biomarker; hypoxia; long noncoding RNA; lung adenocarcinoma; lymphangiogenesis; Molecular Medicine; Oncology; Genetics; Cancer Research
Abstract :
[en] A hypoxic microenvironment promotes the aggressiveness of lung adenocarcinoma (LUAD) through treatment resistance and generation of new lymphatic vessels (i.e., lymphangiogenesis) favoring metastatic dissemination. Transcriptomic analysis of cohorts of LUAD patients highlighted LINC01116, a long noncoding RNA, associated with a bad prognosis, a high rate of recurrence, and induced by hypoxia in tumors. Gain- (overexpression) and loss-of-function (CRISPRi (Clustered Regularly Interspaced Short Palindromic Repeats interference, RNA interference)) approaches performed in LUAD cancer cell lines did not reveal a clear regulatory role for LINC01116 in tumor cells. Analyses of LUAD single-cell RNA sequencing data sets and RNA Fluorescent In Situ Hybridization (RNA-FISH) showed high expression of LINC01116 in lymphatic endothelial cells (LEC) pointing to this transcript as a specific biomarker of tumoral lymphangiogenesis. Efficient knockdown of LINC01116 in LEC in normoxic or hypoxic conditions impacted the proliferation rate under hypoxic stimulation and revealed a gene signature associated with proliferation and hypoxia sensing. Together, our data suggest a role for LINC01116 in pathological lymphangiogenesis of lung tumors.
Disciplines :
Life sciences: Multidisciplinary, general & others
Author, co-author :
Gautier-Isola, Marine; UMR CNRS 7275, INSERM 1323, IPMC, IHU RespirERA Valbonne, Université Côte d'Azur, France
Lopes Goncalves, Rafael; UMR CNRS 7275, INSERM 1323, IPMC, IHU RespirERA Valbonne, Université Côte d'Azur, France
Truchi, Marin; UMR CNRS 7275, INSERM 1323, IPMC, IHU RespirERA Valbonne, Université Côte d'Azur, France
Lacoux, Caroline; UMR CNRS 7275, INSERM 1323, IPMC, IHU RespirERA Valbonne, Université Côte d'Azur, France
Scribe, Célia; UMR CNRS 7275, INSERM 1323, IPMC, IHU RespirERA Valbonne, Université Côte d'Azur, France
Cadis, Hugo; UMR CNRS 7275, INSERM 1323, IPMC, IHU RespirERA Valbonne, Université Côte d'Azur, France
Guardini, Laetitia; UMR CNRS 7275, INSERM 1323, IPMC, IHU RespirERA Valbonne, Université Côte d'Azur, France
Bekisz, Sophie ; Université de Liège - ULiège > Département d'aérospatiale et mécanique > Génie biomécanique ; Laboratory of Biology of Tumor and Development, GIGA-Cancer, Liege University, Belgium
Ilié, Marius ; Laboratory of Clinical and Experimental Pathology and Hospital-Integrated Biobank (BB-0033-00025), CHU Nice, IHU RespirERA, Université Côte d'Azur, France
Hofman, Paul; Laboratory of Clinical and Experimental Pathology and Hospital-Integrated Biobank (BB-0033-00025), CHU Nice, IHU RespirERA, Université Côte d'Azur, France
Vassaux, Georges; UMR CNRS 7275, INSERM 1323, IPMC, IHU RespirERA Valbonne, Université Côte d'Azur, France
Mari, Bernard; UMR CNRS 7275, INSERM 1323, IPMC, IHU RespirERA Valbonne, Université Côte d'Azur, France
Rezzonico, Roger ; UMR CNRS 7275, INSERM 1323, IPMC, IHU RespirERA Valbonne, Université Côte d'Azur, France
We sincerely thank Agn\u00E8s No\u00EBl of GIGA Cancer/Uli\u00E8ge for providing frozen primary human LECs for functional studies. We thank the animal care facility, the UCA GenomiX, the CoBioDA bioinformatics hub and the microscopy facility of IPMC, part of the \u00ABMicroscopie Imagerie Cytom\u00E9trie Azur\u00BB GIS IBiSA labeled platform for their technical support. We also thank the staff from the Nice Hospital\u2010Integrated Biobank (BB\u20100033\u201000025). LEC sequencing was performed by the GenomEast platform, a member of the \u2018France Genomique\u2019 consortium (ANR\u201010\u2010INBS\u20100009). We thank A. Monteil and C. Lemmers from the Vectorology facility, PVM, Biocampus Montpellier, CNRS UMS3426. This work was supported by the Centre National de la Recherche Scientifique (CNRS), Institut National de la Sant\u00E9 et de la Recherche M\u00E9dicale (Inserm), Universit\u00E9 C\u00F4te d'Azur, Plan Cancer 2018 \u00ABARN noncodants en canc\u00E9rologie: du fondamental au translationnel\u00BB(number 18CN045), Canc\u00E9rop\u00F4le PACA, Fondation ARC pour la Recherche sur le Cancer (PJA20191209562), the French Government, through the \u2018IHU RespirERA\u2019 France 2030 program (# ANR\u201023\u2010IAHU\u2010007), Institut National Du Cancer (INCa), grant Number PLBIO 2022\u2010075 (FibroMel) and the UCA J.E.D.I. Investments in the Future project with the reference number ANR\u201015\u2010IDEX\u201001. The graphical abstract is created in BioRender. MARI, B. (2025) https://BioRender.com/b0jq8np .
Chang MY, Mentzer SJ, Colson YL, Linden PA, Jaklitsch MT, Lipsitz SR, et al. Factors predicting poor survival after resection of stage IA non-small cell lung cancer. J Thorac Cardiovasc Surg. 2007;134:850–856.
Liu L, Soler J, Reckamp KL, Sankar K. Emerging targets in non-small cell lung cancer. Int J Mol Sci. 2024;25:10046.
Pouyssegur J, Dayan F, Mazure NM. Hypoxia signalling in cancer and approaches to enforce tumour regression. Nature. 2006;441:437–443.
Holohan C, Van Schaeybroeck S, Longley DB, Johnston PG. Cancer drug resistance: an evolving paradigm. Nat Rev Cancer. 2013;13:714–726.
Mirchandani AS, Sanchez-Garcia MA, Walmsley SR. How oxygenation shapes immune responses: emerging roles for physioxia and pathological hypoxia. Nat Rev Immunol. 2024;25:161–177.
Akagi I, Okayama H, Schetter AJ, Robles AI, Kohno T, Bowman ED, et al. Combination of protein coding and non-coding gene expression as a robust prognostic classifier in stage I lung adenocarcinoma. Cancer Res. 2013;73:3821–3832.
Ilie M, Mazure NM, Hofman V, Ammadi RE, Ortholan C, Bonnetaud C, et al. High levels of carbonic anhydrase IX in tumour tissue and plasma are biomarkers of poor prognostic in patients with non-small cell lung cancer. Br J Cancer. 2010;102:1627–1635.
Tian H, Tang L, Yang Z, Xiang Y, Min Q, Yin M, et al. Current understanding of functional peptides encoded by lncRNA in cancer. Cancer Cell Int. 2024;24:252.
Quinn JJ, Chang HY. Unique features of long non-coding RNA biogenesis and function. Nat Rev Genet. 2016;17:47–62.
Kopp F, Mendell JT. Functional classification and experimental dissection of long noncoding RNAs. Cell. 2018;172:393–407.
Moreno Leon L, Gautier M, Allan R, Ilié M, Nottet N, Pons N, et al. The nuclear hypoxia-regulated NLUCAT1 long non-coding RNA contributes to an aggressive phenotype in lung adenocarcinoma through regulation of oxidative stress. Oncogene. 2019;38:7146–7165.
Xu Y, Yu X, Zhang M, Zheng Q, Sun Z, He Y, et al. Promising advances in LINC01116 related to cancer. Front Cell Dev Biol. 2021;9:736927.
Shang B, Li Z, Li M, Jiang S, Feng Z, Cao Z, et al. Silencing LINC01116 suppresses the development of lung adenocarcinoma via the AKT signaling pathway. Thorac Cancer. 2021;12:2093–2103.
Buffa FM, Harris AL, West CM, Miller CJ. Large meta-analysis of multiple cancers reveals a common, compact and highly prognostic hypoxia metagene. Br J Cancer. 2010;102:428–435.
Yoshihara K, Shahmoradgoli M, Martinez E, Vegesna R, Kim H, Torres-Garcia W, et al. Inferring tumour purity and stromal and immune cell admixture from expression data. Nat Commun. 2013;4:2612.
Truchi M, Lacoux C, Gille C, Fassy J, Magnone V, Lopes Goncalves R, et al. Detecting subtle transcriptomic perturbations induced by lncRNAs knock-down in single-cell CRISPRi screening using a new sparse supervised autoencoder neural network. Front Bioinform. 2024;4:1340339.
Gastaldi C, Bertero T, Xu N, Bourget-Ponzio I, Lebrigand K, Fourre S, et al. miR-193b/365a cluster controls progression of epidermal squamous cell carcinoma. Carcinogenesis. 2014;35:1110–1120.
Bertero T, Bourget-Ponzio I, Puissant A, Loubat A, Mari B, Meneguzzi G, et al. Tumor suppressor function of miR-483-3p on squamous cell carcinomas due to its pro-apoptotic properties. Cell Cycle. 2013;12:2183–2193.
Adams TS, Schupp JC, Poli S, Ayaub EA, Neumark N, Ahangari F, et al. Single-cell RNA-seq reveals ectopic and aberrant lung-resident cell populations in idiopathic pulmonary fibrosis. Sci Adv. 2020;6:eaba1983.
Xiang H, Pan Y, Sze MA, Wlodarska M, Li L, van de Mark KA, et al. Single-cell analysis identifies NOTCH3-mediated interactions between stromal cells that promote microenvironment remodeling and invasion in lung adenocarcinoma. Cancer Res. 2024;84:1410–1425.
Schupp JC, Adams TS, Cosme C Jr, Raredon MSB, Yuan Y, Omote N, et al. Integrated single-cell atlas of endothelial cells of the human lung. Circulation. 2021;144:286–302.
Zeng L, Lyu X, Yuan J, Wang W, Zhao N, Liu B, et al. Long non-coding RNA LINC01116 is overexpressed in lung adenocarcinoma and promotes tumor proliferation and metastasis. Am J Transl Res. 2020;12:4302–4313.
Ji RC. Hypoxia and lymphangiogenesis in tumor microenvironment and metastasis. Cancer Lett. 2014;346:6–16.
Chang YN, Zhang K, Hu ZM, Qi HX, Shi ZM, Han XH, et al. Hypoxia-regulated lncRNAs in cancer. Gene. 2016;575:1–8.
Zhang M, Wang Z, Wu Y, Chen M, Li J, Liu G. Hypoxia-induced factor-1alpha promotes radioresistance of esophageal cancer cells by transcriptionally activating LINC01116 and suppressing miR-3612 under hypoxia. J Biochem Mol Toxicol. 2024;38:e23551.
Jackson AL, Bartz SR, Schelter J, Kobayashi SV, Burchard J, Mao M, et al. Expression profiling reveals off-target gene regulation by RNAi. Nat Biotechnol. 2003;21:635–637.
van Dongen S, Abreu-Goodger C, Enright AJ. Detecting microRNA binding and siRNA off-target effects from expression data. Nat Methods. 2008;5:1023–1025.
Stojic L, Lun ATL, Mangei J, Mascalchi P, Quarantotti V, Barr AR, et al. Specificity of RNAi, LNA and CRISPRi as loss-of-function methods in transcriptional analysis. Nucleic Acids Res. 2018;46:5950–5966.
Jacquet K, Vidal-Cruchez O, Rezzonico R, Nicolini VJ, Mograbi B, Hofman P, et al. New technologies for improved relevance in miRNA research. Trends Genet. 2021;37:1060–1063.
Mattick JS, Amaral PP, Carninci P, Carpenter S, Chang HY, Chen LL, et al. Long non-coding RNAs: definitions, functions, challenges and recommendations. Nat Rev Mol Cell Biol. 2023;24:430–447.
Deforzh E, Uhlmann EJ, Das E, Galitsyna A, Arora R, Saravanan H, et al. Promoter and enhancer RNAs regulate chromatin reorganization and activation of miR-10b/HOXD locus, and neoplastic transformation in glioma. Mol Cell. 2022;82:1894–1908.e5.
Deforzh E, Kharel P, Zhang Y, Karelin A, El Khayari A, Ivanov P, et al. HOXDeRNA activates a cancerous transcription program and super enhancers via genome-wide binding. Mol Cell. 2024;84:3950–3966.e6.
Ye J, Zhu J, Chen H, Qian J, Zhang L, Wan Z, et al. A novel lncRNA-LINC01116 regulates tumorigenesis of glioma by targeting VEGFA. Int J Cancer. 2020;146:248–261.
Alitalo K. The lymphatic vasculature in disease. Nat Med. 2011;17:1371–1380.
Gillot L, Baudin L, Rouaud L, Kridelka F, Noel A. The pre-metastatic niche in lymph nodes: formation and characteristics. Cell Mol Life Sci. 2021;78:5987–6002.
Karaman S, Detmar M. Mechanisms of lymphatic metastasis. J Clin Invest. 2014;124:922–928.
Stacker SA, Williams SP, Karnezis T, Shayan R, Fox SB, Achen MG. Lymphangiogenesis and lymphatic vessel remodelling in cancer. Nat Rev Cancer. 2014;14:159–172.
Cho JK, Hyun SH, Choi N, Kim MJ, Padera TP, Choi JY, et al. Significance of lymph node metastasis in cancer dissemination of head and neck cancer. Transl Oncol. 2015;8:119–125.
Maus RLG, Jakub JW, Hieken TJ, Nevala WK, Christensen TA, Sutor SL, et al. Identification of novel, immune-mediating extracellular vesicles in human lymphatic effluent draining primary cutaneous melanoma. Onco Targets Ther. 2019;8:e1667742.
Dieterich LC, Tacconi C, Ducoli L, Detmar M. Lymphatic vessels in cancer. Physiol Rev. 2022;102:1837–1879.
Paupert J, Sounni NE, Noel A. Lymphangiogenesis in post-natal tissue remodeling: lymphatic endothelial cell connection with its environment. Mol Asp Med. 2011;32:146–158.
Viudez-Pareja C, Kreft E, Garcia-Caballero M. Immunomodulatory properties of the lymphatic endothelium in the tumor microenvironment. Front Immunol. 2023;14:1235812.
Forsythe JA, Jiang BH, Iyer NV, Agani F, Leung SW, Koos RD, et al. Activation of vascular endothelial growth factor gene transcription by hypoxia-inducible factor 1. Mol Cell Biol. 1996;16:4604–4613.
Lin S, Chai Y, Zheng X, Xu X. The role of HIF in angiogenesis, lymphangiogenesis, and tumor microenvironment in urological cancers. Mol Biol Rep. 2023;51:14.
Montenegro-Navarro N, Garcia-Baez C, Garcia-Caballero M. Molecular and metabolic orchestration of the lymphatic vasculature in physiology and pathology. Nat Commun. 2023;14:8389.
Schito L. Hypoxia-dependent angiogenesis and Lymphangiogenesis in cancer. Adv Exp Med Biol. 2019;1136:71–85.
Boehme JT, Morris CJ, Chiacchia SR, Gong W, Wu KY, Kameny RJ, et al. HIF-1alpha promotes cellular growth in lymphatic endothelial cells exposed to chronically elevated pulmonary lymph flow. Sci Rep. 2021;11:1468.
Schito L, Rey S. Hypoxia orchestrates the lymphovascular-immune ensemble in cancer. Trends Cancer. 2022;8:771–784.
Wang Y, He S, Diao M, Zhao R, Ren J, Mei P, et al. Elevated ERbeta expression driven by low ASB8-mediated ubiquitination in lung adenocarcinoma promotes lymph node metastasis via tumor-associated neutrophils. Cell Death Dis. 2025;16:576.
