Single-cell sequencing reveals lung cell fate evolution initiated by smoking to explore gene predictions of correlative diseases

References

• Agudelo CW, Samaha G, Garcia-Arcos I. 2020. Alveolar lipids in pulmonary disease. A review. Lipids Health Dis. 19(1):122. doi: 10.1186/s12944-020-01278-8.
   PubMed Web of Science ®Google Scholar
• Bao Y, Zhu X. 2022. Role of chemokines and inflammatory cells in respiratory allergy. J Asthma Allergy. 15:1805–1822. doi: 10.2147/JAA.S395490.
   PubMed Web of Science ®Google Scholar
• Barrington-Trimis JL, Braymiller JL, Unger JB, McConnell R, Stokes A, Leventhal AM, Sargent JD, Samet JM, Goodwin RD. 2020. Trends in the age of cigarette smoking initiation among young adults in the US from 2002 to 2018. JAMA Netw Open. 3(10):e2019022–e2019022. doi: 10.1001/jamanetworkopen.2020.19022.
   PubMed Web of Science ®Google Scholar
• Bharati S, Podder P, Mondal MRH. 2020. Hybrid deep learning for detecting lung diseases from X-ray images. Inform Med Unlocked. 20:100391. doi: 10.1016/j.imu.2020.100391.
   PubMedGoogle Scholar
• Brouwer KLR, Evers R, Hayden E, Hu S, Li CY, Meyer Zu Schwabedissen HE, Neuhoff S, Oswald S, Piquette-Miller M, Saran C, et al. 2022. Regulation of drug transport proteins—from mechanisms to clinical impact: a white paper on behalf of the international transporter consortium. Clin Pharmacol Ther. 112(3):461–484. doi: 10.1002/cpt.2605.
   PubMed Web of Science ®Google Scholar
• Budinger GRS, Kohanski RA, Gan W, Kobor MS, Amaral LA, Armanios M, Kelsey KT, Pardo A, Tuder R, Macian F, et al. 2017. The intersection of aging biology and the pathobiology of lung diseases: a joint NHLBI/NIA workshop. J Gerontol A Biol Sci Med Sci. 72(11):1492–1500. doi: 10.1093/gerona/glx090.
   PubMed Web of Science ®Google Scholar
• Caliri AW, Tommasi S, Besaratinia A. 2021. Relationships among smoking, oxidative stress, inflammation, macromolecular damage, and cancer. Mutat Res Rev Mutat Res. 787:108365. doi: 10.1016/j.mrrev.2021.108365.
   PubMed Web of Science ®Google Scholar
• Cao X, Coyle JP, Xiong R, Wang Y, Heflich RH, Ren B, Gwinn WM, Hayden P, Rojanasakul L. 2021. Invited review: human air-liquid-interface organotypic airway tissue models derived from primary tracheobronchial epithelial cells—overview and perspectives. In Vitro Cell Dev Biol Anim. 57(2):104–132. doi: 10.1007/s11626-020-00517-7.
   PubMed Web of Science ®Google Scholar
• Carraro G, Stripp BR. 2022. Insights gained in the pathology of lung disease through single‐cell transcriptomics. J Pathol. 257(4):494–500. doi: 10.1002/path.5971.
   PubMed Web of Science ®Google Scholar
• Cui Y, Liu KW, Ip MS, Liang Y, Mak JC. 2020. Protective effect of selegiline on cigarette smoke-induced oxidative stress and inflammation in rat lungs in vivo. Ann Transl Med. 8(21):1418–1418. doi: 10.21037/atm-20-2426.
   PubMed Web of Science ®Google Scholar
• Dawod YT, Cook NE, Graham WB, Madhani-Lovely F, Thao C. 2020. Smoking-associated interstitial lung disease: update and review. Expert Rev Respir Med. 14(8):825–834. doi: 10.1080/17476348.2020.1766971.
   PubMed Web of Science ®Google Scholar
• Duarte R, Paschoal MEM. 2006. Molecular markers in lung cancer: prognostic role and relationship to smoking. J Bras Pneumol. 32(1):56–65. doi: 10.1590/s1806-37132006000100012.
   PubMedGoogle Scholar
• Ebersole J, Samburova V, Son Y, Cappelli D, Demopoulos C, Capurro A, Pinto A, Chrzan B, Kingsley K, Howard K, et al. 2020. Harmful chemicals emitted from electronic cigarettes and potential deleterious effects in the oral cavity. Tob Induc Dis. 18:41. doi: 10.18332/tid/116988.
   PubMed Web of Science ®Google Scholar
• Elisia I, Lam V, Cho B, Hay M, Li MY, Yeung M, Bu L, Jia W, Norton N, Lam S, et al. 2020. The effect of smoking on chronic inflammation, immune function and blood cell composition. Sci Rep. 10(1):19480. doi: 10.1038/s41598-020-76556-7.
   PubMed Web of Science ®Google Scholar
• Gotarredona MS, Herrero SN, Izquierdo LG, Portal JR. 2022. Smoking-related interstitial lung disease. Radiología (English Edition). 64:277–289.
   Web of Science ®Google Scholar
• Gui X, Yang Z, Li MD. 2021. Effect of cigarette smoke on gut microbiota: state of knowledge. Front Physiol. 12:673341. doi: 10.3389/fphys.2021.673341.
   PubMed Web of Science ®Google Scholar
• Hajdusianek W, Żórawik A, Waliszewska-Prosół M, Poręba R, Gać P. 2021. Tobacco and Nervous System Development and Function—New Findings 2015–2020. Brain Sci. 11(6):797. doi: 10.3390/brainsci11060797.
   PubMed Web of Science ®Google Scholar
• Hanley CJ, Waise S, Ellis MJ, Lopez MA, Pun WY, Taylor J, Parker R, Kimbley LM, Chee SJ, Shaw EC, et al. 2023. Single-cell analysis reveals prognostic fibroblast subpopulations linked to molecular and immunological subtypes of lung cancer. Nat Commun. 14(1):387. doi: 10.1038/s41467-023-35832-6.
   PubMed Web of Science ®Google Scholar
• Herrera FG, Romero P, Coukos G. 2022. Lighting up the tumor fire with low-dose irradiation. Trends Immunol. 43(3):173–179. doi: 10.1016/j.it.2022.01.006.
   PubMed Web of Science ®Google Scholar
• Hofman P. 2020. New insights into the interaction of the immune system with non-small cell lung carcinomas. Transl Lung Cancer Res. 9(5):2199–2213. doi: 10.21037/tlcr-20-178.
   PubMed Web of Science ®Google Scholar
• Hou W, Hu S, Li C, Ma H, Wang Q, Meng G, Guo T, Zhang J. 2019. Cigarette smoke induced lung barrier dysfunction, EMT, and tissue remodeling: a possible link between COPD and lung cancer. Biomed Res Int. 2019:2025636–2025610. doi: 10.1155/2019/2025636.
   PubMed Web of Science ®Google Scholar
• Januska MN, Walsh MJ. 2022. Single-cell RNA-sequencing reveals new basic and translational insights in the cystic fibrosis lung. Am J Respir Cell Mol Biol. 68(2):131–139. doi: 10.1165/rcmb.2022-0038TR.
   Web of Science ®Google Scholar
• Knobloch J, Casjens S, Lehnert M, Yanik SD, Körber S, Lotz A, Rupp J, Raulf M, Zschiesche W, Weiss T, et al. 2020. Exposure to welding fumes suppresses the activity of T-helper cells. Environ Res. 189:109913. doi: 10.1016/j.envres.2020.109913.
   PubMed Web of Science ®Google Scholar
• Kozlowski LT. 2021. Nicotine addiction, Maurice Seevers, and the first surgeon general report on cigarette smoking and health: conflicting terms and interests. J Stud Alcohol Drugs. 82(4):536–543.
   PubMed Web of Science ®Google Scholar
• Lang NJ, Gote-Schniering J, Porras-Gonzalez D, Yang L, De Sadeleer LJ, Jentzsch RC, Shitov VA, Zhou S, Ansari M, Agami A. 2023. Ex vivo tissue perturbations coupled to single-cell RNA-seq reveal multilineage cell circuit dynamics in human lung fibrogenesis. Sci Transl Med. 15(725):eadh0908. doi: 10.1126/scitranslmed.adh0908.
   Google Scholar
• Lendahl U, Muhl L, Betsholtz C. 2022. Identification, discrimination and heterogeneity of fibroblasts. Nat Commun. 13(1):3409. doi: 10.1038/s41467-022-30633-9.
   PubMed Web of Science ®Google Scholar
• Lin K, Yang Y, Cao Y, Liang J, Qian J, Wang X, Han Q. 2023. Combining single-cell transcriptomics and Cell tagging to identify differentiation trajectories of human adipose-derived mesenchymal stem cells. Stem Cell Res Ther. 14(1):14. doi: 10.1186/s13287-023-03237-3.
   PubMed Web of Science ®Google Scholar
• Lugg ST, Scott A, Parekh D, Naidu B, Thickett DR. 2022. Cigarette smoke exposure and alveolar macrophages: mechanisms for lung disease. Thorax. 77(1):94–101. doi: 10.1136/thoraxjnl-2020-216296.
   PubMed Web of Science ®Google Scholar
• Mendez R, Banerjee S, Bhattacharya SK, Banerjee S. 2019. Lung inflammation and disease: a perspective on microbial homeostasis and metabolism. Iubmb Life. 71(2):152–165. doi: 10.1002/iub.1969.
   PubMed Web of Science ®Google Scholar
• Park E-J, Park Y-J, Lee SJ, Lee K, Yoon C. 2019. Whole cigarette smoke condensates induce ferroptosis in human bronchial epithelial cells. Toxicol Lett. 303:55–66. doi: 10.1016/j.toxlet.2018.12.007.
   PubMed Web of Science ®Google Scholar
• Paudel KR, Dharwal V, Patel VK, Galvao I, Wadhwa R, Malyla V, Shen SS, Budden KF, Hansbro NG, Vaughan A, et al. 2020. Role of lung microbiome in innate immune response associated with chronic lung diseases. Front Med. 7:554. doi: 10.3389/fmed.2020.00554.
   PubMed Web of Science ®Google Scholar
• Prisk GK. 2020. Ventilation, blood flow, and their inter‐relationships. In: Maynard RL, Pearce SJ, Nemery B, Wagner PD, Cooper BG, editors. Cotes’ Lung Function. p. 259–299. doi: 10.1002/9781118597309.ch16.
   Google Scholar
• Proctor RN. 2012. The history of the discovery of the cigarette–lung cancer link: evidentiary traditions, corporate denial, global toll. Tob Control. 21(2):87–91. doi: 10.1136/tobaccocontrol-2011-050338.
   PubMed Web of Science ®Google Scholar
• Ratnasiri K, Wilk AJ, Lee MJ, Khatri P, Blish CA. 2022. Single-cell RNA-seq methods to interrogate virus-host interactions. Semin Immunopathol. 45(1):71–89. Springer. doi: 10.1007/s00281-022-00972-2.
   Google Scholar
• Reyfman PA, Walter JM, Joshi N, Anekalla KR, McQuattie-Pimentel AC, Chiu S, Fernandez R, Akbarpour M, Chen CI, Ren Z, et al. 2019. Single-cell transcriptomic analysis of human lung provides insights into the pathobiology of pulmonary fibrosis. Am J Respir Crit Care Med. 199(12):1517–1536. doi: 10.1164/rccm.201712-2410OC.
   PubMed Web of Science ®Google Scholar
• Rosell R, Tarón M, O'Brate A. 2001. Predictive molecular markers in non–small cell lung cancer. Curr Opin Oncol. 13(2):101–109. doi: 10.1097/00001622-200103000-00004.
   PubMed Web of Science ®Google Scholar
• Salvi SS, Brashier BB, Londhe J, Pyasi K, Vincent V, Kajale SS, Tambe S, Mandani K, Nair A, Mak SM, et al. 2020. Phenotypic comparison between smoking and non-smoking chronic obstructive pulmonary disease. Respir Res. 21(1):50. doi: 10.1186/s12931-020-1310-9.
   PubMed Web of Science ®Google Scholar
• Sarlak S, Lalou C, Amoedo ND, Rossignol R. 2020. Metabolic reprogramming by tobacco-specific nitrosamines (TSNAs) in cancer. In Seminars in cell & developmental biology, vol. 98, p. 154–166. Academic Press. doi: 10.1016/j.semcdb.2019.09.001.
   Google Scholar
• Schupp JC, Adams TS, Cosme C, Raredon MSB, Yuan Y, Omote N, Poli S, Chioccioli M, Rose K-A, Manning EP, et al. 2021. Integrated single-cell atlas of endothelial cells of the human lung. Circulation. 144(4):286–302. doi: 10.1161/CIRCULATIONAHA.120.052318.
   PubMed Web of Science ®Google Scholar
• Sepand MR, Maghsoudi AS, Shadboorestan A, Mirnia K, Aghsami M, Raoufi M. 2021. Cigarette smoke-induced toxicity consequences of intracellular iron dysregulation and ferroptosis. Life Sci. 281:119799. doi: 10.1016/j.lfs.2021.119799.
   PubMed Web of Science ®Google Scholar
• Shukla SD, Walters EH, Simpson JL, Keely S, Wark PA, O'Toole RF, Hansbro PM. 2020. Hypoxia‐inducible factor and bacterial infections in chronic obstructive pulmonary disease. Respirology. 25(1):53–63. doi: 10.1111/resp.13722.
   PubMed Web of Science ®Google Scholar
• Smith JC, Sausville EL, Girish V, Yuan ML, Vasudevan A, John KM, Sheltzer JM. 2020. Cigarette smoke exposure and inflammatory signaling increase the expression of the SARS-CoV-2 receptor ACE2 in the respiratory tract. Dev Cell. 53(5):514–529. e513. doi: 10.1016/j.devcel.2020.05.012.
   PubMed Web of Science ®Google Scholar
• Song M-A, Freudenheim JL, Brasky TM, Mathe EA, McElroy JP, Nickerson QA, Reisinger SA, Smiraglia DJ, Weng DY, Ying KL, et al. 2020. Biomarkers of exposure and effect in the lungs of smokers, nonsmokers, and electronic cigarette users. Cancer Epidemiol Biomarkers Prev. 29(2):443–451. doi: 10.1158/1055-9965.EPI-19-1245.
   PubMed Web of Science ®Google Scholar
• Song Q, Chen P, Liu X-M. 2021. The role of cigarette smoke-induced pulmonary vascular endothelial cell apoptosis in COPD. Respir Res. 22(1):39. doi: 10.1186/s12931-021-01630-1.
   PubMed Web of Science ®Google Scholar
• Stanojevic S, Kaminsky DA, Miller MR, Thompson B, Aliverti A, Barjaktarevic I, Cooper BG, Culver B, Derom E, Hall GL, et al. 2022. ERS/ATS technical standard on interpretive strategies for routine lung function tests. Eur Respir J. 60(1):2101499. doi: 10.1183/13993003.01499-2021.
   PubMed Web of Science ®Google Scholar
• Talhout R, Schulz T, Florek E, van Benthem J, Wester P, Opperhuizen A. 2011. Hazardous compounds in tobacco smoke. Int J Environ Res Public Health. 8(2):613–628. doi: 10.3390/ijerph8020613.
   PubMed Web of Science ®Google Scholar
• Tommola M, Ilmarinen P, Tuomisto LE, Lehtimäki L, Niemelä O, Nieminen P, Kankaanranta H. 2019. Cumulative effect of smoking on disease burden and multimorbidity in adult-onset asthma. Eur Respir J. 54(3):1801580. doi: 10.1183/13993003.01580-2018.
   PubMed Web of Science ®Google Scholar
• Tonnesen P, Marott JL, Nordestgaard B, Bojesen SE, Lange P. 2019. Secular trends in smoking in relation to prevalent and incident smoking-related disease: a prospective population-based study. Tob Induc Dis. 17:72. doi: 10.18332/tid/112459.
   PubMed Web of Science ®Google Scholar
• Travaglini KJ, Nabhan AN, Penland L, Sinha R, Gillich A, Sit RV, Chang S, Conley SD, Mori Y, Seita J, et al. 2020. A molecular cell atlas of the human lung from single-cell RNA sequencing. Nature. 587(7835):619–625. doi: 10.1038/s41586-020-2922-4.
   PubMed Web of Science ®Google Scholar
• Wadowska K, Bil-Lula I, Trembecki Ł, Śliwińska-Mossoń M. 2020. Genetic markers in lung cancer diagnosis: a review. Int J Mol Sci. 21(13):4569. doi: 10.3390/ijms21134569.
   PubMed Web of Science ®Google Scholar
• Wang D, Zhang S, Liu B, Wang B, He S, Zhang R. 2020. Anti-inflammatory effects of adiponectin in cigarette smoke-activated alveolar macrophage through the COX-2/PGE2 and TLRs signaling pathway. Cytokine. 133:155148. doi: 10.1016/j.cyto.2020.155148.
   PubMed Web of Science ®Google Scholar
• Watanabe N, Fujita Y, Nakayama J, Mori Y, Kadota T, Hayashi Y, Shimomura I, Ohtsuka T, Okamoto K, Araya J, et al. 2022. Anomalous epithelial variations and ectopic inflammatory response in chronic obstructive pulmonary disease. Am J Respir Cell Mol Biol. 67(6):708–719. doi: 10.1165/rcmb.2021-0555OC.
   PubMed Web of Science ®Google Scholar
• Wu T, Xu K, Liu C, Li Y, Li M. 2022. Interleukin-37 ameliorates cigarette smoke-induced lung inflammation in mice. Biomed Pharmacother. 155:113684. doi: 10.1016/j.biopha.2022.113684.
   PubMed Web of Science ®Google Scholar
• Xiang H, Ramil CP, Hai J, Zhang C, Wang H, Watkins AA, Afshar R, Georgiev P, Sze MA, Song XS, et al. 2020. Cancer-associated fibroblasts promote immunosuppression by inducing ROS-generating monocytic MDSCs in lung squamous cell carcinoma CAFs induce immunosuppression in lung cancer. Cancer Immunol Res. 8(4):436–450. doi: 10.1158/2326-6066.CIR-19-0507.
   PubMed Web of Science ®Google Scholar
• Zong D, Liu X, Li J, Ouyang R, Chen P. 2019. The role of cigarette smoke-induced epigenetic alterations in inflammation. Epigenetics Chromatin. 12(1):65. doi: 10.1186/s13072-019-0311-8.
   PubMed Web of Science ®Google Scholar
• Zuo W-L, Rostami M, Shenoy S, LeBlanc M, Salit J, Strulovici-Barel Y, O'Beirne S, Kaner R, Leopold P, Mezey J. 2019. Single cell RNA-sequencing reveals novel cell-specific expression of lung disease-related genes in the human small airway epithelium. In D29. Lung multi-omics to mechanism, p. A6078–A6078. American Thoracic Society. doi: 10.1164/ajrccm-conference.2019.199.1_MeetingAbstracts.A6078.
   Google Scholar