Fine needle aspiration biopsy of breast specimens effectively harvests cells for patient-derived organoids modeling breast ductal carcinoma in situ

Ye, J.; Goldhammer, N.; Vohra, P.; Warhadpande, S.; De Castro, G. C.; Maldonado Rodas, C.; Moasser, M. M.; Ramalingam, K.; Abe, S.; Alvarado, M.; Ewing, C.; Goodwin, K.; Mukhtar, R.; Wong, J.; Esserman, L.; Balassanian, R.; Rosenbluth, J. M.

doi:10.1101/2025.08.12.669895

bioRxiv · 10.1101/2025.08.12.669895

Fine needle aspiration biopsy of breast specimens effectively harvests cells for patient-derived organoids modeling breast ductal carcinoma in situ

Ye, J.·Goldhammer, N.·Vohra, P.·Warhadpande, S.·De Castro, G. C.·Maldonado Rodas, C.·Moasser, M. M.·Ramalingam, K.·Abe, S.·Alvarado, M.·Ewing, C.·Goodwin, K.·Mukhtar, R.·Wong, J.·Esserman, L.·Balassanian, R.·Rosenbluth, J. M.

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Abstract

BackgroundPatient-derived organoids (PDOs) generated from benign breast tissue and breast carcinomas have successfully recapitulated their respective in vivo counterparts. PDOs model tumorigenesis and allow for screening of novel therapeutics personalized to individual patients. However, acquiring cells to generate PDOs is cumbersome. We demonstrate the feasibility of fine needle aspiration biopsy (FNAB) for harvesting cells for PDOs modeling ductal carcinoma in situ (DCIS). MethodsSurgical specimens from patients with biopsy-proven DCIS were used for this study. Core needle biopsy (CNB) was performed on fresh specimens in the operating room, and tissue was mechanically dissociated before culture in basement membrane extract (BME) and organoid medium to generate PDOs. FNAB was performed in the gross room on fresh specimens, and the remaining aspirate was similarly submitted for PDO culture. ResultsPDOs were successfully generated in 15/18 specimens obtained by CNB and 7/11 specimens obtained by FNAB. The average time to initial organoid growth was 4 days for FNAB specimens compared to 19.3 days for CNB specimens. Tumor cells were seen on 7/11 FNAB smears and 16/18 CNB touch preps. Immunofluorescence staining confirmed the presence of both luminal and myoepithelial cells in derived PDOs. ConclusionsFNAB effectively obtains cells for PDOs modeling DCIS. CNB after mincing yielded PDOs with a high success rate, but they were slow to establish. Notably, the time to organoid growth was significantly shorter for FNAB specimens. Thus, FNAB offers an efficient alternative for breast PDO culture and can reduce the time and resources spent on generating PDO cultures.

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Ye, J., Goldhammer, N., Vohra, P., Warhadpande, S., De Castro, G. C., Maldonado Rodas, C., Moasser, M. M., Ramalingam, K., Abe, S., Alvarado, M., Ewing, C., Goodwin, K., Mukhtar, R., Wong, J., Esserman, L., Balassanian, R., Rosenbluth, J. M.. 2025-08-13. Fine needle aspiration biopsy of breast specimens effectively harvests cells for patient-derived organoids modeling breast ductal carcinoma in situ. https://doi.org/10.1101/2025.08.12.669895

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