaneously metastasize, but the immunodeficient host is a caveat, given the known role of the immune system in tumor progression and response to therapy. Thus, we attempted to develop an immune-humanized PDX model of ER+ MBC. Methods NSG-SGM3 mice were immune-humanized with CD34+ hematopoietic stem cells, followed by engraftment of human ER+ endocrine resistant MBC tumor fragments. Strategies for exogenous estrogen supplementation were compared, and immune-humanization in blood, bone marrow, spleen, and tumors was assessed by flow cytometry and tissue immunostaining. Characterization of the new model includes assessment of the human tumor microenvironment performed by immunostaining. Results We describe the development of an immune-humanized PDX model of estrogen-independent endocrine resistant ER+ MBC. Importantly, our model harbors a naturally occurring ESR1 mutation, and immune-humanization recapitulates the lymphocyte-excluded and myeloid-rich tumor microenvironment of human ER+ breast tumors. Conclusion This model sets the stage for development of other clinically relevant models of human breast cancer and should allow future studies on mechanisms of endocrine resistance and tumor-immune interactions in an immune-humanized in vivo setting.

Model systems that recapitulate the complexity of human tumors and the reality of variable treatment responses are urgently needed to better understand cancer biology and to develop more effective cancer therapies. Here we report development and characterization of a large bank of patient-derived xenografts (PDX) and matched organoid cultures from tumors that represent some of the greatest unmet needs in breast cancer research and treatment. These include endocrine-resistant, treatment-refractory, and metastatic breast cancers and, in some cases, multiple tumor collections from the same patients. The models can be grown long-term with high fidelity to the original tumors. We show that development of matched PDX and PDX-derived organoid (PDxO) models facilitates high-throughput drug screening that is feasible and cost-effective, while also allowing in vivo validation of results. Our data reveal consistency between drug screening results in organoids and drug responses in breast cancer PDX. Moreover, we demonstrate the feasibility of using these patient-derived models for precision oncology in real time with patient care, using a case of a triple negative breast cancer with early metastatic recurrence as an example. Our results uncovered an FDA-approved drug with high efficacy against the models. Treatment with the PDxO-directed therapy resulted in a complete response for the patient and a progression-free survival period more than three times longer than her previous therapies. This work provides valuable new methods and resources for functional precision medicine and drug development for human breast cancer.Graphical Abstract

Additional file of Navitoclax enhances the effectiveness of EGFR-targeted antibody-drug conjugates in PDX models of EGFR-expressing triple-negative breast cancer

Additional file 1: Supplementary tables and figures.

Patient-derived xenografts (PDX) are valuable, clinically-relevant models of cancer. Their close genomic, phenotypic, and temporal association with patient tumors makes them well-suited for pre-clinical and co-clinical studies that assess the potential of new therapeutics. However, PDX models are not amenable to large-scale drug sensitivity studies due to their high cost and low throughput capacity. To address this, we established and characterized long-term PDX organoid (PDxO) cultures from breast cancer (BC) PDXs and evaluated their utility in therapeutic studies. To establish PDxO culture conditions, we extensively tested medium supplements, including growth factors, kinase inhibitors, conditioned medium, and antioxidants, along with extracellular matrix composition in 3D gels. Using optimized culture conditions for each BC subtype, we established PDxOs from 16 PDX lines in the HCI series, with a PDX to PDxO success rate of 85%. Around 20% of PDxOs contained aggressive mouse stroma, which had to be eliminated by FACS for long-term culture success. PDxOs were maintained for over 1 year, during which we tracked viability, doubling time, organoid size, genomics, epithelial character, and tumorigenicity. Doubling times stabilized after 60 days of initial culture, with a mean of 6.4±1.7 days for triple negative (TN) lines and 7.2±1 days for ER+ lines. Mean organoid size remained stable, with ER+ PDxOs significantly smaller than TN PDxOs, at 91 and 262 cells/organoid respectively (p=0.0012). PDxOs histologically resembled their PDX counterparts when stained for H&E, Vimentin, and CAM 5.2. RNA-Seq and copy-number variation analyses showed that PDxOs clustered with their PDXs and patient tumors. To assess if culturing affected tumorigenicity, we re-implanted PDxOs into mice following early and late passaging. 5/5 early passage and 5/6 late passage PDxOs engrafted and formed tumors. Resulting tumors showed similar gene expression profiles as their original PDXs by RNA-Seq. These data suggest that PDxOs generally recapitulate the molecular and genomic features of their originating PDXs and patient tumors. Having established PDxO cultures, we evaluated their utility as a therapeutic screening platform. We developed a screen to differentiate compounds with cytotoxic and cytostatic effects. NCI CTEP and clinically-approved BC therapies (n=40) were screened in quadruplicate 8-point dose response curves on all 16 PDxOs across three biological replicates. Drug response profiles were stable across biological replicates, spanning up to 1 year in culture. PDxOs exhibited diverse responses to therapies targeting cIAP1, PI3K, and CHK1/2. Initial work to evaluate concordance between PDxO and in vivo PDX responses returned trending linear correlations between PDxO dose response data and change in PDX growth rate following treatment (R2 = 0.52-0.77; p = 0.045-0.12, across 3 PDXs and 9 compounds). Ongoing work aims to confirm concordance between PDX and PDxO models. Our work demonstrates that PDxO models are cost-efficient, easy to maintain, and grow indefinitely - making them renewable and accessible cancer models. PDxOs are a powerful parallel resource to PDX models, especially useful for efficient determination of PDX drug response. We are currently expanding our PDxO bank to include 100 models which will be deposited with the NCI as part of the PDXNet effort. Citation Format: Katrin P. Guillen, Sandra D. Scherer, Yi Qiao, Satya S. Pathi, James M. Graham, Maihi Fujita, Yoko S. DeRose, Jason Gertz, Gabor T. Marth, Katherine E. Varley, Alana L. Welm, Bryan E. Welm. Predicting breast cancer therapy response using a patient-derived xenograft organoid screening platform [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr LB-038.

Aim Breast cancer is the second leading cause of cancer death in women, yet only a few antigens are available for directing immune therapies to a patient’s breast tumor. In this study we establish a new system for identifying tumor-specific antigens presented by the class I HLA of breast tumors. Our approach relies on generating a breast cancer HLA peptide-ligand reference database coupled with isolation of peptides from the HLA of patient-derived breast cancer xenografts (PDX). This HLA PDX approach can rapidly identify targets for existing and emerging cancer immune therapies. Methods A tumor-specific HLA reference peptide ligand library was constructed using 3 breast epithelial tumor cell lines and 1 healthy breast epithelial line. Cells were transfected to secrete HLA-A∗02:01, secreted HLA was affinity purified, HLA-bound peptides were eluted, separated by HPLC, and HLA-A∗02:01 breast cancer peptides were analyzed by mass spectroscopy. To validate the peptides as relevant targets for human breast tumors in vivo, HLA was extracted from PDX-derived tumors and the presence of specific peptides were confirmed in these primary tumors. Results In 20 PDX tumor lines, 7 of the tumors were A∗02:01, half of which expressed detectable A∗02:01. When evaluated for candidate peptide:HLA expression, the HCI-015 triple negative PDX xenograft expressed high levels of the Macrophage Inhibitory Factor 19–27 (MIF) peptide, a peptide that is expressed solely in breast cancer cell lines and primary tumors but not healthy tissues. We are currently expanding HCI-015 PDX for additional HLA extractions. Conclusions These data suggest that PDX tumors can be used as surrogates to human tumors for the direct identification of tumor-specific antigens. The use of a peptide library generated from several breast cancer cell lines allows peptides to be identified with increased sensitivity. Furthermore, expression of the candidate MIF 19-27 peptide on HCI-015 provides compelling evidence that certain tumor-antigens are conserved among cell lines, tumors, and in vivo models of breast cancer. Such antigens provide a unique therapeutic window that can be exploited for targeted immunotherapies.