Name: Author Spotlight: Advancing Personalized Medicine in Ovarian Cancer
Uploaded: 2024-02-23T14:10:00
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The study is funded by the German Cancer Research Center DKTK, Partner site Munich, a partnership between DKFZ and University Hospital LMU Munich. The study is also supported by the German Cancer Aid grant (#70113426 and #70113433). Paraffin embedding of tissue and organoids has been performed at the Core facility of the Institute of Anatomy, Faculty of Medicine, LMU Munich, Munich. Confocal Imaging has been performed at the Core facility Bioimaging at the Biomedical Center (BMC). The authors want to thank Simone Hofmann, Maria Fischer, Cornelia Herbst, Sabine Fink, and Martina Rahmeh, for technical help.

Tumor tissue specimens from ovarian cancer surgeries were collected and patient-derived organoids were generated in compliance with the Ethics Committee of LMU University (17-471), adhering to the existing applicable EU, national, and local regulations. Each patient involved in the study has consented in written form. When working with fresh tissue samples, Biosafety Level 2 safety permission and Laminar Flow cabinets are required. Given the potentially infectious nature of the tissue samples, which cannot be ruled out d...

Standardizing Ovarian Cancer Organoid Biobanking

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The designed protocol addresses previous challenges of ovarian cancer organoid biobanking with regard to organoid formation and long-term passage potential and ensures the generation of fully expandable lines from the majority of solid tumor deposits. The surgical collection process of tumor samples to be used for organoid generation significantly impacts yield and expansion potential. Tumor tissue samples can be obtained during various procedures, including multi-visceral surgery, diagnostic laparoscopy, or biopsy. The ...

Clinical management of patients with epithelial ovarian cancer remains challenging due to its heterogeneous clinical presentation at advanced stages and high recurrence rates1. Improving our understanding of ovarian cancer development and biological behavior requires research approaches that address the patient-specific variability during the course of the disease, treatment response, and histopathological as well as molecular features2.
Biobanking, characterized by the systematic collection and long-term preservation of tumor samples derived from ovarian cancer patients along with their clinical information offers the preservation of a large patient cohort in different disease stages, including tumor samples from primary debulking surgeries, after neoadjuvant chemotherapy and from recurrent disease. It holds valuable potential for advancing cancer research serving as a resource of promising prognostic biomarkers and therapeutic targets3. However, conventional biobanking methods, such as formalin fixation and freezing, are not amenable to conducting functional studies on the original tumor samples due to the loss of viability and the disruption of the native three-dimensional tissue architecture4,5.
Studies of molecular mechanisms, in oncology and beyond, crucially depend on the use of appropriate experimental models that faithfully reflect the biology of the disease and maintain in vitro properties of the tissue observed in vivo. Patient-derived organoids, based on the preservation of the renewal potential, reproduce in the lab the original structure and function of the epithelium and allow testing in a patient-specific context. Therefore, they have emerged as highly promising tools for cancer research and personalized medicine, bridging the gap between clinical diversity and laboratory research6,7,8,9. Tailored therapeutic strategies based on individual drug responses of organoid lines and testing of the functional relevance of molecular profiles, can potentially be directly applied to patient care10,11. The possibility of long-term cultivation including patient-specific characteristics and the collection of relevant prospective clinical data over time holds great promise to identify novel prognostic and predictive factors involved in disease progression and resistance mechanisms3,9.
Nonetheless, building a biobank that includes organoids from different tumor samples requires a combination of strict adherence to complex methodology and setting up protocols for easy maintenance12. Process standardization ensures that the biobank can be established and maintained efficiently by trained staff even at high turnover, while at the same time adhering to the highest quality standards13. Several studies reported the successful generation of stable ovarian cancer organoid lines corresponding to the mutational and phenotypical profile of the original tumor with varying efficiency rates. Still, routine bio banking remains challenging in practice, particularly for long-term stable growth of lines, which is a prerequisite for large-scale expansion or successful genomic editing.
In particular, the issue of expandability remains vaguely defined in the field as organoids that show slow and limited growth potential are occasionally counted as established lines. As initially demonstrated by Hoffmann et al., a study whose principal findings provided the basis for this further developed protocol, optimal handling of ovarian cancer tissue requires a unique strategy to accommodate heterogeneity14. Phenotypic characterization of the organoids obtained by this method and close similarity with parental tumor tissue were confirmed by panel DNA sequencing and transcriptomics analysis of mature cultures (4-10 months of cultivation) demonstrating the stability of the model8,9,12,14.
In contrast to the paracrine environment that regulates the homeostasis in the healthy fallopian tubes, the epithelial layer, which likely yields high-grade serous ovarian cancer (HGSOC), cancer regeneration potential, and organoid formation capacity, is less dependent on exogenous Wnt supplementation. Moreover, active Bone Morphogenetic Protein (BMP) signaling, characterized by the absence of Noggin in organoid medium, proved to be beneficial for the establishment of long-term cultures from ovarian cancer solid tissue deposits14,15. During systematic biobanking of solid deposits of ovarian cancer, we have confirmed these findings and set up the pipeline, with details outlined in this protocol that ensures sustained long-term expansion in the majority of cases. We find that parallel testing of different media compositions and seeding modalities when working with primary isolates are essential to improve the establishment of long-term stable organoid lines and to increase yields enabling robust propagation and expansion to multi-well formats required for downstream experiments16.
Furthermore, the purity and quality of the samples collected during surgery are of crucial importance for the translational potential of ovarian cancer organoids in basic research and molecular diagnostics. The complexity of the clinical presentation of HGSOC requires close cooperation between the surgeons, oncologists, and the scientists in the lab to ensure that relevant material is correctly identified, transport conditions are kept constant, and organoid lines are generated with high efficiency representing the most important characteristics of the disease of each patient. This protocol provides a standardized but adaptable framework to capture the full potential of ovarian cancer organoids, considering the heterogeneity that characterizes ovarian cancer16,17. Notably, this protocol enables reliable biobanking of the broad spectrum of ovarian cancer clinical presentation, including different histological types (high-grade and low-grade ovarian cancer, LGSOC), different deposits from the same patients who exhibit differences in stemness regulation, tissues from surgeries in post neoadjuvant setting, biopsy material, and samples from surgeries in the recurrent phase of disease progression.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>100 Sterican 26 G</td>
			<td>Braun, Melsungen, Germany</td>
			<td>4657683</td>
			<td></td>
		</tr>
		<tr>
			<td>100 Sterican 27 G</td>
			<td>Braun, Melsungen, Germany</td>
			<td>4657705</td>
			<td></td>
		</tr>
		<tr>
			<td>293T HA Rspo1-Fc</td>
			<td>R&#38;D systems, Minneapolis, USA</td>
			<td>3710-001-01</td>
			<td>Alternative: R-Spondin1 expressing Cell line, Sigma-Aldrich, SC111</td>
		</tr>
		<tr>
			<td>A-83-01 (TGF-b RI Kinase inhibitor IV)</td>
			<td>Merck, Darmstadt, Germany</td>
			<td>616454</td>
			<td></td>
		</tr>
		<tr>
			<td>Advanced DMEM/F-12 Medium&#160;</td>
			<td>Gibco, Thermo Scientific, Waltham, USA</td>
			<td>12634028</td>
			<td></td>
		</tr>
		<tr>
			<td>Anti-p53 antibody (DO1)</td>
			<td>Santa Cruz Biotechnology, Texas, USA</td>
			<td>sc-126</td>
			<td></td>
		</tr>
		<tr>
			<td>Anti-PAX8 antibody</td>
			<td>Proteintech, Manchester, UK&#160;</td>
			<td>10336-1-AP</td>
			<td></td>
		</tr>
		<tr>
			<td>B-27 Supplement (50x)</td>
			<td>Gibco, Thermo Scientific, Waltham, USA</td>
			<td>17504-044</td>
			<td></td>
		</tr>
		<tr>
			<td>Bottle-top vacuum filter 0.2 &#181;m</td>
			<td>Corning, Berlin, Germany&#160;</td>
			<td>430049</td>
			<td></td>
		</tr>
		<tr>
			<td>CELLSTAR cell culture flask, 175 cm2</td>
			<td>Greiner Bio-one, Kremsm&#252;nster, Austria</td>
			<td>661175</td>
			<td></td>
		</tr>
		<tr>
			<td>CELLSTAR cell culture flask, 25 cm2</td>
			<td>Greiner Bio-one, Kremsm&#252;nster, Austria</td>
			<td>690160</td>
			<td></td>
		</tr>
		<tr>
			<td>CELLSTAR cell culture flask, 75 cm2</td>
			<td>Greiner Bio-one, Kremsm&#252;nster, Austria</td>
			<td>658175</td>
			<td></td>
		</tr>
		<tr>
			<td>Collagenase I</td>
			<td>Thermo Scientific, Waltham, USA</td>
			<td>17018029</td>
			<td></td>
		</tr>
		<tr>
			<td>Costar 48-well Clear TC-treated&#160;</td>
			<td>Corning, Berlin, Germany&#160;</td>
			<td>3548</td>
			<td></td>
		</tr>
		<tr>
			<td>Cryo SFM</td>
			<td>PromoCell &#8211; Human Centered Science, Heidelberg, Germany</td>
			<td>C-29912</td>
			<td></td>
		</tr>
		<tr>
			<td>Cultrex Reduced Growth Factor Basement Membrane Extract, Type 2, Pathclear</td>
			<td>R&#38;D systems, Minneapolis, USA</td>
			<td>3533-005-02</td>
			<td>Alternative: Matrigel, Growth Factor Reduced Basement membrane matrix&#160; Corning, 356231&#160;</td>
		</tr>
		<tr>
			<td>Cy5 AffiniPure Donkey Anti-Mouse IgG</td>
			<td>Jackson Immuno</td>
			<td>715-175-151</td>
			<td></td>
		</tr>
		<tr>
			<td>DAKO&#160; Citrate Buffer, pH 6.0, 10x Antigen Retriever</td>
			<td>Sigma-Aldrich, Merck, Darmstadt, Germany</td>
			<td>C9999-1000ML</td>
			<td></td>
		</tr>
		<tr>
			<td>DAPI</td>
			<td>Thermo Scientific, Waltham, USA</td>
			<td>62248</td>
			<td></td>
		</tr>
		<tr>
			<td>Donkey anti rabbit Alexa Fluor Plus 555</td>
			<td>Thermo Scientific, Waltham, USA</td>
			<td>A32794</td>
			<td></td>
		</tr>
		<tr>
			<td>Donkey anti-Goat IgG Alexa Fluor Plus 488</td>
			<td>Thermo Scientific, Waltham, USA</td>
			<td>A32814</td>
			<td></td>
		</tr>
		<tr>
			<td>Dulbecco&#180;s Phosphate-Buffered Saline&#160;</td>
			<td>Gibco, Thermo Scientific, Waltham, USA</td>
			<td>14190-094</td>
			<td></td>
		</tr>
		<tr>
			<td>Epredia Richard-Allan Scientific HistoGel</td>
			<td>Thermo Scientific, Waltham, USA</td>
			<td>Epredia HG-4000-012</td>
			<td></td>
		</tr>
		<tr>
			<td>Falcon 24-well Polystyrene&#160;</td>
			<td>Corning, Berlin, Germany&#160;</td>
			<td>351447</td>
			<td></td>
		</tr>
		<tr>
			<td>Feather scalpel&#160;</td>
			<td>Pfm medical, Cologne, Germany</td>
			<td>200130010</td>
			<td></td>
		</tr>
		<tr>
			<td>Fetal Bovine Serum</td>
			<td>Gibco, Thermo Scientific, Waltham, USA</td>
			<td>10270106</td>
			<td></td>
		</tr>
		<tr>
			<td>Formalin 37% acid free, stabilized</td>
			<td>Morphisto, Offenbach am Main, Germany</td>
			<td>1019205000</td>
			<td></td>
		</tr>
		<tr>
			<td>GlutaMAX</td>
			<td>Gibco, Thermo Scientific, Waltham, USA</td>
			<td>35050038</td>
			<td></td>
		</tr>
		<tr>
			<td>HEPES (1 M)</td>
			<td>Gibco, Thermo Scientific, Waltham, USA</td>
			<td>156630080</td>
			<td></td>
		</tr>
		<tr>
			<td>Human EpCAM/TROP-1 Antibody</td>
			<td>R&#38;D systems, Minneapolis, USA</td>
			<td>AF960</td>
			<td></td>
		</tr>
		<tr>
			<td>Human FGF10</td>
			<td>Peprotech, NJ, USA</td>
			<td>100-26</td>
			<td></td>
		</tr>
		<tr>
			<td>Human recombinant BMP2</td>
			<td>Gibco, Thermo Scientific, Waltham, USA</td>
			<td>PHC7146</td>
			<td></td>
		</tr>
		<tr>
			<td>Human recombinant EGF</td>
			<td>Gibco, Thermo Scientific, Waltham, USA</td>
			<td>PHG0311L</td>
			<td></td>
		</tr>
		<tr>
			<td>Human recombinant Heregulin beta-1</td>
			<td>Peprotech, NJ, USA</td>
			<td>100-03</td>
			<td></td>
		</tr>
		<tr>
			<td>LAS X core Software</td>
			<td>Leica Microsystems</td>
			<td></td>
			<td>https://webshare.leica-microsystems.com/latest/core/widefield/</td>
		</tr>
		<tr>
			<td>Leica TCS SP8 X&#160;White Light Laser Confocal Microscope</td>
			<td>Leica Microsystems</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>N-2 Supplement (100x)</td>
			<td>Gibco, Thermo Scientific, Waltham, USA</td>
			<td>17502-048</td>
			<td></td>
		</tr>
		<tr>
			<td>Nicotinamide</td>
			<td>Sigma-Aldrich, Merck, Darmstadt, Germany</td>
			<td>N0636</td>
			<td></td>
		</tr>
		<tr>
			<td>Omnifix 1 mL</td>
			<td>Braun, Melsungen, Germany</td>
			<td>3570519</td>
			<td></td>
		</tr>
		<tr>
			<td>Paraffin</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Parafilm</td>
			<td>Omnilab, Munich, Germany</td>
			<td>5170002</td>
			<td></td>
		</tr>
		<tr>
			<td>Paraformaldehyd&#160;</td>
			<td>Morphisto, Offenbach am Main, Germany</td>
			<td>1176201000</td>
			<td></td>
		</tr>
		<tr>
			<td>Pen Strep</td>
			<td>Gibco, Thermo Scientific, Waltham, USA</td>
			<td>15140-122</td>
			<td></td>
		</tr>
		<tr>
			<td>Penicillin-Streptomycin (10,000 U/mL)</td>
			<td>Sigma-Aldrich, Merck, Darmstadt, Germany</td>
			<td>P4333-100</td>
			<td></td>
		</tr>
		<tr>
			<td>PluriStrainer 400 &#181;m</td>
			<td>PluriSelect, Leipzig, Germany</td>
			<td>43-50400-01</td>
			<td></td>
		</tr>
		<tr>
			<td>Primocin</td>
			<td>InvivoGen, Toulouse, France</td>
			<td>ant-pm-05</td>
			<td></td>
		</tr>
		<tr>
			<td>Red Blood Cell Lysing Buffer</td>
			<td>Sigma-Aldrich, Merck, Darmstadt, Germany</td>
			<td>11814389001</td>
			<td></td>
		</tr>
		<tr>
			<td>Roticlear</td>
			<td>Carl Roth, Karlsruhe, Germany</td>
			<td>A538.5</td>
			<td></td>
		</tr>
		<tr>
			<td>Surgipath Paraplast</td>
			<td>Leica, Wetzlar, Germany</td>
			<td>39602012</td>
			<td></td>
		</tr>
		<tr>
			<td>Thermo Scientific Nunc Cryovials</td>
			<td>Thermo Scientific, Waltham, USA</td>
			<td>375418PK</td>
			<td></td>
		</tr>
		<tr>
			<td>Triton X-100</td>
			<td>Sigma-Aldrich, Merck, Darmstadt, Germany</td>
			<td>T8787</td>
			<td></td>
		</tr>
		<tr>
			<td>Trypan Blue Stain</td>
			<td>Sigma-Aldrich, Merck, Darmstadt, Germany</td>
			<td>T8154</td>
			<td></td>
		</tr>
		<tr>
			<td>TrypLE Express Enzyme&#160;</td>
			<td>Gibco, Thermo Scientific, Waltham, USA</td>
			<td>12604-013</td>
			<td></td>
		</tr>
		<tr>
			<td>Tween-20</td>
			<td>PanReac AppliChem, Darmstadt, Germany</td>
			<td>A4974-0100</td>
			<td></td>
		</tr>
		<tr>
			<td>Y-27632</td>
			<td>TOCRIS biotechne, Wiesbaden, Germany</td>
			<td>1254</td>
			<td></td>
		</tr>
		<tr>
			<td>Zeocin</td>
			<td>Invitrogen, Thermo Scientific, Waltham, USA</td>
			<td>R25001</td>
			<td></td>
		</tr>
	</tbody>
</table>

strategy for biobanking of ovarian cancer organoids: addressing the interpatient heterogeneity across histological subtypes and disease stages

While the establishment of an ovarian cancer biobank from patient-derived organoids along with their clinical background information promises advances in research and patient care, standardization remains a challenge due to the heterogeneity of this lethal malignancy, combined with the inherent complexity of organoid technology. This adaptable protocol provides a systematic framework to realize the full potential of ovarian cancer organoids considering a patient-specific variability of progenitors. By implementing a structured experimental workflow to select optimal culture conditions and seeding methods, with parallel testing of direct 3D seeding versus a 2D/3D route, we obtain, in most cases, robust long-term expanding lines suitable for a broad range of downstream applications. 
Notably, the protocol has been tested and proven efficient in a great number of cases (N = 120) of highly heterogeneous starting material, including high-grade and low-grade ovarian cancer and stages of the disease with primary debulking, recurrent disease, and post-neoadjuvant surgical specimens. Within a low Wnt, high BMP exogenous signaling environment, we observed progenitors being differently susceptible to the activation of the Heregulin 1 &#223; (HER&#223;-1)-pathway, with HER&#223;-1 promoting organoid formation in some while inhibiting it in others. For a subset of the patient's samples, optimal organoid formation and long-term growth necessitate the addition of fibroblast growth factor 10 and R-Spondin 1 to the medium. 
Further, we highlight the critical steps of tissue digestion and progenitor isolation and point to examples where brief cultivation in 2D on plastic is beneficial for subsequent organoid formation in the Basement Membrane Extract type 2 matrix. Overall, optimal biobanking requires systematic testing of all main conditions in parallel to identify an adequate growth environment for individual lines. The protocol also describes the handling procedure for efficient embedding, sectioning, and staining to obtain high-resolution images of organoids, which is required for comprehensive phenotyping.

Author Spotlight: Advancing Personalized Medicine in Ovarian Cancer 

Strategy for Biobanking of Ovarian Cancer Organoids: Addressing the Interpatient Heterogeneity across Histological Subtypes and Disease Stages

The best clinical management in cutting-edge translational research for patients with advanced ovarian cancer has highest priority at our institution. With the biobanking of patient-derived organoids, we have achieved major progress towards individually-tailored management. This enables us to evaluate patient-specific characteristics and to identify predictive biomarkers.We have made significant advances in recent years in improving radical multivisceral surgery, chemotherapy, anti-angiogenic therapy, and also PARP inhibitor therapy in patients with advanced ovarian cancer and improved survival rates even with that. Now, the next big step would be to better predict which patient would benefit from which specific treatment. Currently, clinical treatment decisions are based on general histopathological features and on information on homologous recommendation deficiency or tested in paraffin-embedded tumor tissue.Biologic models that evaluate specific responses to chemotherapy and to targeted treatments have not yet been implemented in clinical routine. We have identified key characteristics of ovarian cancer tissue, specifically the culture requirements necessary to sustain its renewal potential in vitro, and use this knowledge to achieve robust long-term growth of organoid lines and establish biobank from samples at various stages of the disease. Our day-to-day experience in biobanking of ovarian cancer organoids effectively shows a remarkable heterogeneity in the biology of this malignancy, which could pave the way to new classification or provide the basis for new therapeutic solutions targeting STEMI's potential.

After initial tissue dissociation, filtration, and counting, cells are seeded in parallel directly in 3D format, as explained above, as well as the suspension in the flask for brief 2D expansion. In some cases, the transient 2D expansion positively influences the organoid formation, and the long-term line is successfully established via this route while comparative parallel 3D seeding can result in growth arrest (Figure 1). For each donor tissue that is processed, the cells are tested accord...

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This protocol offers a systematic framework for the establishment of ovarian cancer organoids from different disease stages and addresses the challenges of patient-specific variability to increase yield and enable robust long-term expansion for subsequent applications. It includes detailed steps for tissue processing, seeding, adjusting media requirements, and immunofluorescence staining.

While the establishment of an ovarian cancer biobank from patient-derived organoids along with their clinical background information promises advances in ...