Patient-derived epithelial cell organoids mimic the phenotypic complexity of endometriosis subtypes.

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Can patient-derived organoid models be reliably established from diverse surgical phenotypes of endometriosis, and how do clinical factors such as hormonal treatment affect their growth success and morphology? Endometriosis organoids can be established across all major surgical phenotypes with variable efficiency, and hormonal treatment at the time of biospecimen collection significantly reduces organoid establishment success. Organoid cultures have been developed from eutopic endometrium and select endometriosis tissue biospecimens previously, but their feasibility as pre-clinical models of endometriosis across diverse tissue types and clinical presentations remains unclear. Twenty-eight endometriosis tissue biospecimens were obtained from 23 patients undergoing surgery, with organoid cultures assessed through successive stages of establishment, passage, and cryopreservation. Endometriosis biospecimens, including deep infiltrating endometriosis (DIE), ovarian endometrioma (OMA), and superficial peritoneal (SUP) biospecimens, were processed into organoid cultures using a validated low-Wnt culture system. Organoid viability, morphology, hormone receptor expression, and cellular composition were evaluated by microscopy, immunohistochemistry, and quantitative morphometric analysis. Overall, 22/28 (78.6%) biospecimens established 3-dimensional structures, with 15/28 (53.6%) remaining viable after cryopreservation. Establishment success differed by phenotype (OMA 71.4%, DIE 63.6%, SUP 30%). Progesterone receptor expression was retained in SUP and DIE-derived organoids (7/7, 100%), while OMA-derived organoids showed substantial reductions (4/5 cases). Biospecimens from patients receiving hormonal treatment were smaller (P = 0.038) and had reduced organoid establishment success (3/13, 23.1% vs 12/15, 80.0%, P = 0.003). Organoids exhibited distinct morphological patterns correlating with disease phenotype. Uniform culture conditions may limit growth of certain subtypes, and the in vitro organoid models may not fully represent in vivo tissue complexity. Sample sizes were modest, and pooling tissues from the same patient could mask intra-patient heterogeneity. These organoid models offer a promising platform for studying subtype-specific endometriosis biology, including hormone resistance mechanisms, and could inform personalized therapeutic development. The impact of hormonal treatment on organoid viability underscores the need to consider clinical context in pre-clinical models of endometriosis. This work was supported by the National Endometriosis Clinical and Scientific Trials (NECST) Network, funded by the Australian Government Department of Health and Aged Care (Grant 4-I66SNMA), and by a research grant from Endometriosis Australia to C.E.F., D.L., and J.A.A. K.G. is supported by an Australian Government Research Training Program Scholarship and a NECST Network Top-Up Scholarship, which did not influence the conduct or outcomes of this study. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. J.A.A. has received consulting fees from Hologic, Gedeon Richter, and BD, personal payments from Hologic, Bayer, Organon, and Gedeon Richter, travel support from Gedeon Richter, and participated on data safety monitoring advisory boards for Hologic and Gideon Richter. He was the former chair of the Australian Endometriosis Guideline Committee and is the Co-Editor-in-Chief of the Journal of Minimally Invasive Gynaecology. All other authors declare no competing interests. N/A.

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  • 10.1097/pgp.0000000000000522
Immunohistochemical Analysis of Somatostatin Receptors in Endometriosis Tissue Samples: A Retrospective Study.
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Three types of endometriosis are described: superficial peritoneal endometriosis (SPE), ovarian endometrioma (OMA), and deep infiltrating endometriosis (DIE). The expression of somatostatin receptors (SSTR1, 2, and 5) in human endometrial tissue and its ectopic form has been previously studied and may be different in each type of endometriosis. The aim of this study was to assess the immunohistochemical expression of SSTR1, 2, and 5 in tissue samples of SPE, OMA, and DIE. We performed a retrospective analysis in the pathology department database. Patients aged <50 yr and diagnosed with endometriosis have been identified and sorted into 3 groups according to their endometriosis type: SPE, OMA, and DIE. For each selected patient, formalin-fixed paraffin-embedded blocks were retrieved in order to make new sections to be incubated with polyclonal rabbit antibodies anti-SSTR1, 2, and 5. Receptor status was considered as positive on the sections when >50% of the cells showed immunostaining. Seventy-six patients were included in the analysis. SSTR1 and 5 were expressed in 95.4% and 77.2% of SPE, respectively, in 95.8% and 83.3% of OMA, respectively, and in 100% and 80% of DIE, respectively. There was no significant difference between SPE, OMA, and DIE with regard to the SSTR1 (P=0.5) and SSTR5 (P=0.9) expression. We observed a significant difference between SPE (9.0%), OMA (16.6%), and DIE (63.3%) with regard to SSTR2 expression (P<0.05). The present study identifies 2 different immunohistochemical patterns of endometriosis lesions with regard to their SSTR expression: SSTR1+/SSTR2-/SSTR5+ for SPE and OMA, and SSTR1+/SSTR2+/SSTR5+ for DIE.

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Abstract 3079: Development of an automated platform for screening patient-derived organoid models
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Isolation and Characterization of Patient-derived Pancreatic Ductal Adenocarcinoma Organoid Models.
  • Jan 14, 2020
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Pancreatic ductal adenocarcinoma (PDAC) is amongst the most lethal malignancies. Recently, next-generation organoid culture methods enabling the 3-dimensional (3D) modeling of this disease have been described. Patient-derived organoid (PDO) models can be isolated from both surgical specimens as well as small biopsies and form rapidly in culture. Importantly, organoid models preserve the pathogenic genetic alterations detected in the patient's tumor and are predictive of the patient's treatment response, thus enabling translational studies. Here, we provide comprehensive protocols for adapting tissue culture workflow to study 3D, matrix embedded, organoid models. We detail methods and considerations for isolating and propagating primary PDAC organoids. Furthermore, we describe how bespoke organoid media is prepared and quality controlled in the laboratory. Finally, we describe assays for downstream characterization of the organoid models such as isolation of nucleic acids (DNA and RNA), and drug testing. Importantly we provide critical considerations for implementing organoid methodology in a research laboratory.

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  • Cite Count Icon 2
  • 10.1007/s12015-024-10733-3
Translational Utility of Organoid Models for Biomedical Research on Gastrointestinal Diseases.
  • May 17, 2024
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  • Pratibha Banerjee + 1 more

Organoid models have recently been utilized to study 3D human-derived tissue systems to uncover tissuearchitecture and adultstem cellbiology. Patient-derived organoids unambiguously provide the most suitable in vitro system to study disease biology with the actual genetic background. With the advent of much improved and innovative approaches, patient-derived organoids can potentially be used in regenerative medicine. Various human tissues were explored to develop organoids due to their multifold advantage over the conventional in vitro cell line culture approach and in vivo models. Gastrointestinal (GI) tissues have been widely studied to establish organoids and organ-on-chip for screening drugs, nutraceuticals, and other small molecules having therapeutic potential. The function of channel proteins, transporters, and transmembrane proteins was also explained. The successful application of genome editing in organoids using the CRISPR-Cas approach has been reported recently. GI diseases such as Celiac disease (CeD), Inflammatory bowel disease (IBD), and common GI cancers have been investigated using several patient-derived organoid models. Recent advancements on organoid bio-banking and 3D bio-printing contributed significantly in personalized disease management and therapeutics. This article reviews the available literature on investigations and translational applications of patient-derived GI organoid models, notably on elucidating gut-microbial interaction and epigenetic modifications.

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  • Research Article
  • Cite Count Icon 12
  • 10.1186/s12905-020-00974-y
Lesion distribution characteristics of deep infiltrating endometriosis with ovarian endometrioma: an observational clinical study
  • May 20, 2020
  • BMC Women's Health
  • Hungling Kwok + 7 more

BackgroundTo investigate the characteristics of deep infiltrating endometriosis (DIE) lesion distribution when associated with ovarian endometrioma (OEM).MethodsThe present study analyzed retrospective data obtained by the First Affiliated Hospital of Sun Yat-sen University, between June 2008 to June 2016. A total of 304 patients underwent laparoscopic surgery for complete removal of endometriosis by one experienced surgeon, and histological confirmation of OEM associated with DIE was conducted for each patient. Clinical data were recorded for each patient from medical, operative and pathological reports. Patients were then divided into two groups according to unilateral or bilateral OEM. Patients with unilateral OEM were subsequently divided into two subgroups according to OEM location (left- or right-hand side) and the diameter of the OEM (≤50 and > 50 mm). The distribution characteristics of DIE lesions were then compared between the groups.ResultsDIE lesions were widely distributed, 30 anatomical sites were involved. Patients with associated unilateral OEM (n = 184 patients) had a significantly increased number of DIE lesions when compared with patients with bilateral OEM (n = 120 patients; 2.76 ± 1.52 vs. 2.33 ± 1.34; P = 0.006). Compared with bilateral OEM with DIE, there was a higher rate of intestinal (39.1% vs. 18.3%; P < 0.01) and vaginal (17.4% vs. 6.7%; P < 0.01) infiltration by DIE lesions in unilateral OEM with DIE. The mean number of DIE lesions was not significantly correlated with the location or size of the OEM (2.83 ± 1.56 vs. 2.74 ± 1.53; P = 0.678; and 2.65 ± 1.42 vs. 2.80 ± 1.43; P = 0.518, respectively). There was no significant difference between the groups with OEM ≤50 mm and > 50 mm.ConclusionLesion distribution characteristics in women diagnosed with histologically proven OEM associated with DIE were frequently multifocal and severe.

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  • Cite Count Icon 1
  • 10.1158/1538-7445.am2020-3916
Abstract 3916: Patient-derived organoid and cell culture models from the NCI Patient-Derived Models Repository (NCI PDMR) preserve genomic stability and heterogeneity of patient tumor specimens
  • Aug 13, 2020
  • Cancer Research
  • Biswajit Das + 41 more

Background: The National Cancer Institute (NCI) has developed a Patient-Derived Models Repository (PDMR; https://pdmr.cancer.gov) of preclinical models including patient-derived xenografts (PDX), organoids (PDOrg) and patient-derived cell cultures (PDC). Extensive clinical annotation and genomic datasets are available for these preclinical models. However, it is unclear if the molecular profiles of the corresponding patient tumors are stably propagated in these models. We have previously demonstrated that PDX models from the NCI PDMR faithfully represent the patient tumors both in terms of genomic stability and tumor heterogeneity. Here, we conduct an in-depth investigation of genomic representation of patient tumors in the PDOrgs and PDCs. Methods: PDOrgs (n=64) and PDCs (n=94) were established from tumor fragments (i.e., initiator specimens) obtained either from patient specimens or from PDX specimens of early passage. For some models (n=19), both PDOrgs and PDCs were generated from the same tumor tissue; in fewer cases (n=4), PDCs were established from organoids derived from patient specimens. Whole Exome Sequencing and RNA-Seq were performed on all PDCs and PDOrgs, and data were compared with patient specimens or early passage PDXs. Results: A majority of the PDOrgs and PDCs have stably inherited the genome of the corresponding patient specimens based on the following observations: (1) &amp;gt;87% of PDOrgs and PDCs maintained similar copy number alteration profiles compared with the initiator specimens of the preclinical model; (2) the variant allele frequency (VAF) of clinically relevant mutations remained consistent between the PDOrgs, PDCs, and the initiator specimens, with none of the PDCs or PDOrgs deviating by &amp;gt;15% VAF; and (3) clinically relevant biomarkers (e.g., MSI, LOH, mutational signatures etc.) are concordant amongst the PDOrgs, PDCs, and the initiator specimens. We observed that the majority of SNVs and indels present in the initiator specimens were also found in the PDOrgs and PDCs, suggesting almost all the tumor heterogeneity was preserved in these preclinical models. Conclusions: This large and histologically diverse set of PDOrgs and PDCs from the NCI PDMR exhibited genomic stability and faithfully represented the tumor heterogeneity observed in corresponding patient specimens. These preclinical models thus represent a valuable resource for researchers interested in pre-clinical drug or other studies. Citation Format: Biswajit Das, Yvonne A. Evrard, Li Chen, Rajesh Patidar, Tomas Vilimas, Justine N. McCutcheon, Amanda L. Peach, Nikitha V. Nair, Thomas D. Forbes, Brandie A. Fullmer, Anna J. Lee Fong, Luis E. Romero, Alyssa K. Chapman, Kelsey A. Conley, Robin D. Harrington, Shahanawaz S. Jiwani, Peng Wang, Michelle M. Gottholm-Ahalt, Erin N. Cantu, Gloryvee Rivera, Lindsay M. Dutko, Kelly M. Benauer, Vishnuprabha R. Kannan, Carrie A. Bonomi, Kelly M. Dougherty, Joseph P. Geraghty, Marion V. Gibson, Savanna S. Styers, Abigail J. Walke, Jenna E. Moyer, Anna Wade, Mariah L. Baldwin, Kaitlyn A. Arthur, Kevin J. Plater, Luke Stockwin, Matthew R. Murphy, Michael E. Mullendore, Dianne L. Newton, Melinda G. Hollingshead, Chris A. Karlovich, Paul M. Williams, James H. Doroshow. Patient-derived organoid and cell culture models from the NCI Patient-Derived Models Repository (NCI PDMR) preserve genomic stability and heterogeneity of patient tumor specimens [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3916.

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  • Research Article
  • Cite Count Icon 7
  • 10.1155/2014/140413
Endometriosis: Novel Models, Diagnosis, and Treatment
  • Jan 1, 2014
  • BioMed Research International
  • Renato Seracchioli + 3 more

Endometriosis: Novel Models, Diagnosis, and Treatment

  • Research Article
  • 10.1093/neuonc/noac174.100
P02.07.B Patient-derived glioblastoma organoids: Elucidating the mechanisms of glioblastoma therapeutic resistance in the context of tumor microenvironment
  • Sep 5, 2022
  • Neuro-Oncology
  • A Habič + 7 more

Background Intratumoral heterogeneity plays an important role in glioblastoma (GB) resistance to standard therapy consisting of irradiation and chemotherapy with temozolomide (TMZ). However, classical in vitro GB models fail to represent the complex cellular composition of tumors in vivo, which hinders relevant examination of GB therapeutic response. To overcome these limitations, we studied the effects of irradiation and TMZ in a novel patient-derived organoid model. Material and Methods We established a patient-derived GB organoid model by a protocol recently published by Jacob et al. Original tumor tissue and tissue-derived organoids were compared by immunofluorescence staining of selected cell type markers and qPCR analysis of expression levels of a panel of selected target genes, including 15 genes defining GB subtypes. To analyze GB therapeutic response, organoids from 11 patients were exposed to a single dose of irradiation (10 Gy), one-week treatment with TMZ (50 µM) or their combination. The effects of therapy were assessed by viability and invasion assays. Expression levels of a number of genes related to GB subtypes, epithelial-mesenchymal transition, stemness, DNA damage responses, cell cycle, cytokines, and cell markers of the tumor microenvironment (TME) were compared between treated organoids and untreated controls. In addition, the heterogeneity of the TME and its responses to treatment were investigated by spatially resolved transcriptomics with in situ sequencing (ISS) methodology. Results Organoids recapitulate inter-patient variability and reflect the cellular composition and gene expression levels of the tumor tissue from which they were derived. GB stem cells and differentiated cancer cells are present in organoids along with various cells of the TME, e.g., macrophages and microglia, lymphocytes, and endothelial cells. Irradiation and TMZ showed no significant effects on organoid viability and invasion. However, some target genes were differentially expressed in the treated organoids, such as E3 ubiquitin-protein ligase MDM2 and cyclin-dependent kinase inhibitor 1A (CDKN1A). To our knowledge, we are the first to apply spatially resolved transcriptomics (ISS) to formalin-fixed, paraffin-embedded sections of (un)treated GB organoids. Our results elucidate the role of the TME in GB therapeutic response and shed light on potential mechanism underlying GB therapy resistance. Conclusion Patient-derived GB organoids recapitulate the key characteristics and complex composition of patient’s tumor tissue, providing a valuable platform for studies of GB therapeutic response and resistance.

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  • Research Article
  • Cite Count Icon 77
  • 10.3390/jcm9020496
Recurrence Patterns after Surgery in Patients with Different Endometriosis Subtypes: A Long-Term Hospital-Based Cohort Study
  • Feb 11, 2020
  • Journal of Clinical Medicine
  • Konstantinos Nirgianakis + 3 more

Recurrence of endometriosis after surgery constitutes a serious challenge. Whether there is an evolution of lesion subtypes with each recurrence and whether certain lesions subtypes tend to recur faster than others is not adequately addressed. Medical records of all patients who underwent surgery for endometriosis between 1997 and 2018 in the Department of Gynecology and Obstetrics, University of Bern, were reviewed. Inclusion criteria was surgically confirmed endometriosis recurrence, defined as a subsequent surgery for endometriosis after a previous complete surgical excision of endometriosis lesions. Three subtypes of endometriosis were defined: superficial peritoneal endometriosis (SUP), ovarian endometrioma (OMA), and deep infiltrating endometriosis (DIE). Time to recurrence and variation in endometriosis subtype between the first and recurrent surgeries were the primary outcome measures. Out of the 322 patients with recurrent surgery that were identified, for 234 of them, the endometriosis subtype at first surgery was confirmed and classified (SUP = 56, OMA = 124, DIE = 54). No statistically significant difference was found for time to recurrence between lesion subtypes. SUP compared to the other groups had a higher possibility of presenting with SUP at recurrence (Odds Ratio (OR): 3.65, 95% confidence interval (CI): 1.74–7.51) and OMA compared to the other groups had a higher possibility of presenting with OMA at recurrence (OR: 3.72, 95% CI: 2.04–6.74). Nevertheless, a large number of SUP patients subsequently presented with OMA (10/56: 17.9%) or DIE (27/56: 48.2%) lesions at recurrence. Similarly, a large number of OMA patients subsequently presented with DIE (49/124: 39.5%) lesions at recurrence. In conclusion, although SUP and OMA patients compared to the others are more likely to present with the same subtype at recurrence, increasing lesion subtype severity occurs in a substantial proportion of patients. Time to recurrence is independent from the lesion subtype at first surgery.

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