<p>Dear Editor,</p><p>Breast cancer organoids (BCOs) are increasingly recognised as crucial tools in personalised medicine,<span><sup>1</sup></span> yet a significant gap remains between the need for precise drug sensitivity assessments and the biological disparities observed between BCOs and primary breast cancer (PBC) tissues.<span><sup>2, 3</sup></span> Our extensive analysis of paired single-cell RNA sequencing data has revealed a substantial preservation of molecular characteristics in hormone receptor-positive (HR-positive) and HER2-positive breast cancers. However, in triple-negative breast cancer (TNBC), we observed marked variability in cell subpopulations, likely influenced by oxygen-enriched culture conditions.</p><p>To investigate the preservation of characteristics across different molecular subtypes of breast cancer, we cultured six BCOs representing three subtypes: two HR-positive, two HER2-positive, and two TNBCs derived from surgical samples without prior adjuvant treatments (for study design, see Figure S1; for images of successfully established organoids, see Figure S2; patient clinical characteristics are detailed in the Supplementary Table). Following establishment, single-cell RNA sequencing was performed on matched PBCs and BCOs, yielding 66,920 quality-controlled cells (Figure 1A; for contributions of samples, molecular subtypes, and sample sources, see Figure S3). Our analysis of cell type composition revealed a significant reduction in immune and stromal cells in BCOs compared to PBCs (adjusted <i>p</i> < 0.001; Figure 1B), while epithelial cells proportions nearly doubled (<i>p</i> = 0.031, median fold change = 0.96, IQR = 0.94-1.78, Figure 1C). This suggests that organoid culture better preserves epithelial cells, and co-culture systems are required for the preservation of the tumour microenvironment (TME).<span><sup>4</sup></span> Further analyses demonstrated reductions in both the proportions and functionality of all immune and stromal cell subpopulations (Figure 1D-F). Notably, both malignant and non-malignant epithelial cells were amplified in BCOs while maintaining key functional characteristics (Figure 1G-I; see Methods section in Supplementary Materials for malignancy determination). Thus, despite the observed differences in cell type distribution, these findings did not diminish the value of organoids as robust in vitro models for studying epithelial components of tumours.</p><p>To assess genomic concordance in PDOs,<sup>5</sup> we analysed copy number variation (CNV) as a genomic marker between BCOs and PBCs using both paired and unpaired comparisons. Our findings revealed that BCOs effectively preserved cellular-level CNVs from PBCs in five out of six cases (Figure 2A), with an average retention rate of 71.6%. This preservation was particularly robust in HR-positive breast cancer at 88.2%, though it was less pronounced in TNBC at 62.4% (Figure 2B and C). Moreover, BCOs demonstrated the ability to amplify
{"title":"Distinct discrepancy in breast cancer organoids recapitulation among molecular subtypes revealed by single-cell transcriptomes analysis","authors":"Ziqi Jia, Hengyi Xu, Yaru Zhang, Heng Cao, Chunyu Deng, Longchen Xu, Yuning Sun, Jiayi Li, Yansong Huang, Pengming Pu, Tongxuan Shang, Xiang Wang, Jianzhong Su, Jiaqi Liu","doi":"10.1002/ctm2.70023","DOIUrl":"https://doi.org/10.1002/ctm2.70023","url":null,"abstract":"<p>Dear Editor,</p><p>Breast cancer organoids (BCOs) are increasingly recognised as crucial tools in personalised medicine,<span><sup>1</sup></span> yet a significant gap remains between the need for precise drug sensitivity assessments and the biological disparities observed between BCOs and primary breast cancer (PBC) tissues.<span><sup>2, 3</sup></span> Our extensive analysis of paired single-cell RNA sequencing data has revealed a substantial preservation of molecular characteristics in hormone receptor-positive (HR-positive) and HER2-positive breast cancers. However, in triple-negative breast cancer (TNBC), we observed marked variability in cell subpopulations, likely influenced by oxygen-enriched culture conditions.</p><p>To investigate the preservation of characteristics across different molecular subtypes of breast cancer, we cultured six BCOs representing three subtypes: two HR-positive, two HER2-positive, and two TNBCs derived from surgical samples without prior adjuvant treatments (for study design, see Figure S1; for images of successfully established organoids, see Figure S2; patient clinical characteristics are detailed in the Supplementary Table). Following establishment, single-cell RNA sequencing was performed on matched PBCs and BCOs, yielding 66,920 quality-controlled cells (Figure 1A; for contributions of samples, molecular subtypes, and sample sources, see Figure S3). Our analysis of cell type composition revealed a significant reduction in immune and stromal cells in BCOs compared to PBCs (adjusted <i>p</i> < 0.001; Figure 1B), while epithelial cells proportions nearly doubled (<i>p</i> = 0.031, median fold change = 0.96, IQR = 0.94-1.78, Figure 1C). This suggests that organoid culture better preserves epithelial cells, and co-culture systems are required for the preservation of the tumour microenvironment (TME).<span><sup>4</sup></span> Further analyses demonstrated reductions in both the proportions and functionality of all immune and stromal cell subpopulations (Figure 1D-F). Notably, both malignant and non-malignant epithelial cells were amplified in BCOs while maintaining key functional characteristics (Figure 1G-I; see Methods section in Supplementary Materials for malignancy determination). Thus, despite the observed differences in cell type distribution, these findings did not diminish the value of organoids as robust in vitro models for studying epithelial components of tumours.</p><p>To assess genomic concordance in PDOs,<sup>5</sup> we analysed copy number variation (CNV) as a genomic marker between BCOs and PBCs using both paired and unpaired comparisons. Our findings revealed that BCOs effectively preserved cellular-level CNVs from PBCs in five out of six cases (Figure 2A), with an average retention rate of 71.6%. This preservation was particularly robust in HR-positive breast cancer at 88.2%, though it was less pronounced in TNBC at 62.4% (Figure 2B and C). Moreover, BCOs demonstrated the ability to amplify ","PeriodicalId":10189,"journal":{"name":"Clinical and Translational Medicine","volume":"14 9","pages":""},"PeriodicalIF":7.9,"publicationDate":"2024-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ctm2.70023","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142276619","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}