Hi-C profiling of cancer spheroids identifies 3D-growth-specific chromatin interactions in breast cancer endocrine resistance

Jingwei Li, Kun Fang, Lavanya Choppavarapu, Ke Yang, Yini Yang, Junbai Wang, Ruifeng Cao, Ismail Jatoi, Victor X. Jin

Research output: Contribution to journalArticlepeer-review

9 Scopus citations


Background: Organoids or spheroids have emerged as a physiologically relevant in vitro preclinical model to study patient-specific diseases. A recent study used spheroids of MCF10 cells to model breast cancer progression and identified targetable alterations more similar to those in vivo. Thus, it is practical and essential to explore and characterize the spheroids of the commonly used human breast cancer (BC) cells. Methods: In this study, we conducted Hi-C analyses in three-dimensional (3D) spheroids of MCF10A, MCF7 and MCF7TR cells and compared TADs and looping genes with those in 2D monolayers. Furthermore, we performed in silico functional analysis on 3D-growth-specific looping genes and to compare patient outcomes with or without endocrinal therapy. Finally, we performed 3C/RT-qPCR validations in 3D spheroids and 3D-FISH confirmations in organoids of breast cancer patient tissues. Results: We found that chromatin structures have experienced drastic changes during the 3D culture growth of BC cells although there is not much change in the quantity of chromatin domains. We also observed that the strengths of looping genes were statistically different between 2D monolayers and 3D spheroids. We further identified novel 3D growth-specific looping genes within Hippo relevant pathways, of which two genes showed potential prognostic values in measuring the outcome of the endocrine treatment. We finally confirmed a few selected genes in Hippo relevant pathways with enhanced looping in organoids of breast cancer patient tissues. Conclusions: Hence, our work has provided significant insights into our understanding of 3D-growth-specific chromatin architecture in tamoxifen-resistant breast cancer. Our analyses suggest that the strengthened looping-mediated Hippo relevant pathways may contribute to endocrine therapy resistance in breast cancer patients.

Original languageEnglish (US)
Article number175
JournalClinical Epigenetics
Issue number1
StatePublished - Dec 2021


  • 3D spheroids
  • Hi-C
  • Looping genes
  • Organoids
  • Tamoxifen-resistant breast cancer

ASJC Scopus subject areas

  • Genetics(clinical)
  • Genetics
  • Molecular Biology
  • Developmental Biology


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