Sequencing of 3D Organoids Derived From Colorectal Cancer Patients

This study focuses on the whole-exome sequencing (WES) of patient-derived organoids (PDOs) established from colorectal cancer (CRC) tumors collected at Columbia University. CRC remains a major cause of cancer-related mortality due to its metastatic progression and resistance to therapy. To model CRC at the patient level, we generated 3D organoid cultures from primary and metastatic tumors, preserving their genetic and phenotypic characteristics. The study cohort consists of 9 CRC patients with microsatellite-stable adenocarcinomas from the ascending, transverse, and descending colon, as well as the rectum, with differentiation statuses ranging from well to moderate and moderate-poor. Notably, for one patient, we generated organoids from both the primary tumor and matched liver metastases, allowing for a comparative analysis of tumor evolution. PDOs were derived from these tumors and subjected to WES at early passage to profile somatic mutations, copy number variations, and other genomic alterations to identify mutational signatures. Mutations identified in the PDOs were cross-referenced and confirmed with mutational data from the Columbia Solid Tumor Panel, which was conducted on all tumor tissues prior to organoid establishment. Molecular technologies employed include next-generation sequencing (NGS) for WES, enabling high-resolution characterization of the genomic landscape of CRC PDOs. WES of PDOs allowed us to classify tumor samples based on oncogenic mutations and mutation types, with a specific focus on PIK3CA. Notably, the efficacy of PI3Kα-specific pharmacologic inhibitors in suppressing organoid growth was dependent on the mutational status of KRAS and PIK3CA, underscoring the importance of genomic context in therapeutic response. The dataset available through dbGaP includes raw WES data from CRC PDOs.]]>
Inclusion Criteria:Diagnosis: Patients diagnosed with microsatellite-stable (MSS) colorectal adenocarcinoma.Tumor source: Primary and/or metastatic CRC tumor tissues obtained for organoid generation.Tumor location: Tumors originating from the ascending, transverse, and descending colon, or rectum.Patient sample availability: Tumor tissues must be available for patient-derived organoid (PDO) establishment.Consent: Patients must have provided informed consent for tumor tissue collection, genetic sequencing, and data sharing for research purposes.Molecular analysis: Tumor samples must have undergone Columbia Solid Tumor Panel analysis prior to PDO establishment.Exclusion Criteria:Molecular instability: Patients with microsatellite instability-high (MSI-H) tumors are excluded.Non-adenocarcinoma histology: Patients with non-adenocarcinoma CRC subtypes (e.g., neuroendocrine, squamous cell carcinoma) are excluded.Insufficient tumor material: Samples with inadequate tumor tissue for PDO establishment.Neoadjuvant therapy impact: Tumors that underwent extensive pre-treatment (chemotherapy/radiotherapy) prior to organoid establishment, if treatment significantly altered the tumor's genomic profile.Lack of consent: Patients who did not provide explicit consent for genetic sequencing and data sharing.]]>