The co-location of CD14+APOE+ cells and MMP7+ tumour cells contributed to worse immunotherapy response in non-small cell lung cancer

Abstract

Intra-tumour immune infiltration is a crucial determinant affecting immunotherapy response in non-small cell lung cancer (NSCLC). However, its phenotype and related spatial structure have remained elusive. To overcome these restrictions, we undertook a comprehensive study comprising spatial transcriptomic (ST) data (28 712 spots from six samples). We identified two distinct intra-tumour infiltration patterns: immune exclusion (characterised by myeloid cells) and immune activation (characterised by plasma cells). The immune exclusion and immune activation signatures showed adverse and favourable roles in NSCLC patients’ survival, respectively. Notably, CD14+APOE+ cells were recognised as the main cell type in immune exclusion samples, with increased epithelial‒mesenchymal transition and decreased immune activities. The co-location of CD14+APOE+ cells and MMP7+ tumour cells was observed in both ST and bulk transcriptomics data, validated by multiplex immunofluorescence performed on 20 NSCLC samples. The co-location area exhibited the upregulation of proliferation-related pathways and hypoxia activities. This co-localisation inhibited T-cell infiltration and the formation of tertiary lymphoid structures. Both CD14+APOE+ cells and MMP7+ tumour cells were associated with worse survival. In an immunotherapy cohort from the ORIENT-3 clinical trial, NSCLC patients who responded unfavourably exhibited higher infiltration of CD14+APOE+ cells and MMP7+ tumour cells. Within the co-location area, the MK, SEMA3 and Macrophage migration inhibitory factor (MIF) signalling pathway was most active in cell‒cell communication. This study identified immune exclusion and activation patterns in NSCLC and the co-location of CD14+APOE+ cells and MMP7+ tumour cells as contributors to immune resistance.

Keywords

intra-tumour immune infiltration / non-small cell lung cancer / spatial structure / spatial transcriptomics

References

[1] LiuS-YM, ZhengM-M, PanY, LiuS-Y, LiY, WuY-L. Emerging evidence and treatment paradigm of non-small cell lung cancer. J Hematol Oncol. 2023; 16: 40.

[2] SungH, FerlayJ, SiegelRL, et al. Global cancer statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J Clin. 2021; 71: 209-249.

[3] LahiriA, MajiA, PotdarPD, et al. Lung cancer immunotherapy: progress, pitfalls, and promises. Mol Cancer. 2023; 22: 40.

[4] GenovaC, Dellepiane C, CarregaP, et al. Therapeutic implications of tumor microenvironment in lung cancer: focus on immune checkpoint blockade. Front Immunol. 2021; 12: 799455.

[5] LambrechtsD, Wauters E, BoeckxB, et al. Phenotype molding of stromal cells in the lung tumor microenvironment. Nat Med. 2018; 24: 1277-1289.

[6] LiuW, PowellCA, WangQ. Tumor microenvironment in lung cancer-derived brain metastasis. Chin Med J. 2022; 135: 1781-1791.

[7] HorvathL, Thienpont B, ZhaoL, WolfD, Pircher A. Overcoming immunotherapy resistance in non-small cell lung cancer (NSCLC)—novel approaches and future outlook. Mol Cancer. 2020; 19: 141.

[8] ZhaoY, GuoS, DengJ, et al. VEGF/VEGFR-targeted therapy and immunotherapy in non-small cell lung cancer: targeting the tumor microenvironment. Int J Biol Sci. 2022; 18: 3845-3858.

[9] SunD, LiuJ, ZhouH, et al. Classification of tumor immune microenvironment according to programmed death-ligand 1 expression and immune infiltration predicts response to immunotherapy plus chemotherapy in advanced patients with NSCLC. J Thorac Oncol. 2023; 18: 869-881.

[10] StankovicB, Bjørhovde HAK, SkarshaugR, et al. Immune cell composition in human non-small cell lung cancer. Front Immunol. 2018; 9: 3101.

[11] ZhangQi, AbdoR, IosefC, et al. The spatial transcriptomic landscape of non-small cell lung cancer brain metastasis. Nat Commun. 2022; 13: 5983.

[12] LarroquetteM, GueganJ-P, BesseB, et al. Spatial transcriptomics of macrophage infiltration in non-small cell lung cancer reveals determinants of sensitivity and resistance to anti-PD1/PD-L1 antibodies. J Immunother Cancer. 2022; 10: e003890.

[13] Sandström GerdtssonA, KnulstM, Botling J, MezheyeuskiA, MickeP, EkS. Phenotypic characterization of spatial immune infiltration niches in non-small cell lung cancer. Oncoimmunology. 2023; 12: 2206725.

[14] ChengC, NguyenTT, TangM, et al. Immune infiltration in tumor and adjacent non-neoplastic regions codetermines patient clinical outcomes in early-stage lung cancer. J Thorac Oncol. 2023; 18: 1184-1198.

[15] TianY, LiQ, YangZ, et al. Single-cell transcriptomic profiling reveals the tumor heterogeneity of small-cell lung cancer. Signal Transduct Target Ther. 2022; 7: 346.

[16] MaynardA, Mccoach CE, RotowJK, et al. Therapy-induced evolution of human lung cancer revealed by single-cell RNA sequencing. Cell. 2020; 182: 1232-1251. e1222.

[17] WangY, LiuB, MinQ, et al. Spatial transcriptomics delineates molecular features and cellular plasticity in lung adenocarcinoma progression. Cell Discov. 2023; 9: 96.

[18] FanG, XieT, LiL, TangLe, HanX, ShiY. Single-cell and spatial analyses revealed the co-location of cancer stem cells and SPP1+ macrophage in hypoxic region that determines the poor prognosis in hepatocellular carcinoma. NPJ Precis Oncol. 2024; 8: 75.

[19] KrausgruberT, RedlA, BarrecaD, et al. Single-cell and spatial transcriptomics reveal aberrant lymphoid developmental programs driving granuloma formation. Immunity. 2023; 56: 289-306. e287.

[20] WangYe, LiuB, ZhaoG, et al. Spatial transcriptomics: technologies, applications and experimental considerations. Genomics. 2023; 115: 110671.

[21] TianL, ChenF, MacoskoEZ. The expanding vistas of spatial transcriptomics. Nat Biotechnol. 2023; 41: 773-782.

[22] ZhangY, HuJ, JiK, et al. CD39 inhibition and VISTA blockade may overcome radiotherapy resistance by targeting exhausted CD8+ T cells and immunosuppressive myeloid cells. Cell Rep Med. 2023; 4: 101151.

[23] TuE, McGlinchey K, WangJ, et al. Anti-PD-L1 and anti-CD73 combination therapy promotes T cell response to EGFR-mutated NSCLC. JCI Insight. 2022; 7: e142843.

[24] KimSS, SumnerWA, MiyauchiS, Cohen EEW, CalifanoJA, SharabiAB. Role of B cells in responses to checkpoint blockade immunotherapy and overall survival of cancer patients. Clin Cancer Res. 2021; 27: 6075-6082.

[25] PatilNS, NabetBY, MüllerS, et al. Intratumoral plasma cells predict outcomes to PD-L1 blockade in non-small cell lung cancer. Cancer Cell. 2022; 40: 289-300. e284.

[26] MeylanM, Petitprez F, BechtE, et al. Tertiary lymphoid structures generate and propagate anti-tumor antibody-producing plasma cells in renal cell cancer. Immunity. 2022; 55: 527-541. e525.

[27] FridmanWH, MeylanM, PetitprezF, Sun C-M, ItalianoA, Sautès-FridmanC. B cells and tertiary lymphoid structures as determinants of tumour immune contexture and clinical outcome. Nat Rev Clin Oncol. 2022; 19: 441-457.

[28] Sautès-FridmanC, Petitprez F, CalderaroJ, FridmanWH. Tertiary lymphoid structures in the era of cancer immunotherapy. Nat Rev Cancer. 2019; 19: 307-325.

[29] ShenX, ZhouS, YangY, et al. CD14+ cells-targeted reeducation for enhanced cancer immunotherapy: mechanism and recent progress. Front Oncol. 2022; 12: 1034842.

[30] PuY, JiQ. Tumor-associated macrophages regulate PD-1/PD-L1 immunosuppression. Front Immunol. 2022; 13: 874589.

[31] WuF, FanJ, HeY, et al. Single-cell profiling of tumor heterogeneity and the microenvironment in advanced non-small cell lung cancer. Nat Commun. 2021; 12: 2540.

[32] ZilionisR, Engblom C, PfirschkeC, et al. Single-cell transcriptomics of human and mouse lung cancers reveals conserved myeloid populations across individuals and species. Immunity. 2019; 50: 1317-1334. e1310.

[33] KimN, KimHK, LeeK, et al. Single-cell RNA sequencing demonstrates the molecular and cellular reprogramming of metastatic lung adenocarcinoma. Nat Commun. 2020; 11: 2285.

[34] JiaY, ZhangB, ZhangC, et al. Single-cell transcriptomic analysis of primary and metastatic tumor ecosystems in esophageal squamous cell carcinoma. Adv Sci (Weinh). 2023; 10: e2204565.

[35] WongHY, ShengQ, HesterbergAB, et al. Single cell analysis of cribriform prostate cancer reveals cell intrinsic and tumor microenvironmental pathways of aggressive disease. Nat Commun. 2022; 13: 6036.

[36] MezheyeuskiA, Backman M, MattssonJ, et al. An immune score reflecting pro-and anti-tumoural balance of tumour microenvironment has major prognostic impact and predicts immunotherapy response in solid cancers. EBioMedicine. 2023; 88: 104452.

[37] KettererS, Mitschke J, KetscherA, et al. Cathepsin D deficiency in mammary epithelium transiently stalls breast cancer by interference with mTORC1 signaling. Nat Commun. 2020; 11: 5133.

[38] JiangS, LiW, YangJ, et al. Cathepsin B-responsive programmed brain targeted delivery system for chemo-immunotherapy combination therapy of glioblastoma. ACS Nano. 2024; 18: 6445-6462.

[39] FangX, RaoK, WeiZ, ChengJ. SOX10 modulated SMARCA4 dysregulation alleviates DNA replication stress in cutaneous melanoma. J Cell Mol Med. 2022; 26: 5846-5857.

[40] OhguchiH, Hideshima T, BhasinMK, et al. The KDM3A-KLF2-IRF4 axis maintains myeloma cell survival. Nat Commun. 2016; 7: 10258.

[41] PiJ, TaoT, ZhuangT, et al. A microRNA302-367-Erk1/2-Klf2-S1pr1 pathway prevents tumor growth via restricting angiogenesis and improving vascular stability. Circ Res. 2017; 120: 85-98.

[42] WangY, HuL, ZhengY, Guo L. HMGA1 in cancer: cancer classification by location. J Cell Mol Med. 2019; 23: 2293-2302.

[43] ZhangQ, LiuS, ParajuliKR, et al. Interleukin-17 promotes prostate cancer via MMP7-induced epithelial-to-mesenchymal transition. Oncogene. 2017; 36: 687-699.

[44] FukumuraD, Kloepper J, AmoozgarZ, DudaDG, JainRK. Enhancing cancer immunotherapy using antiangiogenics: opportunities and challenges. Nat Rev Clin Oncol. 2018; 15: 325-340.

[45] SikderMOF, Sivaprakasam S, BrownTP, ThangarajuM, BhutiaYD, GanapathyV. SLC6A14, a Na+/Cl-coupled amino acid transporter, functions as a tumor promoter in colon and is a target for Wnt signaling. Biochem J. 2020; 477: 1409-1425.

[46] CaoJ-H, CaoC-H, LinJ-L, et al. NEIL1 drives the initiation of colorectal cancer through transcriptional regulation of COL17A1. Cell Rep. 2024; 43: 113654.

[47] WangW, McDonald MCL, KimC, et al. The complementary roles of STAT3 and STAT1 in cancer biology: insights into tumor pathogenesis and therapeutic strategies. Front Immunol. 2023; 14: 1265818.

[48] LiongueC, SobahML, WardAC. Signal transducer and activator of transcription proteins at the nexus of immunodeficiency, autoimmunity and cancer. Biomedicines. 2023; 12:45.

[49] MouSI, Sultana T, ChatterjeeD, FarukMO, HosenMI. Comprehensive characterization of coding and non-coding single nucleotide polymorphisms of the Myoneurin (MYNN) gene using molecular dynamics simulation and docking approaches. PLoS One. 2024; 19: e0296361.

[50] ShiY, WuL, YuX, et al. Sintilimab versus docetaxel as second-line treatment in advanced or metastatic squamous non-small-cell lung cancer: an open-label, randomized controlled phase 3 trial (ORIENT-3). Cancer Commun (Lond). 2022; 42: 1314-1330.

[51] ZhengN, WangT, LuoQ, et al. M2 macrophage-derived exosomes suppress tumor intrinsic immunogenicity to confer immunotherapy resistance. Oncoimmunology. 2023; 12: 2210959.

[52] WeiJ, YuW, ChenJ, et al. Single-cell and spatial analyses reveal the association between gene expression of gluCD14+ cellsine synthetase with the immunosuppressive phenotype of APOE+CTSZ+CD14+ cells in cancers. Mol Oncol. 2023; 17: 611-628.

[53] RevelM, Sautès-Fridman C, FridmanW-H, RoumeninaLT. C1q+ macrophages: passengers or drivers of cancer progression. Trends Cancer. 2022; 8: 517-526.

[54] ShoucairS, ChenJ, MartinsonJR, et al. Association of matrix metalloproteinase 7 expression with pathologic response after neoadjuvant treatment in patients with resected pancreatic ductal adenocarcinoma. JAMA Surg. 2022; 157: e221362.

[55] XiaoXY, LangXP. Correlation between MMP-7 and bFGF expressions in non-small cell lung cancer tissue and clinicopathologic features. Cell Biochem Biophys. 2015; 73: 427-432.

[56] LiaoH-Y, DaC-M, LiaoB, Zhang H-H. Roles of matrix metalloproteinase-7 (MMP-7) in cancer. Clin Biochem. 2021; 92: 9-18.

[57] OuS, ChenH, WangH, et al. Fusobacterium nucleatum upregulates MMP7 to promote metastasis-related characteristics of colorectal cancer cell via activating MAPK(JNK)-AP1 axis. J Transl Med. 2023; 21: 604.

[58] LiuM, HuangL, LiuY, et al. Identification of the MMP family as therapeutic targets and prognostic biomarkers in the microenvironment of head and neck squamous cell carcinoma. J Transl Med. 2023; 21: 208.

[59] YanL, WuM, WangT, et al. Breast cancer stem cells secrete MIF to mediate tumor metabolic reprogramming that drives immune evasion. Cancer Res. 2024; 84(8): 1270-1285.

[60] WangY, ChenY, WangC, et al. MIF is a 3′ flap nuclease that facilitates DNA replication and promotes tumor growth. Nat Commun. 2021; 12: 2954.

[61] WuL, GaoY, XieS, et al. The level of macrophage migration inhibitory factor is negatively correlated with the efficacy of PD-1 blockade immunotherapy combined with chemotherapy as a neoadjuvant therapy for esophageal squamous cell carcinoma. Transl Oncol. 2023; 37: 101775.

[62] LiaoY, WuC, LiY, WenJ, ZhaoD. MIF is a critical regulator of mononuclear phagocytic infiltration in hepatocellular carcinoma. iScience. 2023; 26: 107273.

[63] ZhuG-Q, TangZ, HuangR, et al. CD36(+) cancer-associated fibroblasts provide immunosuppressive microenvironment for hepatocellular carcinoma via secretion of macrophage migration inhibitory factor. Cell Discov. 2023; 9: 25.

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2024 The Author(s). Clinical and Translational Medicine published by John Wiley & Sons Australia, Ltd on behalf of Shanghai Institute of Clinical Bioinformatics.