Individualized Breast Cancer Characterization through Single-Cell Analysis of Tumor and Adjacent Normal Cells

Anjanappa, Manjushree; Cardoso, Angelo A.; Cheng, Lijun; Mohamad, Safa; Gunawan, Andrea; Rice, Susan; Dong, Yan; Li, Lang; Sandusky, George E.; Srour, Edward F.; Nakshatri, Harikrishna

doi:10.1158/0008-5472.can-16-3308

Cited by 17 publications

(20 citation statements)

References 37 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Because gene expression in normal tissues shows interindividual variations due to SNP in the gene regulatory regions (27), we had recently proposed that normal cells from the same patient need to be used to determine cancer-specific gene expression changes (28). Although the use of cells from normal tissues adjacent to tumor is far from perfect because of cancer-induced field defects on adjoining cells (29,30), it is still better to use those cells or from the unaffected contralateral breast than normal cells from unrelated individuals as controls to identify cancer-specific gene expression changes.…”

Section: Individualizing Tumor Characterization Through Propagation Omentioning

confidence: 99%

Dual TGFβ/BMP Pathway Inhibition Enables Expansion and Characterization of Multiple Epithelial Cell Types of the Normal and Cancerous Breast

Prasad

Kumar

Bhat‐Nakshatri

et al. 2019

Molecular Cancer Research

Self Cite

View full text Add to dashboard Cite

Functional modeling of normal breast epithelial hierarchy and stromal-epithelial cell interactions have been difficult due to inability to obtain sufficient stem-progenitor-mature epithelial and stromal cells. Recently reported epithelial reprogramming assay has partially overcome this limitation, but cross-contamination of cells from the feeder layer is a concern. The purpose of this study was to develop a feeder-layerindependent and inexpensive method to propagate multiple cell types from limited tissue resources. Cells obtained after enzymatic digestion of tissues collected at surgery or by coreneedle biopsies were plated on tissue culture dishes precoated with laminin-5-rich-conditioned media from the rat bladder tumor cell line 804G and a defined growth media with inhibitors of ROCK, TGFb, and BMP signaling. Cells were characterized by flow cytometry, mammosphere assay, 3D cultures, and xenograft studies. Cells from the healthy breasts included CD10 þ /EpCAM À basal/myoepithelial, CD49f þ /EpCAM þ luminal progenitor, CD49f À /EpCAM þ mature luminal, CD73 þ /EpCAM þ /CD90 À rare endogenous pluripotent somatic stem, CD73 þ /CD90 þ /EpCAM À , estrogen receptor alpha-expressing ALCAM (CD166) þ /EpCAM þ , and ALDFLUOR þ stem/luminal progenitor subpopulations. Epithelial cells were luminal (KRT19 þ ), basal (KRT14 þ ), or dual-positive luminal/basal hybrid cells. While breast cells derived from BRCA1, BRCA2, and PALB2 mutation carriers did not display unique characteristics, cells from women with breast cancer-protective alleles showed enhanced differentiation. Cells could also be propagated from primary tumors and metastasis of breast, ovarian, and pancreatic cancerneuroendocrine subtype. Xenograft studies confirmed tumorigenic properties of tumor-derived cells.Implications: Our method expands the scope of individualized studies of patient-derived cells and provides resources to model epithelial-stromal interactions under normal and pathologic conditions.

show abstract

Section: Individualizing Tumor Characterization Through Propagation Omentioning

confidence: 99%

Dual TGFβ/BMP Pathway Inhibition Enables Expansion and Characterization of Multiple Epithelial Cell Types of the Normal and Cancerous Breast

Prasad

Kumar

Bhat‐Nakshatri

et al. 2019

Molecular Cancer Research

Self Cite

View full text Add to dashboard Cite

show abstract

“…scRNA-seq reports in the past years have provided useful information in this respect. Different types of CAFs have been reported in breast and colorectal tumors, which is likely to be associated with different cell origins [34][35][36]. Additionally, each group of CAFs has special functions in the recruitment of immune cells and in the induction of the epithelial-mesenchymal transition (EMT) in tumor cells [24,29,34,36].…”

Section: Tumor Microenvironmentmentioning

confidence: 99%

Tumor Functional Heterogeneity Unraveled by scRNA-seq Technologies

2020

View full text Add to dashboard Cite

Effective cancer treatment has been precluded by the presence of various forms of intratumoral complexity that drive treatment resistance and metastasis. Recent single-cell sequencing technologies are significantly facilitating the characterization of tumor internal architecture during disease progression. New applications and advances occurring at a fast pace predict an imminent broad application of these technologies in many research areas. As occurred with next-generation sequencing (NGS) technologies, once applied to clinical samples across tumor types, single-cell sequencing technologies could trigger an exponential increase in knowledge of the molecular pathways involved in cancer progression and contribute to the improvement of cancer treatment. Multifaceted Heterogeneity and Its Impact on Cancer ProgressionTumors comprise various cell populations in constant evolution. Some of this complex heterogeneity derives from genetic diversification and Darwinian selection of tumor cells as they adapt to variable environments. Next-generation sequencing (NGS; see Glossary) used for the past decade had enough sensitivity to detect mutations present in minor cell populations and, combined with multisampling of human tumors (multisampling sequencing), fostered many studies that characterized intratumor heterogeneity in various cancers [1]. The level of intratumor heterogeneity is considered a main driver of therapy resistance and metastasis and is associated with poor prognosis [2].In addition, human cancers frequently have tumor cell populations with different transcriptional programs. This functional diversity is likely associated with the genetic heterogeneity described above but is also the result of many other factors. First, the presence of a hierarchical structure, where a group of quiescent stem-like cells fosters the growth of a tumor comprising cells in different differentiation states, was demonstrated in various tumor types [3]. Additionally, different transcriptional programs can be activated in tumor cells as a response to stochastic factors or to a variable tumor microenvironment. This functional diversity provides tumors with a plasticity that grants a high capacity for adaptation [4].Finally, human tumors comprise not only malignant/transformed cells but also a plethora of different cell types recruited from the surrounding tissue and the immune system. The tumor microenvironment shows also genetic and transcriptional diversity and plays important roles in tumor progression, metastasis, and treatment resistance [1,5].Fine characterization of these levels of tumor heterogeneity is essential to the successful treatment of cancer patients. The recent development of technologies based on sequencing individual cells (single-cell sequencing technologies) opens new ways for the characterization of tumor heterogeneity. At the genetic level, single-cell DNA-seq technologies offer higher sensitivity in the detection of minority clones, the reconstruction of clone structure, and the identification of concurrent ...

show abstract

“…From a basic research point of view, results presented here provides an opportunity to determine whether a gene is truly differentially expressed in tumors compared to normal, as the expression pattern of a specific gene in the tumor could be a reflection of its cell-of-origin. Using single cell RT-PCR of tumor adjacent normal and tumor cells from the same individual, we had previously demonstrated that elevated expression of few genes in tumor can be attributed to cellof-origin of tumor instead due to tumor-specific genomic aberration (Anjanappa et al, 2017).…”

Section: Gene Signatures Of Epithelial Clusters and Their Relevance Tmentioning

confidence: 99%

“…While HER2+ breast cancers may originate from luminal progenitors and mature luminal cells, luminal-A/B breast cancers likely originate from mature luminal cells (Prat and Perou, 2009). However, it is acknowledged that heterogeneity exists within basal/stem, luminal progenitors and mature luminal cells as defined by CD49f/EpCAM cell surface marker profiling (Anjanappa et al, 2017;Colacino et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

A single cell atlas of the healthy breast tissues reveal clinically relevant clusters of breast epithelial cells

Bhat‐Nakshatri

Gao

McGuire

et al. 2020

Preprint

Self Cite

View full text Add to dashboard Cite

Significance:This study elucidates different epithelial cell types of the normal breasts and identifies a minor subpopulation of cells from which the majority of breast cancers may originate. This observation should help to develop methods to characterize breast tumors based on cell-of-origin. Although it was suggested that intrinsic subtypes of breast cancers have distinct cells of origins, this study suggests multiple cell-of-origin for an intrinsic subtype of breast cancer, including for hormone responsive breast cancers. Cell-of-origin signatures allowed survival-associated subclassification of intrinsic subtypes. Critically, this normal breast cell atlas would allow for the classification of genes differentially expressed in a breast tumor compared to normal breast due to the cell-of-origin of tumor and those that are acquired due to genomic aberrations.

show abstract

Individualized Breast Cancer Characterization through Single-Cell Analysis of Tumor and Adjacent Normal Cells

Cited by 17 publications

References 37 publications

Dual TGFβ/BMP Pathway Inhibition Enables Expansion and Characterization of Multiple Epithelial Cell Types of the Normal and Cancerous Breast

Dual TGFβ/BMP Pathway Inhibition Enables Expansion and Characterization of Multiple Epithelial Cell Types of the Normal and Cancerous Breast

Tumor Functional Heterogeneity Unraveled by scRNA-seq Technologies

A single cell atlas of the healthy breast tissues reveal clinically relevant clusters of breast epithelial cells

Contact Info

Product

Resources

About