Integrated spatial multi-omics profiling of Fusobacterium nucleatum in breast cancer unveils its role in tumour microenvironment modulation and cancer progression

Feng Zhao , Rui An , Yilei Ma , Shaobo Yu , Yuzhen Gao , Yanzhong Wang , Haitao Yu , Xinyou Xie , Jun Zhang

Clinical and Translational Medicine ›› 2025, Vol. 15 ›› Issue (3) : e70273

PDF
Clinical and Translational Medicine ›› 2025, Vol. 15 ›› Issue (3) : e70273 DOI: 10.1002/ctm2.70273
RESEARCH ARTICLE

Integrated spatial multi-omics profiling of Fusobacterium nucleatum in breast cancer unveils its role in tumour microenvironment modulation and cancer progression

Author information +
History +
PDF

Abstract

•Intratumoral Fusobacterium nucleatum exhibits significant spatial heterogeneity within breast cancer tissues.

F. nucleatum colonization alters the expression of key proteins involved in tumour progression and migration.

•The MAPK signalling pathway is a critical mediator of F. nucleatum-induced breast cancer cell proliferation and migration.

•VEGFD and PAK1 are potential therapeutic targets to mitigate F. nucleatum-induced tumour progression.

Keywords

breast cancer / Fusobacterium nucleatum / intratumoral microbiota / spatial multi-omics / tumour microenvironment

Cite this article

Download citation ▾
Feng Zhao, Rui An, Yilei Ma, Shaobo Yu, Yuzhen Gao, Yanzhong Wang, Haitao Yu, Xinyou Xie, Jun Zhang. Integrated spatial multi-omics profiling of Fusobacterium nucleatum in breast cancer unveils its role in tumour microenvironment modulation and cancer progression. Clinical and Translational Medicine, 2025, 15(3): e70273 DOI:10.1002/ctm2.70273

登录浏览全文

4963

注册一个新账户 忘记密码

References

[1]

Farc O, Cristea V, An overview of the tumor microenvironment, from cells to complex networks (review). Exp Ther Med. 2021;21(1):96.

[2]

Hirata E, Sahai E, tumor microenvironment and differential responses to therapy. Cold Spring Harb Perspect Med. 2017;7(7):a026781.

[3]

Petitprez F, Meylan M, de Reyniès A, Sautès-Fridman C, Fridman WH, The tumor microenvironment in the response to immune checkpoint blockade therapies. Front Immunol. 2020;11:784.

[4]

Nejman D, Livyatan I, Fuks G, et al. The human tumor microbiome is composed of tumor type-specific intracellular bacteria. Science. 2020;368(6494):973-980.

[5]

Bullman S, Pedamallu CS, Sicinska E, et al. Analysis of Fusobacterium persistence and antibiotic response in colorectal cancer. Science. 2017;358(6369):1443-1448.

[6]

Riquelme E, Zhang Y, Zhang L, et al. Tumor microbiome diversity and composition influence pancreatic cancer outcomes. Cell. 2019;178(4):795-806.e12.

[7]

Kalaora S, Nagler A, Nejman D, et al. Identification of bacteria-derived HLA-bound peptides in melanoma. Nature. 2021;592(7852):138-143.

[8]

Kwon S, Thi-Thu Ngo H, Son J, Hong Y, Min J, Exploiting bacteria for cancer immunotherapy. Nat Rev Clin Oncol. 2024;21(8):569-589

[9]

Xavier JB, Young VB, Skufca J, et al. The cancer microbiome: distinguishing direct and indirect effects requires a systemic view. Trends Cancer. 2020;6(3):192-204.

[10]

Long J, Wang J, Xiao C, You F, Jiang Y, Li X, Intratumoral microbiota in colorectal cancer: focus on specific distribution and potential mechanisms. Cell Commun Signal. 2024;22(1):455.

[11]

Flemer B, Lynch DB, Brown JMR, et al. Tumour-associated and non-tumour-associated microbiota in colorectal cancer. Gut. 2017;66(4):633-643.

[12]

Jin C, Lagoudas GK, Zhao C, et al. Commensal microbiota promote lung cancer development via gammadelta T cells. Cell. 2019;176(5):998-1013.e16.

[13]

Pushalkar S, Hundeyin M, Daley D, et al. The pancreatic cancer microbiome promotes oncogenesis by induction of innate and adaptive immune suppression. Cancer Discov. 2018;8(4):403-416.

[14]

Urbaniak C, Gloor GB, Brackstone M, Scott L, Tangney M, Reid G, The microbiota of breast tissue and its association with breast cancer. Appl Environ Microbiol. 2016;82(16):5039-5048.

[15]

LaCourse K, Johnston C, Bullman S, The relationship between gastrointestinal cancers and the microbiota. Lancet Gastroenterol Hepatol. 2021;6(6):498-509.

[16]

Parhi L, Alon-Maimon T, Sol A, et al. Breast cancer colonization by Fusobacterium nucleatum accelerates tumor growth and metastatic progression. Nat Commun. 2020;11(1):3259.

[17]

Fu A, Yao B, Dong T, et al. Tumor-resident intracellular microbiota promotes metastatic colonization in breast cancer. Cell. 2022;185(8):1356-1372 e26.

[18]

Yu T, Guo F, Yu Y, et al. Fusobacterium nucleatum promotes chemoresistance to colorectal cancer by modulating autophagy. Cell. 2017;170(3):548-563 e16.

[19]

Geller LT, Barzily-Rokni M, Danino T, et al. Potential role of intratumor bacteria in mediating tumor resistance to the chemotherapeutic drug gemcitabine. Science. 2017;357(6356):1156-1160.

[20]

Sung H, Ferlay J, Siegel RL, 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(3):209-249.

[21]

Agostinetto E, Gligorov J, Piccart M, Systemic therapy for early-stage breast cancer: learning from the past to build the future. Nat Rev Clin Oncol. 2022;19(12):763-774.

[22]

Zheng C, Zhang W, Wang J, et al. Lenvatinib-and Vadimezan-loaded synthetic high-density lipoprotein for combinational immunochemotherapy of metastatic triple-negative breast cancer. Acta Pharm Sin B. 2022;12(9):3726-3738

[23]

Xue C, Chu Q, Zheng Q, et al. Current understanding of the intratumoral microbiome in various tumors. Cell Rep Med. 2023;4(1):100884.

[24]

Vitorino M, Alpuim Costa D, Vicente R, Caleça T, Santos C, Local breast microbiota: a “new” player on the block. Cancers (Basel). 2022;14(15):3811.

[25]

Tzeng A, Sangwan N, Jia M, et al, Human breast microbiome correlates with prognostic features and immunological signatures in breast cancer. Genome Med. 2021;13(1):60.

[26]

Xie Y, Xie F, Zhou X, et al. Microbiota in tumors: from understanding to application. Adv Sci (Weinh). 2022;9(21):e2200470.

[27]

Gong Y, Huang X, Wang M, Liang X, Intratumor microbiota: a novel tumor component. J Cancer Res Clin Oncol. 2023;149(9):6675-6691.

[28]

Rao Malla R, Marni R, Kumari S, Chakraborty A, Lalitha P, Microbiome assisted tumor microenvironment: emerging target of breast cancer. Clin Breast Cancer. 2022;22(3):200-211.

[29]

Garcia-Carretero R, Lopez-Lomba M, Carrasco-Fernandez B, Duran-Valle MT, Clinical features and outcomes of fusobacterium species infections in a ten-year follow-up. J Crit Care Med (Targu Mures). 2017;3(4):141-147.

[30]

Strauss J, Kaplan GG, Beck PL, et al. Invasive potential of gut mucosa-derived Fusobacterium nucleatum positively correlates with IBD status of the host. Inflamm Bowel Dis. 2011;17(9):1971-1978.

[31]

Yang Y, Weng W, Peng J, et al. Fusobacterium nucleatum increases proliferation of colorectal cancer cells and tumor development in mice by activating toll-like receptor 4 signaling to nuclear factor-kappaB, and up-regulating expression of microRNA-21. Gastroenterology. 2017;152(4):851-866 e24.

[32]

Xu M, Yamada M, Li M, Liu H, Chen SG, Han YW, FadA from Fusobacterium nucleatum utilizes both secreted and nonsecreted forms for functional oligomerization for attachment and invasion of host cells. J Biol Chem. 2007;282(34):25000-25009.

[33]

GURSOY UK, KÖNÖNEN E, UITTO V, Intracellular replication of fusobacteria requires new actin filament formation of epithelial cells. APMIS. 2008;116(12):1063-1070.

[34]

Dagogo-Jack I, Shaw A, Tumour heterogeneity and resistance to cancer therapies. Nat Rev Clin Oncol. 2018;15(2):81-94.

[35]

van der Bruggen P, Traversari C, Chomez P, et al. A gene encoding an antigen recognized by cytolytic T lymphocytes on a human melanoma. Science. 1991;254(5038):1643-1647.

[36]

Dvorak H. Tumors: wounds that do not heal. Similarities between tumor stroma generation and wound healing. N Engl J Med. 1986;315(26):1650-1659.

[37]

Anderson N, Simon M, The tumor microenvironment. Curr Biol. 2020;30(16):R921-R925.

[38]

Joyce J, Fearon D, T cell exclusion, immune privilege, and the tumor microenvironment. Science. 2015;348(6230):74-80.

[39]

Kieffer Y, Hocine HR, Gentric G, et al. Single-cell analysis reveals fibroblast clusters linked to immunotherapy resistance in cancer. Cancer Discov. 2020;10(9):1330-1351.

[40]

Qian J, Olbrecht S, Boeckx B, et al. A pan-cancer blueprint of the heterogeneous tumor microenvironment revealed by single-cell profiling. Cell Res. 2020;30(9):745-762.

[41]

Wu F, Fan J, He Y, et al. Single-cell profiling of tumor heterogeneity and the microenvironment in advanced non-small cell lung cancer. Nat Commun. 2021;12(1):2540.

[42]

Dohlman AB, Klug J, Mesko M, et al. A pan-cancer mycobiome analysis reveals fungal involvement in gastrointestinal and lung tumors. Cell. 2022;185(20):3807-3822 e12.

[43]

Galeano Niño JL, Wu H, LaCourse KD, et al. Effect of the intratumoral microbiota on spatial and cellular heterogeneity in cancer. Nature. 2022;611(7937):810-817.

[44]

Narunsky-Haziza L, Sepich-Poore GD, Livyatan I, et al. Pan-cancer analyses reveal cancer-type-specific fungal ecologies and bacteriome interactions. Cell. 2022;185(20):3789-3806 e17.

[45]

Serna G, Ruiz-Pace F, Hernando J, et al. Fusobacterium nucleatum persistence and risk of recurrence after preoperative treatment in locally advanced rectal cancer. Ann Oncol. 2020;31(10):1366-1375.

[46]

Pernigoni N, Zagato E, Calcinotto A, et al. Commensal bacteria promote endocrine resistance in prostate cancer through androgen biosynthesis. Science. 2021;374(6564):216-224.

[47]

Hunter MV, Moncada R, Weiss JM, Yanai I, White RM, Spatially resolved transcriptomics reveals the architecture of the tumor-microenvironment interface. Nat Commun. 2021;12(1):6278.

[48]

Whitmore S, Lamont R, Oral bacteria and cancer. PLoS Pathog. 2014;10(3):e1003933.

[49]

Fitzsimonds Z, Rodriguez-Hernandez C, Bagaitkar J, Lamont R, From beyond the pale to the pale riders: the emerging association of bacteria with oral cancer. J Dent Res. 2020;99(6):604-612.

[50]

Hajishengallis G, Chavakis T, Local and systemic mechanisms linking periodontal disease and inflammatory comorbidities. Nat Rev Immunol. 2021;21(7):426-440.

[51]

Kostic AD, Gevers D, Pedamallu CS, et al. Genomic analysis identifies association of Fusobacterium with colorectal carcinoma. Genome Res. 2012;22(2):292-298.

[52]

Castellarin M, Warren RL, Freeman JD, et al. Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma. Genome Res. 2012;22(2):299-306.

[53]

Mitsuhashi K, Nosho K, Sukawa Y, et al. Association of Fusobacterium species in pancreatic cancer tissues with molecular features and prognosis. Oncotarget. 2015;6(9):7209-7220.

[54]

Gaiser RA, Halimi A, Alkharaan H, et al. Enrichment of oral microbiota in early cystic precursors to invasive pancreatic cancer. Gut. 2019;68(12):2186-2194.

[55]

Yamamura K, Baba Y, Nakagawa S, et al. Human microbiome Fusobacterium nucleatum in esophageal cancer tissue is associated with prognosis. Clin Cancer Res. 2016;22(22):5574-5581.

[56]

Yamamura K, Izumi D, Kandimalla R, et al. Intratumoral Fusobacterium nucleatum levels predict therapeutic response to neoadjuvant chemotherapy in esophageal squamous cell carcinoma. Clin Cancer Res. 2019;25(20):6170-6179.

[57]

Hieken TJ, Chen J, Hoskin TL, t al. The microbiome of aseptically collected human breast tissue in benign and malignant disease. Sci Rep. 2016;6:30751.

[58]

Mima K, Nishihara R, Qian ZR, et al. Fusobacterium nucleatum in colorectal carcinoma tissue and patient prognosis. Gut. 2016;65(12):1973-1980.

[59]

Gethings-Behncke C, Coleman HG, Jordao HW, et al. Fusobacterium nucleatum in the colorectum and its association with cancer risk and survival: a systematic review and meta-analysis. Cancer Epidemiol Biomarkers Prev. 2020;29(3):539-548.

[60]

Lamont R, Koo H, Hajishengallis G, The oral microbiota: dynamic communities and host interactions. Nat Rev Microbiol. 2018;16(12):745-759.

[61]

Kostic A, Chun E, Robertson L, et al. Fusobacterium nucleatum potentiates intestinal tumorigenesis and modulates the tumor-immune microenvironment. Cell Host Microbe. 2013;14(2):207-215.

[62]

Abed J, Emgård J, Zamir G, et al. Fap2 Mediates Fusobacterium nucleatum colorectal adenocarcinoma enrichment by binding to tumor-expressed Gal-GalNAc. Cell Host Microbe. 2016;20(2):215-225.

[63]

Abed J, Maalouf N, Parhi L, Chaushu S, Mandelboim O, Bachrach G, Tumor targeting by Fusobacterium nucleatum: a pilot study and future perspectives. Front Cell Infect Microbiol. 2017;7:295.

[64]

Yue B, Yang H, Wu J, et al. Characterization and transcriptome analysis of exosomal and nonexosomal RNAs in bovine adipocytes. Int J Mol Sci. 2020;21(23):9313.

[65]

Kim E, Choi E, Pathological roles of MAPK signaling pathways in human diseases. Biochim Biophys Acta. 2010;1802(4):396-405.

[66]

Yokota T, Wang Y, p38 MAP kinases in the heart. Gene. 2016;575(2 Pt 2):369-376.

[67]

Uddin S, Ah-Kang J, Ulaszek J, Mahmud D, Wickrema A, Differentiation stage-specific activation of p38 mitogen-activated protein kinase isoforms in primary human erythroid cells. Proc Natl Acad Sci USA. 2004;101(1):147-152.

[68]

Sahu V, Nigam L, Agnihotri V, et al. Diagnostic significance of p38 isoforms (p38alpha, p38beta, p38gamma, p38delta) in head and neck squamous cell carcinoma: comparative serum level evaluation and design of novel peptide inhibitor targeting the same. Cancer Res Treat. 2019;51(1):313-325.

[69]

Cánovas B, Igea A, Sartori AA, et al. Targeting p38alpha increases DNA damage, chromosome instability, and the anti-tumoral response to taxanes in breast cancer cells. Cancer Cell. 2018;33(6):1094-1110 e8.

[70]

Gupta J, del Barco Barrantes I, Igea A, et al. Dual function of p38alpha MAPK in colon cancer: suppression of colitis-associated tumor initiation but requirement for cancer cell survival. Cancer Cell. 2014;25(4):484-500.

[71]

Vitos-Faleato J, Real SM, Gutierrez-Prat N, et al. Requirement for epithelial p38alpha in KRAS-driven lung tumor progression. Proc Natl Acad Sci USA. 2020;117(5):2588-2596.

[72]

Basu S, Chaudhary N, Shah S, Braggs C, et al. Plakophilin3 loss leads to an increase in lipocalin2 expression, which is required for tumour formation. Exp Cell Res. 2018;369(2):251-265.

[73]

Győrffy B, Survival analysis across the entire transcriptome identifies biomarkers with the highest prognostic power in breast cancer. Comput Struct Biotechnol J. 2021;19:4101-4109.

[74]

Ősz Á, Lánczky A, Győrffy B, Survival analysis in breast cancer using proteomic data from four independent datasets. Sci Rep. 2021;11(1):16787.

[75]

Trempolec N, Dave-Coll N, Nebreda A, SnapShot: p38 MAPK signaling. Cell. 2013;152(3):656-656 e1.

[76]

Kappelmann M, Bosserhoff A, Kuphal S, AP-1/c-Jun transcription factors: regulation and function in malignant melanoma. Eur J Cell Biol. 2014;93(1-2):76-81.

[77]

Sundqvist A, Zieba A, Vasilaki E, et al. Specific interactions between Smad proteins and AP-1 components determine TGFbeta-induced breast cancer cell invasion. Oncogene. 2013;32(31):3606-3615.

[78]

Gao X, Shi X, Fu X, et al. Human Tudor staphylococcal nuclease (Tudor-SN) protein modulates the kinetics of AGTR1-3’UTR granule formation. FEBS Lett. 2014;588(13):2154-2161.

[79]

Sundqvist A, Vasilaki E, Voytyuk O, et al. TGFbeta and EGF signaling orchestrates the AP-1-and p63 transcriptional regulation of breast cancer invasiveness. Oncogene. 2020;39(22):4436-4449.

[80]

Ou S, Chen H, Wang H, 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(1):704.

[81]

Hafner A, Bulyk ML, Jambhekar A, Lahav G, The multiple mechanisms that regulate p53 activity and cell fate. Nat Rev Mol Cell Biol. 2019;20(4):199-210.

[82]

Timofeev O, Editorial: mutant p53 in cancer progression and personalized therapeutic treatments. Front Oncol. 2021;11:740578.

[83]

Mendola La, Trincavelli ML, Martini C, Angiogenesis in disease. Int J Mol Sci. 2022;23(18):10962.

[84]

Liu X, Zhao H, Hou S, et al. Recent development of multi-target VEGFR-2 inhibitors for the cancer therapy. Bioorg Chem. 2023;133:106425.

[85]

Achen MG, Williams RA, Baldwin ME, et al. The angiogenic and lymphangiogenic factor vascular endothelial growth factor-D exhibits a paracrine mode of action in cancer. Growth Factors. 2002;20(2):99-107.

[86]

Yokoyama Y, Charnock-Jones DS, Licence D, et al., Expression of vascular endothelial growth factor (VEGF)-D and its receptor, VEGF receptor 3, as a prognostic factor in endometrial carcinoma. Clin Cancer Res. 2003;9(4):1361-1369.

[87]

Yu H, Zhang S, Zhang R, Zhang L, The role of VEGF-C/D and Flt-4 in the lymphatic metastasis of early-stage invasive cervical carcinoma. J Exp Clin Cancer Res. 2009;28(1):98.

[88]

Kong X, Zhang Y, Xiang L, et al. Fusobacterium nucleatum-triggered neutrophil extracellular traps facilitate colorectal carcinoma progression. J Exp Clin Cancer Res. 2023;42(1):236.

[89]

Guo Y, Pan WW, Liu SB, Shen ZF, Xu Y, ERK/MAPK signalling pathway and tumorigenesis. Exp Ther Med. 2020;19(3):1997-2007.

[90]

Bagheri-Yarmand R, Vadlamudi RK, Wang R, Mendelsohn J, Kumar R, Vascular endothelial growth factor up-regulation via p21-activated kinase-1 signaling regulates heregulin-beta1-mediated angiogenesis. J Biol Chem. 2000;275(50):39451-39457.

[91]

Chau CH, Chen K, Deng H, et al. Coordinating Etk/Bmx activation and VEGF upregulation to promote cell survival and proliferation. Oncogene. 2002;21(57):8817-8829.

[92]

Kumar R, Gururaj A, Barnes C, p21-activated kinases in cancer. Nat Rev Cancer. 2006;6(6):459-471.

[93]

Ong CC, Jubb AM, Haverty PM, et al. Targeting p21-activated kinase 1 (PAK1) to induce apoptosis of tumor cells. Proc Natl Acad Sci U S A. 2011;108(17):7177-7182.

[94]

Radu M, Semenova G, Kosoff R, Chernoff J, PAK signalling during the development and progression of cancer. Nat Rev Cancer. 2014;14(1):13-25.

[95]

Manser E, Leung T, Salihuddin H, Zhao Z, Lim L, A brain serine/threonine protein kinase activated by Cdc42 and Rac1. Nature. 1994;367(6458):40-46.

[96]

Vadlamudi RK, Adam L, Wang R, et al. Regulatable expression of p21-activated kinase-1 promotes anchorage-independent growth and abnormal organization of mitotic spindles in human epithelial breast cancer cells. J Biol Chem. 2000;275(46):36238-36244.

[97]

Wang Z, Fu M, Wang L, et al. p21-activated kinase 1 (PAK1) can promote ERK activation in a kinase-independent manner. J Biol Chem. 2013;288(27):20093-20099.

[98]

Slack-Davis JK, Eblen ST, Zecevic M, et al. PAK1 phosphorylation of MEK1 regulates fibronectin-stimulated MAPK activation. J Cell Biol. 2003;162(2):281-291.

[99]

Shrestha Y, Schafer EJ, Boehm JS, et al. PAK1 is a breast cancer oncogene that coordinately activates MAPK and MET signaling. Oncogene. 2012;31(29):3397-3408.

[100]

Fuks G, Elgart M, Amir A, et al. Combining 16S rRNA gene variable regions enables high-resolution microbial community profiling. Microbiome. 2018;6(1):17.

[101]

Chong J, Liu P, Zhou G, Xia J, Using Microbiome analyst for comprehensive statistical, functional, and meta-analysis of microbiome data. Nat Protoc. 2020;15(3):799-821.

[102]

Wang Y, Zeng J, Wu W, et al. Nicotinamide N-methyltransferase enhances chemoresistance in breast cancer through SIRT1 protein stabilization. Breast Cancer Res. 2019;21(1):64.

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.

AI Summary AI Mindmap
PDF

122

Accesses

0

Citation

Detail

Sections
Recommended

AI思维导图

/