Dissection of triple-negative breast cancer microenvironment and identification of potential therapeutic drugs using single-cell RNA sequencing analysis

Weilun Cheng; Wanqi Mi; Shiyuan Wang; Xinran Wang; Hui Jiang; Jing Chen; Kaiyue Yang; Wenqi Jiang; Jun Ye; Baoliang Guo; Yunpeng Zhang

doi:10.1016/j.jpha.2024.100975

Volume 14 Issue 8

Aug. 2024

Turn off MathJax

Article Contents

Article Navigation > Journal of Pharmaceutical Analysis > 2024 > 14(8): 100975

Weilun Cheng, Wanqi Mi, Shiyuan Wang, Xinran Wang, Hui Jiang, Jing Chen, Kaiyue Yang, Wenqi Jiang, Jun Ye, Baoliang Guo, Yunpeng Zhang. Dissection of triple-negative breast cancer microenvironment and identification of potential therapeutic drugs using single-cell RNA sequencing analysis[J]. Journal of Pharmaceutical Analysis, 2024, 14(8): 100975. doi: 10.1016/j.jpha.2024.100975

Citation:

Weilun Cheng, Wanqi Mi, Shiyuan Wang, Xinran Wang, Hui Jiang, Jing Chen, Kaiyue Yang, Wenqi Jiang, Jun Ye, Baoliang Guo, Yunpeng Zhang. Dissection of triple-negative breast cancer microenvironment and identification of potential therapeutic drugs using single-cell RNA sequencing analysis[J]. Journal of Pharmaceutical Analysis, 2024, 14(8): 100975. doi: 10.1016/j.jpha.2024.100975

Citation:

Weilun Cheng, Wanqi Mi, Shiyuan Wang, Xinran Wang, Hui Jiang, Jing Chen, Kaiyue Yang, Wenqi Jiang, Jun Ye, Baoliang Guo, Yunpeng Zhang. Dissection of triple-negative breast cancer microenvironment and identification of potential therapeutic drugs using single-cell RNA sequencing analysis[J]. Journal of Pharmaceutical Analysis, 2024, 14(8): 100975. doi: 10.1016/j.jpha.2024.100975

PDF( 9454 KB)

Dissection of triple-negative breast cancer microenvironment and identification of potential therapeutic drugs using single-cell RNA sequencing analysis

doi: 10.1016/j.jpha.2024.100975

a. Department of General Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150001, China;
b. College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China;
c. State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China

Funds:

This research was funded by the National Natural Science Foundation of China (Grant Nos: 62172131 and 81872135) and the Outstanding Youth Foundation of Heilongjiang Province of China (Grant No.: YQ2021C026).

Received Date: Feb. 02, 2024
Accepted Date: Mar. 30, 2024
Rev Recd Date: Mar. 28, 2024
Publish Date: Apr. 02, 2024

Abstract

Abstract

Breast cancer remains a leading cause of mortality in women worldwide. Triple-negative breast cancer (TNBC) is a particularly aggressive subtype characterized by rapid progression, poor prognosis, and lack of clear therapeutic targets. In the clinic, delineation of tumor heterogeneity and development of effective drugs continue to pose considerable challenges. Within the scope of our study, high heterogeneity inherent to breast cancer was uncovered based on the landscape constructed from both tumor and healthy breast tissue samples. Notably, TNBC exhibited significant specificity regarding cell proliferation, differentiation, and disease progression. Significant associations between tumor grade, prognosis, and TNBC oncogenes were established via pseudotime trajectory analysis. Consequently, we further performed comprehensive characterization of the TNBC microenvironment. A crucial epithelial subcluster, E8, was identified as highly malignant and strongly associated with tumor cell proliferation in TNBC. Additionally, epithelial-mesenchymal transition (EMT)-associated fibroblast and M2 macrophage subclusters exerted an influence on E8 through cellular interactions, contributing to tumor growth. Characteristic genes in these three cluster cells could therefore serve as potential therapeutic targets for TNBC. The collective findings provided valuable insights that assisted in the screening of a series of therapeutic drugs, such as pelitinib. We further confirmed the anti-cancer effect of pelitinib in an orthotopic 4T1 tumor-bearing mouse model. Overall, our study sheds light on the unique characteristics of TNBC at single-cell resolution and the crucial cell types associated with tumor cell proliferation that may serve as potent tools in the development of effective anti-cancer drugs.
- Triple-negative breast cancer,
- Single-cell RNA sequencing,
- Epithelial-mesenchymal transition,
- Macrophage polarization,
- Therapeutic drugs,
- Bioinformatics

FullText(HTML)

References(82)

References

[1]	H. Sung, J. Ferlay, R.L. Siegel, et al., Global cancer statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries, CA Cancer J. Clin. 71(2021) 209-249.
[2]	C.M. Perou, T. Soerlie, M.B. Eisen, et al., Molecular portraits of human breast tumours, Nature 406(2000) 747-752.
[3]	A. Goldhirsch, W.C. Wood, A.S. Coates, et al., Strategies for subtypes - Dealing with the diversity of breast cancer: Highlights of the St. Gallen International Expert Consensus on the Primary Therapy of Early Breast Cancer 2011, Ann. Oncol. 22(2011) 1736-1747.
[4]	F.M. Howard, O.I. Olopade, Epidemiology of triple-negative breast cancer: A review, Cancer J. 27(2021) 8-16.
[5]	N. Harbeck, M. Gnant, Breast cancer, Lancet 389(2017) 1134-1150.
[6]	W.J. Gradishar, M.S. Moran, J. Abraham, et al., NCCN guidelines^® insights: Breast cancer, version 4.2023, J. Natl. Compr. Canc. Netw. 21(2023) 594-608.
[7]	Y. Li, H. Zhang, Y. Merkher, et al., Recent advances in therapeutic strategies for triple-negative breast cancer, J. Hematol. Oncol. 15(2022), 121.
[8]	S. Ding, X. Chen, K. Shen, Single-cell RNA sequencing in breast cancer: Understanding tumor heterogeneity and paving roads to individualized therapy, Cancer Commun. (Lond.) 40(2020) 329-344.
[9]	R. Sklavenitis-Pistofidis, G. Getz, I. Ghobrial, Single-cell RNA sequencing: One step closer to the clinic, Nat. Med. 27(2021) 375-376.
[10]	Y. Zhang, H. Chen, H. Mo, et al., Single-cell analyses reveal key immune cell subsets associated with response to PD-L1 blockade in triple-negative breast cancer, Cancer Cell 39(2021) 1578-1593.e8.
[11]	T. Liu, C. Liu, M. Yan, et al., Single cell profiling of primary and paired metastatic lymph node tumors in breast cancer patients, Nat. Commun. 13(2022), 6823.
[12]	M. Karaayvaz, S. Cristea, S.M. Gillespie, et al., Unravelling subclonal heterogeneity and aggressive disease states in TNBC through single-cell RNA-seq, Nat. Commun. 9(2018), 3588.
[13]	A. Sebastian, N.R. Hum, K.A. Martin, et al., Single-cell transcriptomic analysis of tumor-derived fibroblasts and normal tissue-resident fibroblasts reveals fibroblast heterogeneity in breast cancer, Cancers 12(2020), 1307.
[14]	C. Curtis, S.P. Shah, S.-F. Chin, et al., The genomic and transcriptomic architecture of 2, 000 breast tumours reveals novel subgroups, Nature 486(2012) 346-352.
[15]	E. Cerami, J. Gao, U. Dogrusoz, et al., The cBio cancer genomics portal: An open platform for exploring multidimensional cancer genomics data, Cancer Discov. 2(2012) 401-404.
[16]	Y. Hao, T. Stuart, M.H. Kowalski, et al., Dictionary learning for integrative, multimodal and scalable single-cell analysis, Nat. Biotechnol. 42(2024) 293-304.
[17]	I. Korsunsky, N. Millard, J. Fan, et al., Fast, sensitive and accurate integration of single-cell data with Harmony, Nat. Meth. 16(2019) 1289-1296.
[18]	A. Subramanian, P. Tamayo, V.K. Mootha, et al., Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles, Proc. Natl. Acad. Sci. U. S. A. 102(2005) 15545-15550.
[19]	T. Wu, E. Hu, S. Xu, et al., clusterProfiler 4.0: A universal enrichment tool for interpreting omics data, Innovation (Camb) 2(2021), 100141.
[20]	M. Kanehisa, M. Furumichi, Y. Sato, et al., KEGG for taxonomy-based analysis of pathways and genomes, Nucleic Acids Res. 51(2023) D587-D592.
[21]	A.P. Patel, I. Tirosh, J.J. Trombetta, et al., Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma, Science 344(2014) 1396-1401.
[22]	R. Gao, S. Bai, Y.C. Henderson, et al., Delineating copy number and clonal substructure in human tumors from single-cell transcriptomes, Nat. Biotechnol. 39(2021) 599-608.
[23]	J. Cao, M. Spielmann, X. Qiu, et al., The single-cell transcriptional landscape of mammalian organogenesis, Nature 566(2019) 496-502.
[24]	K. Yoshihara, M. Shahmoradgoli, E. Martinez, et al., Inferring tumour purity and stromal and immune cell admixture from expression data, Nat. Commun. 4(2013), 2612.
[25]	S. Morabito, F. Reese, N. Rahimzadeh, et al., hdWGCNA identifies co-expression networks in high-dimensional transcriptomics data, Cell Rep. Methods 3(2023), 100498.
[26]	L. Garcia-Alonso, V. Lorenzi, C.I. Mazzeo, et al., Single-cell roadmap of human gonadal development, Nature 607(2022) 540-547.
[27]	P. Shannon, A. Markiel, O. Ozier, et al., Cytoscape: A software environment for integrated models of biomolecular interaction networks, Genome Res. 13(2003) 2498-2504.
[28]	B. He, Y. Xiao, H. Liang, et al., ASGARD is A single-cell guided pipeline to aid repurposing of drugs, Nat. Commun. 14(2023), 993.
[29]	S. Detre, G. Saclani Jotti, M. Dowsett, A “quickscore” method for immunohistochemical semiquantitation: Validation for oestrogen receptor in breast carcinomas, J. Clin. Pathol. 48(1995) 876-878.
[30]	C. Hu, T. Li, Y. Xu, et al., CellMarker 2.0: An updated database of manually curated cell markers in human/mouse and web tools based on scRNA-seq data, Nucleic Acids Res. 51(2023) D870-D876.
[31]	W.C. Huang, J.H. Yen, Y.W. Sung, et al., Novel function of THEMIS2 in the enhancement of cancer stemness and chemoresistance by releasing PTP1B from MET, Oncogene 41(2022) 997-1010.
[32]	V.G. LeBlanc, D.L. Trinh, S. Aslanpour, et al., Single-cell landscapes of primary glioblastomas and matched explants and cell lines show variable retention of inter- and intratumor heterogeneity, Cancer Cell 40(2022) 379-392.e9.
[33]	S. Zheng, Y. Zou, Y. Tang, et al., Landscape of cancer-associated fibroblasts identifies the secreted biglycan as a protumor and immunosuppressive factor in triple-negative breast cancer, Oncoimmunology 11(2022), 2020984.
[34]	L. Hu, L. Su, H. Cheng, et al., Single-cell RNA sequencing reveals the cellular origin and evolution of breast cancer in BRCA1 mutation carriers, Cancer Res. 81(2021) 2600-2611.
[35]	X. Yan, Y. Xie, F. Yang, et al., Comprehensive description of the current breast cancer microenvironment advancements via single-cell analysis, J. Exp. Clin. Cancer Res. 40(2021), 142.
[36]	M. Pecoraro, S. Marzocco, S. Franceschelli, et al., Trastuzumab and doxorubicin sequential administration increases oxidative stress and phosphorylation of connexin 43 on Ser368, Int. J. Mol. Sci. 23(2022), 6375.
[37]	S. Heublein, D. Mayr, A. Meindl, et al., Vitamin D receptor, Retinoid X receptor and peroxisome proliferator-activated receptor γ are overexpressed in BRCA1 mutated breast cancer and predict prognosis, J. Exp. Clin. Cancer Res. 36(2017), 57.
[38]	M. Anurag, E.J. Jaehnig, K. Krug, et al., Proteogenomic markers of chemotherapy resistance and response in triple-negative breast cancer, Cancer Discov. 12(2022) 2586-2605.
[39]	S. Vegunta, J.M. Kling, E. Kapoor, Androgen therapy in women, J. Womens Health (Larchmt) 29(2020) 57-64.
[40]	D.N. Edwards, V.M. Ngwa, A.L. Raybuck, et al., Selective glutamine metabolism inhibition in tumor cells improves antitumor T lymphocyte activity in triple-negative breast cancer, J. Clin. Invest. 131(2021), e140100.
[41]	K.G.K. Deepak, R. Vempati, G.P. Nagaraju, et al., Tumor microenvironment: Challenges and opportunities in targeting metastasis of triple negative breast cancer, Pharmacol. Res. 153(2020), 104683.
[42]	J.R. Whittle, F. Vaillant, E. Surgenor, et al., Dual targeting of CDK4/6 and BCL2 pathways augments tumor response in estrogen receptor-positive breast cancer, Clin. Cancer Res. 26(2020) 4120-4134.
[43]	V.S. Periasamy, A. Riyasdeen, V. Rajendiran, et al., Induction of redox-mediated cell death in ER-positive and ER-negative breast cancer cells by a copper(II)-phenolate complex: An in vitro and in silico study, Molecules 25(2020), 4504.
[44]	S. Taurin, H. Alkhalifa, Breast cancers, mammary stem cells, and cancer stem cells, characteristics, and hypotheses, Neoplasia 22(2020) 663-678.
[45]	R. Vishnubalaji, N.M. Alajez, Epigenetic regulation of triple negative breast cancer (TNBC) by TGF-β signaling, Sci. Rep. 11(2021), 15410.
[46]	W. Bocker, WHO classification of breast tumors and tumors of the female genital organs: Pathology and genetics, Verh. Dtsch Ges. Pathol. 86(2002) 116-119.
[47]	N. Liu, X. Wang, Z. Zhu, et al., Selected ideal natural ligand against TNBC by inhibiting CDC20, using bioinformatics and molecular biology, Aging 13(2021) 23702-23725.
[48]	Y. Liu, L. Teng, S. Fu, et al., Highly heterogeneous-related genes of triple-negative breast cancer: Potential diagnostic and prognostic biomarkers, BMC Cancer 21(2021), 644.
[49]	J. Li, X. Gao, Z. Zhang, et al., CircCD44 plays oncogenic roles in triple-negative breast cancer by modulating the miR-502-5p/KRAS and IGF2BP2/Myc axes, Mol. Cancer 20(2021), 138.
[50]	W. Li, T. Tanikawa, I. Kryczek, et al., Aerobic glycolysis controls myeloid-derived suppressor cells and tumor immunity via a specific CEBPB isoform in triple-negative breast cancer, Cell Metab. 28(2018) 87-103.e6.
[51]	K.W. Evans, E. Yuca, S.S. Scott, et al., Oxidative phosphorylation is a metabolic vulnerability in chemotherapy-resistant triple-negative breast cancer, Cancer Res. 81(2021) 5572-5581.
[52]	Q. Wu, D.Y. Nie, W. Ba-Alawi, et al., PRMT inhibition induces a viral mimicry response in triple-negative breast cancer, Nat. Chem. Biol. 18(2022) 821-830.
[53]	C.H. O’Flanagan, K.R. Campbell, A.W. Zhang, et al., Dissociation of solid tumor tissues with cold active protease for single-cell RNA-seq minimizes conserved collagenase-associated stress responses, Genome Biol. 20(2019), 210.
[54]	G.K. Gray, C.M. Li, J.M. Rosenbluth, et al., A human breast atlas integrating single-cell proteomics and transcriptomics, Dev. Cell 57(2022) 1400-1420.e7.
[55]	H.K. Yoon, T.H. Kim, S. Park, et al., Effect of anthracycline and taxane on the expression of programmed cell death ligand-1 and galectin-9 in triple-negative breast cancer, Pathol. Res. Pract. 214(2018) 1626-1631.
[56]	S. Saeed, J. Quintin, H.H.D. Kerstens, et al., Epigenetic programming of monocyte-to-macrophage differentiation and trained innate immunity, Science 345(2014), 1251086.
[57]	K.K. To, D.C. Poon, Y. Wei, et al., Pelitinib (EKB-569) targets the up-regulation of ABCB1 and ABCG2 induced by hyperthermia to eradicate lung cancer, Br. J. Pharmacol. 172(2015) 4089-4106.
[58]	S. Lee, E. Kang, U. Lee, et al., Role of pelitinib in the regulation of migration and invasion of hepatocellular carcinoma cells via inhibition of Twist1, BMC Cancer 23(2023), 703.
[59]	X. Lv, Y. Jia, J. Li, et al., The construction of a prognostic model of cervical cancer based on four immune-related LncRNAs and an exploration of the correlations between the model and oxidative stress, Front. Pharmacol. 14(2023), 1234181.
[60]	F. Derakhshan, J.S. Reis-Filho, Pathogenesis of triple-negative breast cancer, Annu. Rev. Pathol. 17(2022) 181-204.
[61]	S.Z. Wu, G.Al-Eryani, D.L. Roden, et al., A single-cell and spatially resolved atlas of human breast cancers, Nat. Genet. 53(2021) 1334-1347.
[62]	B. Pal, Y. Chen, F. Vaillant, et al., A single-cell RNA expression atlas of normal, preneoplastic and tumorigenic states in the human breast, EMBO J. 40(2021), e107333.
[63]	J.A. Sparano, R.J. Gray, D.F. Makower, et al., Prospective validation of a 21-gene expression assay in breast cancer, N. Engl. J. Med. 373(2015) 2005-2014.
[64]	A. Dongre, R.A. Weinberg, New insights into the mechanisms of epithelial-mesenchymal transition and implications for cancer, Nat. Rev. Mol. Cell Biol. 20(2019) 69-84.
[65]	C.P. Bracken, G.J. Goodall, The many regulators of epithelial-mesenchymal transition, Nat. Rev. Mol. Cell Biol. 23(2022) 89-90.
[66]	J. Yuan, Y. Zhang, Y. Liu, et al., Diffusion behaviors of integrins in single cells altered by epithelial to mesenchymal transition, Small 18(2022), e2106498.
[67]	Y. Chen, S. Zhang, Q. Wang, et al., Tumor-recruited M2 macrophages promote gastric and breast cancer metastasis via M2 macrophage-secreted CHI3L1 protein, J. Hematol. Oncol. 10(2017), 36.
[68]	A. Mantovani, F. Marchesi, A. Malesci, et al., Tumour-associated macrophages as treatment targets in oncology, Nat. Rev. Clin. Oncol. 14(2017) 399-416.
[69]	X. Zhao, Q. Di, H. Liu, et al., MEF2C promotes M1 macrophage polarization and Th1 responses, Cell. Mol. Immunol. 19(2022) 540-553.
[70]	X. Zhu, R. Liang, T. Lan, et al., Tumor-associated macrophage-specific CD155 contributes to M2-phenotype transition, immunosuppression, and tumor progression in colorectal cancer, J. Immunother. Cancer 10(2022), e004219.
[71]	K.C. Wheeler, M.K. Jena, B.S. Pradhan, et al., VEGF may contribute to macrophage recruitment and M2 polarization in the decidua, PLoS One 13(2018), e0191040.
[72]	X. Chen, A. Gao, F. Zhang, et al., ILT4 inhibition prevents TAM- and dysfunctional T cell-mediated immunosuppression and enhances the efficacy of anti-PD-L1 therapy in NSCLC with EGFR activation, Theranostics 11(2021) 3392-3416.
[73]	D.V. Maybee, N.L. Ink, M.A.M. Ali, Novel roles of MT1-MMP and MMP-2: Beyond the extracellular milieu, Int. J. Mol. Sci. 23(2022), 9513.
[74]	K.T. Flaherty, C. Robert, P. Hersey, et al., Improved survival with MEK inhibition in BRAF-mutated melanoma, N Engl J. Med. 367(2012) 107-114.
[75]	M. Maio, M.S. Carlino, A.M. Joshua, et al., KEYNOTE-022: Pembrolizumab with trametinib in patients with BRAF wild-type melanoma or advanced solid tumours irrespective of BRAF mutation, Eur. J. Cancer 160(2022) 1-11.
[76]	T. Seo, E. Noguchi, M. Yoshida, et al., Response to dabrafenib and trametinib of a patient with metaplastic breast carcinoma harboring a BRAF V600E mutation, Case Rep. Oncol. Med. 2020(2020), 2518383.
[77]	M.C. Schmid, C.J. Avraamides, H.C. Dippold, et al., Receptor tyrosine kinases and TLR/IL1Rs unexpectedly activate myeloid cell PI3Kγ, a single convergent point promoting tumor inflammation and progression, Cancer Cell 19(2011) 715-727.
[78]	M. Li, V. Sala, M.C. De Santis, et al., Phosphoinositide 3-kinase gamma inhibition protects from anthracycline cardiotoxicity and reduces tumor growth, Circulation 138(2018) 696-711.
[79]	Z. Zhang, H. Li, C. Zhou, et al., Non-benzoquinone geldanamycin analogs trigger various forms of death in human breast cancer cells, J. Exp. Clin. Cancer Res. 35(2016), 149.
[80]	M. Zhang, L. Zhang, R. Hei, et al., CDK inhibitors in cancer therapy, an overview of recent development, Am. J. Cancer Res. 11(2021) 1913-1935.
[81]	J. Cicenas, K. Kalyan, A. Sorokinas, et al., Roscovitine in cancer and other diseases, Ann. Transl. Med. 3(2015), 135.
[82]	S. Houze, N.T. Hoang, O. Lozach, et al., Several human cyclin-dependent kinase inhibitors, structurally related to roscovitine, are new anti-malarial agents, Molecules 19(2014) 15237-15257.