Browse
Submit Data
Databases
API
Help

Dataset Information

41 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Obtaining patient-derived cancer organoid cultures via fine-needle aspiration.

ABSTRACT: Patient-derived tumor organoid cultures are an essential and innovative methodology for translational research. However, current techniques to establish these cultures are cumbersome, expensive, and often require irreplaceable clinical tissue from surgery or core biopsies. Fine-needle aspiration (FNA) provides a minimally invasive biopsy technique commonly performed in clinical settings. Here, we provide a protocol for FNA. We have found that FNA provides a cost-effective, rapid, and streamlined method for tissue acquisition for cancer organoid culture. For complete details on the use and execution of this protocol, please refer to Lee et al. (2020) and Vilgelm et al. (2020).

SUBMITTER: Phifer CJ

PROVIDER: S-EPMC7758553 | biostudies-literature | 2021 Mar

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Obtaining patient-derived cancer organoid cultures via fine-needle aspiration.

Phifer Courtney J CJ Bergdorf Kensey N KN Bechard Matthew E ME Vilgelm Anna A Baregamian Naira N McDonald Oliver G OG Lee Ethan E Weiss Vivian L VL

STAR protocols 20201221 1

Patient-derived tumor organoid cultures are an essential and innovative methodology for translational research. However, current techniques to establish these cultures are cumbersome, expensive, and often require irreplaceable clinical tissue from surgery or core biopsies. Fine-needle aspiration (FNA) provides a minimally invasive biopsy technique commonly performed in clinical settings. Here, we provide a protocol for FNA. We have found that FNA provides a cost-effective, rapid, and streamlined ...[more]

PMID: 33377121

Similar Datasets

Fine-Needle Aspiration-Based Patient-Derived Cancer Organoids.

Project description:Patient-derived cancer organoids hold great potential to accurately model and predict therapeutic responses. Efficient organoid isolation methods that minimize post-collection manipulation of tissues would improve adaptability, accuracy, and applicability to both experimental and real-time clinical settings. Here we present a simple and minimally invasive fine-needle aspiration (FNA)-based organoid culture technique using a variety of tumor types including gastrointestinal, thyroid, melanoma, and kidney. This method isolates organoids directly from patients at the bedside or from resected tissues, requiring minimal tissue processing while preserving the histologic growth patterns and infiltrating immune cells. Finally, we illustrate diverse downstream applications of this technique including in vitro high-throughput chemotherapeutic screens, in situ immune cell characterization, and in vivo patient-derived xenografts. Thus, routine clinical FNA-based collection techniques represent an unappreciated substantial source of material that can be exploited to generate tumor organoids from a variety of tumor types for both discovery and clinical applications.

| S-EPMC7415927 | biostudies-literature

Establishment of Patient-Derived Pancreatic Cancer Organoids from Endoscopic Ultrasound-Guided Fine-Needle Aspiration Biopsies.

Project description:Background/aimsThree-dimensional cultures of human pancreatic cancer tissue also known as "organoids" have largely been developed from surgical specimens. Given that most patients present with locally advanced and/or metastatic disease, such organoids are not representative of the majority of patients. Therefore, we used endoscopic ultrasound-guided fine-needle aspiration (EUS-FNA) to collect pancreatic cancer tissues from patients with advanced pancreatic cancer to create organoids, and evaluated their utility in pancreatic cancer research.MethodsSingle-pass EUS-FNA samplings were employed to obtain the tissue for organoid generation. After establishment of the organoid, we compared the core biopsy tissues with organoids using hematoxylin and eosin staining, and performed whole exome sequencing (WES) to detect mutational variants. Furthermore, we compared patient outcome with the organoid drug response to determine the potential utility of the clinical application of such organoid-based assays.ResultsOrganoids were successfully generated in 14 of 20 tumors (70%) and were able to be passaged greater than 5 times in 12 of 20 tumors (60%). Among them, we selected eight pairs of organoid and core biopsy tissues for detailed analyses. They showed similar patterns in hematoxylin and eosin staining. WES revealed mutations in KRAS, TP53, CDKN2A, SMAD4, BRCA1, and BRCA2 which were 93% homologous, and the mean nonreference discordance rate was 5.47%. We observed moderate drug response correlations between the organoids and clinical outcomes in patients who underwent FOLFIRINOX chemotherapy.ConclusionsThe established organoids from EUS-FNA core biopsies can be used for a suitable model system for pancreatic cancer research.

| S-EPMC9289822 | biostudies-literature

Immunofluorescent staining of cancer spheroids and fine-needle aspiration-derived organoids.

Project description:Our organoid generation technique has allowed for the development of downstream organoid applications. Here, we detail an accessible, straightforward protocol for immunofluorescent staining and imaging of thyroid cancer organoids, particularly those with tumor de-differentiation. Immunofluorescence is a powerful tool to help understand the localization of cell types within organoids and determine the interactions between those cells. As organoids have been shown to recapitulate patient tumor morphology, immunofluorescent staining and imaging of organoids allows for enhanced understanding of near in vivo structures. For complete details on the use and execution of this protocol, please refer to Lee et al. (2020) and Vilgelm et al. (2020).

| S-EPMC8182106 | biostudies-literature

Analysis of the Pancreatic Cancer Microbiome Using Endoscopic Ultrasound-Guided Fine-Needle Aspiration-Derived Samples.

Project description:ObjectivesMost previous studies have analyzed bacteria in tumors using resected pancreatic cancer (PC) tissues, because it is difficult to obtain tissue samples from unresectable advanced PC. We aimed to determine whether minimal tissue obtained by endoscopic ultrasound-guided fine-needle aspiration is useful for microbiome analysis.MethodsThirty PC and matched duodenal and stomach tissues (N = 90) were prospectively collected from 30 patients who underwent endoscopic ultrasound-guided fine-needle aspiration. Bacterial DNA was extracted, and 16S rRNA sequencing was performed. The primary outcome was the success rate of bacterial detection in tumors. Bacterial diversity and structure were investigated.ResultsThe bacterial detection rates were 80%, 100%, and 97% in PC, gastric, and duodenal samples, respectively. Pancreatic cancer tissues showed a lower α-diversity and a significantly different microbial structure than stomach and duodenal tissues. Proteobacteria were more abundant, whereas Firmicutes, Bacteroidetes, and Fusobacteria were less abundant in PC tissues than in stomach and duodenal tissues. Acinetobacter was more abundant in PC tissues than in stomach and duodenal tissues, and Delftia was more frequently detected in resectable PC.ConclusionsEndoscopic ultrasound-guided fine-needle aspiration samples were valuable for PC microbiome analysis, revealing that the bacterial composition of PC is different from that of the stomach and duodenum.

| S-EPMC9257056 | biostudies-literature

Diagnostic sensitivity of fine-needle aspiration cytology in thyroid cancer.

Project description:Introduction Fine-needle aspiration cytology (FNAC) is an effective tool in the diagnostic work-up of patients with thyroid nodules. The aim of our study was to assess the diagnostic sensitivity of FNAC in thyroid cancer (TC) in Sweden by correlating the findings of preoperative FNAC with those obtained through final histology of the surgical specimen. Methods A Swedish nationwide cohort of patients having surgery for TC (n = 2519) from the Scandinavian Quality Register for Thyroid, Parathyroid and Adrenal surgery between 2004 and 2013 was obtained. Data was validated through scrutinizing patient FNAC and histology reports. Results Among the 2519 cases operated with a final diagnosis of TC, the diagnosis was substantiated and validated through the histology report in 2332 cases (92.6%), included in the present study. Among these, 1679 patients (72%) were female and the median age at TC diagnosis was 52.3 years (range 18-94.6). In 353 cases (15.1%) FNAC was not performed at all; whereas in the remaining 1965 cases, the diagnostic sensitivity of FNAC was 81.6%. In lesions > 1 cm, FNAC diagnostic sensitivity reached 86.5%, whereas in lesions < 1 cm, FNAC yielded a sensitivity of 61.5%. Approximately 85% of FNACs (n = 1981/2332) were performed using ultra-sonographic (US) guidance. In TC lesions > 1 cm, the diagnostic sensitivity of US-guided FNAC (n = 1504) was 86.9% as compared to 76.9% in clinically applied FNAC without US utilization (n = 118). Conclusions FNAC is performed in most patients operated for TC in Sweden (85%) and retains its value as a tool in TC diagnostic work-up with an overall sensitivity of 82%, reaching 87% in lesions > 1 cm, that harbor clinically relevant TC.

| S-EPMC11484879 | biostudies-literature

Patient-Derived Cancer Organoid Cultures to Predict Sensitivity to Chemotherapy and Radiation.

Project description:PurposeCancer treatment is limited by inaccurate predictors of patient-specific therapeutic response. Therefore, some patients are exposed to unnecessary side effects and delays in starting effective therapy. A clinical tool that predicts treatment sensitivity for individual patients is needed.Experimental designPatient-derived cancer organoids were derived across multiple histologies. The histologic characteristics, mutation profile, clonal structure, and response to chemotherapy and radiation were assessed using bright-field and optical metabolic imaging on spheroid and single-cell levels, respectively.ResultsWe demonstrate that patient-derived cancer organoids represent the cancers from which they were derived, including key histologic and molecular features. These cultures were generated from numerous cancers, various biopsy sample types, and in different clinical settings. Next-generation sequencing reveals the presence of subclonal populations within the organoid cultures. These cultures allow for the detection of clonal heterogeneity with a greater sensitivity than bulk tumor sequencing. Optical metabolic imaging of these organoids provides cell-level quantification of treatment response and tumor heterogeneity allowing for resolution of therapeutic differences between patient samples. Using this technology, we prospectively predict treatment response for a patient with metastatic colorectal cancer.ConclusionsThese studies add to the literature demonstrating feasibility to grow clinical patient-derived organotypic cultures for treatment effectiveness testing. Together, these culture methods and response assessment techniques hold great promise to predict treatment sensitivity for patients with cancer undergoing chemotherapy and/or radiation.

| S-EPMC6726566 | biostudies-literature

Expression data from paired matched breast cancer Fine needle aspiration (FNA) or Core needle biopsies (CBX)

Project description:Paired FNA and CBX specimens were prospectively collected from 37 breast cancers before any systemic therapy during a biomarker discovery study at The University of Texas M. D. Anderson Cancer Center. We identified 293 probe sets overexpressed in core biopsies; these included five highly coexpressed gene clusters (metagenes) corresponding to immune functions and extracellular matrix components. We compared gene expression profiles of pairs of fine-needle (stroma-poor) and core-needle (stroma-rich) biopsies from 37 cancers to identify stroma-associated genes

2011-10-31 | GSE32518 | GEO

Expression data from Fine Needle Aspiration (FNA) biopsies from breast cancer patients

Project description:This is a stage-matched case control study. Cases with clinical diagnosis of Inflammatory Breast Cancer (IBC) were selected after reviewing all medical records of the 440 FNA samples. IBC was defined as signs of erythema and edema (peau d’orange) involving at least one third of the skin and rapid clinical presentation. Presence of tumor emboli in the dermal lymphatics of the involved skin in the pathology report was not required for inclusion as IBC. Controls were selected to match for T stage, all T4a-c tumors in the data set were included as controls. IBC breast cancer are all T4d breast cancer. We examined if gene expression differences exist between IBC and stage-matched Non-IBC stratified according to hormone receptor and HER2 status.

2011-07-01 | GSE22597 | GEO

Ultrasound-Guided Fine-Needle Aspiration Versus Fine-Needle Capillary Sampling in Evaluation of Lymph Node Metastasis of Thyroid Cancer.

Project description:BackgroundTo compare the sampling adequacy and diagnostic efficiency of ultrasound-guided fine-needle aspiration with 22-, 25-gauge needles and capillary sampling with 22-gauge needle in the biopsy of cervical lymph node.MethodsA total of 130 cervical lymph nodes from 103 patients were consecutively included in the prospective study. Each suspected lymph node was aspirated with a 22-gauge needle, capillary sampled with a 22-gauge needle and aspirated with a 25-gauge needle. The adequacy rates and nondiagnostic rates of obtained specimen were calculated.ResultsOf the 130 suspected lymph nodes, there were 77 lymph nodes<6.0 mm and 53 lymph nodes≥6.0mm in the smallest dimension. Both FNA22G and FNC22G got significantly higher sampling adequacy than FNA25G for the total lymph nodes. For lymph nodes<6.0 mm, the sampling adequacy was significantly higher with FNA22G than with FNA25G for each parameter and the cumulative score (all P<0.05), while no difference were seen between FNA22G and FNC22G, and between FNC22G and FNA25G. There were higher nondiagnostic rates for FNA25G compared with FNA22G and FNC22G in all lymph nodes and in each size subgroups. FNA25G yielded more diagnostically inadequate specimens than FNA22G and FNC22G did in the total lymph nodes (P=0.002), in lymph nodes<6.0 mm (P=0.014), and in those ≥ 6.0 mm (P=0.000).ConclusionsFNA22G and FNC22G obtained more diagnostically adequate specimens than FNA25G in cervical lymph nodes. FNA22G and FNC22G may be more suitable than FNA25G in diagnosing cervical lymph nodes. FNA22G and FNC22G may yield specimens with similar quality.

| S-EPMC8079778 | biostudies-literature

Expression data from Fine Needle Aspiration (FNA) biopsies from breast cancer patients

2011-07-01 | E-GEOD-22597 | biostudies-arrayexpress