A rapid platform for 3D patient-derived cutaneous neurofibroma organoid establishment and screening

Abstract

Localized cutaneous neurofibromas (cNFs) are benign tumors that arise in the dermis of patients affected by Neurofibromatosis Type 1 syndrome (NF1). cNFs are fundamentally benign lesions: they do not undergo malignant transformation or metastasize. Nevertheless, in NF1 patients, they can cover a significant proportion of the body, with some individuals developing hundreds to thousands of lesions. cNFs can cause pain, itching, and disfigurement with substantial socio-emotional repercussions. To date, surgical removal or laser desiccation are the only treatment options, but can result in scarring and the leave a potential for regrowth. To support drug discovery efforts focused on identifying effective systemic therapies for cNF, we introduce an approach to routinely establish and screen cNF tumor organoids. We optimized conditions to support ex vivo growth of genomically-diverse cNFs. Patient-derived cNF organoids closely recapitulate the molecular and cellular heterogeneity of these tumors as measured by immunohistopathology, DNA methylation, RNA-seq and flow cytometry. Our tractable patient-derived cNF organoid platform enables rapid screening of hundreds of compounds in a patient- and tumor-specific manner.

The landscape of drug sensitivity and resistance in sarcoma

“…The specimens included in this study were procured through the UCLA Pathology Department and expedited to the lab for processing following our published protocols as described in the Methods section (Figure 1A) 17,26,[28][29][30] . Given that there is no a priori sorting of tumor cells, we performed a detailed histopathological analysis of all organoids and parental tissue to verify that tumor cells are present and all main features are maintained ex vivo 26,29 (Figure 1A and 2).…”

“…A total of 40 samples were frozen, including 19 that were procured during COVID-related shutdowns and interruptions. The remaining n=124 samples corresponding to 80% of all samples that were processed, were used to generate mini-rings 17,26,[28][29][30] in 96 well plates for high throughput drug screening. These encompassed 21 different sarcoma diagnoses.…”

“…The drug library utilized in our study includes over 400 compounds and drug combinations in different stages of clinical and pre-clinical development (Figure 3A-B) 26,28,29 . For each sample, we customized a panel of drugs to be screened based on sample characteristics, histology, a priori patient-specific information, and clinical data.…”

“…We have procured n=194 specimens from 126 patients undergoing biopsies or surgical resections at UCLA Health Hospitals and successfully generated PDTOs from over 121 samples originating from primary, recurrent and metastatic bone and soft tissue sarcomas. Here we describe our pipeline for procuring and generating sarcoma PDTOs which include histopathology to characterize both the parent tumor and PDTOs as well as sequencing and high throughput drug testing leveraging our rapid 3D organoid screening platform 17,26,[28][29][30] . The drug sensitivity and resistance patterns observed across 24 sarcoma types pinpointed both subtype-specific and patient-specific vulnerabilities.…”