Single-cell RNA-sequencing and spatial transcriptomic analysis reveal a distinct population of APOE^– cells yielding pathological lymph node metastasis in papillary thyroid cancer

Abstract

	•A subpopulation of tumor cells with lower expression levels of APOE was strongly associated with more advanced stages and metastasis of PTC.
	•APOE-negative (APOE–) cellsoverall exhibited weaker interactions with immune cells.
	•A machine-learning bioinformatics model based on scRNA-seq data of in-situ thyroid cancer tissue was established to predict lymph node metastasis.

Keywords

APOE-ABCA1-LXR axis / lymph node metastasis / papillary thyroid carcinoma / single-cell RNAsequencing

References

[1] Deng Y, Li H, Wang M, et al. Global burden of thyroid cancer from 1990 to 2017. JAMA Netw Open. 2020;3(6):e208759.

[2] Cabanillas ME, McFadden DG, Durante C. Thyroid cancer. Lancet. 2016;388(10061):2783-2795

[3] Tarabichi M, Demetter P, Craciun L, Maenhaut C, Detours V. Thyroid cancer under the scope of emerging technologies. Mol Cell Endocrinol. 2022;541:111491.

[4] Vaccarella S, Franceschi S, Bray F, Wild CP, Plummer M, Dal Maso L. Worldwide thyroid-cancer epidemic? The increasing impact of overdiagnosis. New Engl J Med. 2016;375(7):614-617.

[5] La Vecchia C, Malvezzi M, Bosetti C, et al. Thyroid cancer mortality and incidence: a global overview. Int J Cancer. 2015;136(9):2187-2195.

[6] Ferrari SM, Fallahi P, Galdiero MR, et al. Immune and inflammatory cells in thyroid cancer microenvironment. Int J Mol Sci. 2019;20(18):4413.

[7] Ham J, Wang B, Po JW, Singh A, Niles N, Lee CS. Cancer-associated fibroblasts (CAFs) in thyroid papillary carcinoma: molecular networks and interactions. J Clin Pathol. 2021;74(12):759-765.

[8] Gill KS, Tassone P, Hamilton J, et al. Thyroid cancer metabolism: a review. J Thyroid Disord Ther. 2016;5(1):200.

[9] Xie Z, Li X, He Y, et al. Immune cell confrontation in the papillary thyroid carcinoma microenvironment. Front Endocrinol. 2020;11:570604.

[10] Strickaert A, Saiselet M, Dom G, et al. Cancer heterogeneity is not compatible with one unique cancer cell metabolic map. Oncogene. 2017;36(19):2637-2642.

[11] Wen L, Li G, Huang T, et al. Single-cell technologies: from research to application. Innovation (Camb). 2022;3(6):100342.

[12] Longo SK, Guo MG, Ji AL, Khavari PA. Integrating single-cell and spatial transcriptomics to elucidate intercellular tissue dynamics. Nat Rev Genet. 2021;22(10):627-644.

[13] Pu W, Shi X, Yu P, et al. Single-cell transcriptomic analysis of the tumor ecosystems underlying initiation and progression of papillary thyroid carcinoma. Nat Commun. 2021;12(1):6058.

[14] Hu J, Li X, Coleman K, et al. SpaGCN: integrating gene expression, spatial location and histology to identify spatial domains and spatially variable genes by graph convolutional network. Nat Methods. 2021;18(11):1342-1351.

[15] Hu J, Coleman K, Zhang D, et al. Deciphering tumor ecosystems at super resolution from spatial transcriptomics with TESLA. Cell Syst. 2023;14(5):404-417.

[16] Rawat V, Wang S, Sima J, et al. ApoE4 alters ABCA1 membrane trafficking in astrocytes. J Neurosci. 2019;39(48):9611-9622.

[17] Tavazoie MF, Pollack I, Tanqueco R, et al. LXR/ApoE activation restricts innate immune suppression in cancer. Cell. 2018;172(4):825-840.

[18] Zeng L, Yang T, Yang K, et al. Efficacy and safety of curcumin and curcuma longa extract in the treatment of arthritis: a systematic review and meta-analysis of randomized controlled trial. Front Immunol. 2022;13:891822.

[19] Iannacone M, Guidotti LG. Immunobiology and pathogenesis of hepatitis B virus infection. Nat Rev Immunol. 2022;22(1):19-32.

[20] Wei R, He S, Bai S, et al. Spatial charting of single-cell transcriptomes in tissues. Nat Biotechnol. 2022;40(8):1190-1199.

[21] Gao R, Bai S, Henderson YC, et al. Delineating copy number and clonal substructure in human tumors from single-cell transcriptomes. Nat Biotechnol. 2021;39(5):599-608.

[22] Qiu X, Mao Q, Tang Y, et al. Reversed graph embedding resolves complex single-cell trajectories. Nat Methods. 2017;14(10):979-982.

[23] Jin S, Guerrero-Juarez CF, Zhang L, et al. Inference and analysis of cell−cell communication using CellChat. Nat Commun. 2021;12(1):1088.

[24] Bray NL, Pimentel H, Melsted P, Pachter L. Near-optimal probabilistic RNA-seq quantification. Nat Biotechnol. 2016;34(5):525-527.

[25] Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15(12):550.

[26] Subramanian A, Tamayo P, Mootha VK, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA. 2005;102(43):15545-15550.

[27] Xiao G, Wei Y, Xie R, et al. Citric acid promotes SPARC release in pancreatic cancer cells and inhibits the progression of pancreatic tumors in mice on a high-fat diet. FEBS J. 2024;291(8):1699-1718.

[28] Gliemann J. Receptors of the low density lipoprotein (LDL) receptor family in man. Multiple functions of the large family members via interaction with complex ligands. Biol Chem. 1998;379(8-9):951-964.

[29] Lin X, Zhang J, Zhao RH, Zhang WJ, Wu JF, Xue G. APOE is a prognostic biomarker and correlates with immune infiltrates in papillary thyroid carcinoma. J Cancer. 2022;13(5):1652-1663.

[30] Nan BY, Xiong GF, Zhao ZR, Gu X, Huang XS. Comprehensive identification of potential crucial genes and miRNA-mRNA regulatory networks in papillary thyroid cancer. Biomed Res Int. 2021;2021:6752141.

[31] Huang J, Sun W, Wang Z, et al. FTO suppresses glycolysis and growth of papillary thyroid cancer via decreasing stability of APOE mRNA in an N6-methyladenosine-dependent manner. J Exp Clin Canc Res. 2022;41(1):42.

[32] Jiang Q, Feng W, Xiong C, Lv Y. Integrated bioinformatics analysis of the association between apolipoprotein E expression and patient prognosis in papillary thyroid carcinoma. Oncol Lett. 2020;19(3):2295-2305.

[33] Rusinek D, Pfeifer A, Krajewska J, et al. Coexistence of TERT promoter mutations and the BRAF V600E alteration and its impact on histopathological features of papillary thyroid carcinoma in a selected series of Polish patients. Int J Mol Sci. 2018;19(9):2647.

[34] Yu J, Deng Y, Liu T, et al. Lymph node metastasis prediction of papillary thyroid carcinoma based on transfer learning radiomics. Nat Commun. 2020;11(1):4807.

[35] Machens A, Hinze R, Thomusch O, Dralle H. Pattern of nodal metastasis for primary and reoperative thyroid cancer. World J Surg. 2002;26(1):22-28.

[36] An HJ, Koh HM, Song DH. Apolipoprotein E is a predictive marker for assessing non-small cell lung cancer patients with lymph node metastasis. Pathol Res Pract. 2019;215(10):152607.

[37] Pencheva N, Tran H, Buss C, et al. Convergent multi-miRNA targeting of ApoE drives LRP1/LRP8-dependent melanoma metastasis and angiogenesis. Cell. 2012;151(5):1068-1082.

[38] Pasello M, Manara MC, Scotlandi K. CD99 at the crossroads of physiology and pathology. J Cell Commun Signal. 2018;12(1):55-68.

[39] Manara MC, Pasello M, Scotlandi K. CD99: a cell surface protein with an oncojanus role in tumors. Genes-Basel. 2018;9(3):159.

[40] Takheaw N, Earwong P, Laopajon W, Pata S, Kasinrerk W. Interaction of CD99 and its ligand upregulates IL-6 and TNF-alpha upon T cell activation. PLoS One. 2019;14(5):e217393.

[41] Ruth JH, Gurrea-Rubio M, Athukorala KS, et al. CD6 is a target for cancer immunotherapy. JCI Insight. 2021;6(5):e145662.

[42] Gurrea-Rubio M, Fox DA. The dual role of CD6 as a therapeutic target in cancer and autoimmune disease. Front Med. 2022;9:1026521.

[43] Saadat M. Apolipoprotein E (APOE) polymorphisms and susceptibility to breast cancer: a meta-analysis. Cancer Res Treat. 2012;44(2):121-126.

[44] Sakashita K, Tanaka F, Zhang X, et al. Clinical significance of ApoE expression in human gastric cancer. Oncol Rep. 2008;20(6):1313-1319.

[45] Goodison S, Chang M, Dai Y, Urquidi V, Rosser CJ. A multi-analyte assay for the non-invasive detection of bladder cancer. PLoS One. 2012;7(10):e47469.

[46] Wu C, Li T, Cheng W. The correlation between APOE expression and the clinical characteristics and prognosis of patients with endometrial cancer. Medicine. 2022;101(37):e30536.

[47] Chen J, Wu W, Zhen C, et al. Expression and clinical significance of complement C3, complement C4b1 and apolipoprotein E in pancreatic cancer. Oncol Lett. 2013;6(1):43-48.

[48] Yencilek F, Yilmaz SG, Yildirim A, et al. Apolipoprotein E genotypes in patients with prostate cancer. Anticancer Res. 2016;36(2):707-711.

[49] Liutkeviciene R, Auzelyte J, Liutkevicius V, et al. The role of ApoE serum levels and ApoE gene polymorphisms in patients with laryngeal squamous cell carcinoma. Biomolecules. 2022;12(8):1013.

[50] Ruiz E, Niu T, Zerfaoui M, et al. A novel gene panel for prediction of lymph-node metastasis and recurrence in patients with thyroid cancer. Surgery. 2020;167(1):73-79.

RIGHTS & PERMISSIONS

2025 The Author(s). Clinical and Translational Medicine published by John Wiley & Sons Australia, Ltd on behalf of Shanghai Institute of Clinical Bioinformatics.