Datasets from "Circulating miRNA and Lung Cancer: - a More Comprehensive Analysis of Available Data"

A collection of datasets on miRNA and lung cancer used in Berg, O.F.B.: Circulating miRNA and Lung Cancer: - a More Comprehensive Analysis of Available Data. NTNU Open (2022) The datasets in this collection are processed and normalized from available raw datasets. The processing code that was used can be found on https://github.com/OleFredrik1/masterthesis. The raw datasets are: Asakura2020: Asakura, K., Kadota, T., Matsuzaki, J., Yoshida, Y., Yamamoto, Y., Nakagawa, K., Takizawa, S., Aoki, Y., Nakamura, E., Miura, J., Sakamoto, H., Kato, K., Watanabe, S.-i., and Ochiya, T. (2020). A miRNA-based diagnostic model predicts resectable lung cancer in humans with high accuracy. Communications Biology, 3(1):1–9. Accession ID: GSE137140 Link: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE137140 Bianchi2011: Bianchi, F., Nicassio, F., Marzi, M., Belloni, E., Dall’Olio, V., Bernard, L., Pelosi, G., Maisonneuve, P., Veronesi, G., and Di Fiore, P. P. (2011). A serum circulating miRNA diagnostic test to identify asymptomatic high-risk individuals with early stage lung cancer. EMBO Molecular Medicine, 3(8):495–503. Link: https://www.embopress.org/action/downloadSupplement?doi=10.1002%2Femmm.201100154&file=emmm_201100154_sm_suppdata2.xls Chen2019: Accession ID: GSE71661 Link: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE71661 Duan2021: Duan, X., Qiao, S., Li, D., Li, S., Zheng, Z., Wang, Q., and Zhu, X. (2021). Circulating miRNAs in Serum as Biomarkers for Early Diagnosis of Non-small Cell Lung Cancer. Frontiers in Genetics, 12:987. Accession ID: GSE137140 Link: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE137140 Fehlmann2020: Fehlmann, T., Kahraman, M., Ludwig, N., Backes, C., Galata, V., Keller, V., Geffers, L., Mercaldo, N., Hornung, D., Weis, T., Kayvanpour, E., Abu-Halima, M., Deuschle, C., Schulte, C., Suenkel, U., von Thaler, A.-K., Maetzler, W., Herr, C., Fähndrich, S., Vogelmeier, C., Guimaraes, P., Hecksteden, A., Meyer, T., Metzger, F., Diener, C., Deutscher, S., Abdul-Khaliq, H., Stehle, I., Haeusler, S., Meiser, A., Groesdonk, H. V., Volk, T., Lenhof, H.-P., Katus, H., Balling, R., Meder, B., Kruger, R., Huwer, H., Bals, R., Meese, E., and Keller, A. (2020). Evaluating the Use of Circulating MicroRNA Profiles for Lung Cancer Detection in Symptomatic Patients. JAMA oncology, 6(5):714–723. Accession ID: E-MTAB-8026 Link: https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-8026/ Halvorsen2016: Halvorsen, A. R., Bjaanæs, M., LeBlanc, M., Holm, A. M., Bolstad, N., Rubio, L., Peñalver, J. C., Cervera, J., Mojarrieta, J. C., López-Guerrero, J. A., Brustugun, O. T., and Helland, Å. (2016). A unique set of 6 circulating microRNAs for early detection of non-small cell lung cancer. Oncotarget, 7(24):37250–37259. Accession ID: GSE70080 Link: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE70080 Jin2017: Jin, X., Chen, Y., Chen, H., Fei, S., Chen, D., Cai, X., Liu, L., Lin, B., Su, H., Zhao, L., Su, M., Pan, H., Shen, L., Xie, D., and Xie, C. (2017). Evaluation of Tumor-Derived Exosomal miRNA as Potential Diagnostic Biomarkers for Early-Stage Non–Small Cell Lung Cancer Using Next-Generation Sequencing. Clinical Cancer Research, 23(17):5311–5319. Link: https://aacrjournals.org/clincancerres/article/23/17/5311/123048/Evaluation-of-Tumor-Derived-Exosomal-miRNA-as (table s1) Keller2009: Keller, A., Leidinger, P., Borries, A., Wendschlag, A., Wucherpfennig, F., Scheffler, M., Huwer, H., Lenhof, H.-P., and Meese, E. (2009). miRNAs in lung cancer - Studying complex fingerprints in patient’s blood cells by microarray experiments. BMC Cancer, 9(1):353. Accession ID: GSE17681 Link: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE17681 Keller2014: Keller, A., Leidinger, P., Vogel, B., Backes, C., ElSharawy, A., Galata, V., Mueller, S. C., Marquart, S., Schrauder, M. G., Strick, R., Bauer, A., Wischhusen, J., Beier, M., Kohlhaas, J., Katus, H. A., Hoheisel, J., Franke, A., Meder, B., and Meese, E. (2014). miRNAs can be generally associated with human pathologies as exemplified for miR-144*. BMC Medicine, 12(1):224. Accession ID: GSE61741 Link: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE61741 Keller2020: Keller, A., Fehlmann, T., Backes, C., Kern, F., Gislefoss, R., Langseth, H., Rounge, T. B., Ludwig, N., and Meese, E. (2020). Competitive learning suggests circulating miRNA profiles for cancers decades prior to diagnosis. RNA Biology, 17(10):1416–1426. Link: https://www.tandfonline.com/doi/full/10.1080/15476286.2020.1771945 (Supplemental Table 9) Kryczka2021: Kryczka, J., Migdalska-Sęk, M., Kordiak, J., Kiszałkiewicz, J. M., PastuszakLewandoska, D., Antczak, A., and Brzeziańska-Lasota, E. (2021). Serum Extracellular Vesicle-Derived miRNAs in Patients with Non-Small Cell Lung Cancer—Search for Non-Invasive Diagnostic Biomarkers. Diagnostics, 11(3):425. Link: https://www.mdpi.com/2075-4418/11/3/425/s1 Leidinger2011: Leidinger, P., Keller, A., Borries, A., Huwer, H., Rohling, M., Huebers, J., Lenhof, H.-P., and Meese, E. (2011). Specific peripheral miRNA profiles for distinguishing lung cancer from COPD. Lung Cancer, 74(1):41–47. Accession ID: GSE24709 Link: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24709 Leidinger2014: Leidinger, P., Backes, C., Dahmke, I. N., Galata, V., Huwer, H., Stehle, I., Bals, R., Keller, A., and Meese, E. (2014). What makes a blood cell based miRNA expression pattern disease specific? - A miRNome analysis of blood cell subsets in lung cancer patients and healthy controls. Oncotarget, 5(19):9484–9497. Accession ID: GSE55993 Link: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE55993 Leidinger2016: Leidinger, P., Brefort, T., Backes, C., Krapp, M., Galata, V., Beier, M., Kohlhaas, J., Huwer, H., Meese, E., and Keller, A. (2016). High-throughput qRT-PCR validation of blood microRNAs in non-small cell lung cancer. Oncotarget, 7(4):4611–4623. Link: https://www.oncotarget.com/article/6566/text/ (supplementary files) Li2017: Li, L.-L., Qu, L.-L., Fu, H.-J., Zheng, X.-F., Tang, C.-H., Li, X.-Y., Chen, J., Wang, W.-X., Yang, S.-X., Wang, L., Zhao, G.-H., Lv, P.-P., Zhang, M., Lei, Y.-Y., Qin, H.-F., Wang, H., Gao, H.-J., and Liu, X.-Q. (2017). Circulating microRNAs as novel biomarkers of ALK-positive non-small cell lung cancer and predictors of response to crizotinib therapy. Oncotarget, 8(28):45399–45414. Accession ID: GSE94536 Link: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE94536 Marzi2016: Marzi, M. J., Montani, F., Carletti, R. M., Dezi, F., Dama, E., Bonizzi, G., Sandri, M. T., Rampinelli, C., Bellomi, M., Maisonneuve, P., Spaggiari, L., Veronesi, G., Bianchi, F., Di Fiore, P. P., and Nicassio, F. (2016). Optimization and Standardization of Circulating MicroRNA Detection for Clinical Application: The miR-Test Case. Clinical Chemistry, 62(5):743–754 Accession ID: GSE76462 Link: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE76462 Nigita2018: Nigita, G., Distefano, R., Veneziano, D., Romano, G., Rahman, M., Wang, K., Pass, H., Croce, C. M., Acunzo, M., and Nana-Sinkam, P. (2018). Tissue and exosomal miRNA editing in Non-Small Cell Lung Cancer. Scientific Reports, 8(1):10222. Accession ID: GSE114711 Link: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE114711 Patnaik2012: Patnaik, S. K., Yendamuri, S., Kannisto, E., Kucharczuk, J. C., Singhal, S., and Vachani, A. (2012). MicroRNA Expression Profiles of Whole Blood in Lung Adenocarcinoma. PLOS ONE, 7(9):e46045. Accession ID: GSE27486 Link: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE27486 Patnaik2017: Patnaik, S. K., Kannisto, E. D., Mallick, R., Vachani, A., and Yendamuri, S. (2017). Whole blood microRNA expression may not be useful for screening non-small cell lung cancer. PLOS ONE, 12(7):e0181926. Accession ID: GSE40738 Link: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40738 Qu2017: Qu, L., Li, L., Zheng, X., Fu, H., Tang, C., Qin, H., Li, X., Wang, H., Li, J., Wang, W., Yang, S., Wang, L., Zhao, G., Lv, P., Lei, Y., Zhang, M., Gao, H., Song, S., and Liu, X. (2017). Circulating plasma microRNAs as potential markers to identify EGFR mutation status and to monitor epidermal growth factor receptor-tyrosine kinase inhibitor treatment in patients with advanced non-small cell lung cancer. Oncotarget, 8(28):45807–45824. Accession ID: GSE93300 Link: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE93300 Reis2020: Reis, P. P., Drigo, S. A., Carvalho, R. F., Lopez Lapa, R. M., Felix, T. F., Patel, D., Cheng, D., Pintilie, M., Liu, G., and Tsao, M.-S. (2020). Circulating miR-16-5p, miR-92a-3p, and miR-451a in Plasma from Lung Cancer Patients: Potential Application in Early Detection and a Regulatory Role in Tumorigenesis Pathways. Cancers, 12(8):2071. Accession ID: GSE152702 Link: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE152702 Wozniak2015: Wozniak, M. B., Scelo, G., Muller, D. C., Mukeria, A., Zaridze, D., and Brennan, P. (2015). Circulating MicroRNAs as Non-Invasive Biomarkers for Early Detection of Non-Small-Cell Lung Cancer. PLOS ONE, 10(5):e0125026. Accession ID: GSE64591 Link: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE64591 Yao2019: Yao, B., Qu, S., Hu, R., Gao, W., Jin, S., Liu, M., and Zhao, Q. (2019). A panel of miRNAs derived from plasma extracellular vesicles as novel diagnostic biomarkers of lung adenocarcinoma. FEBS Open Bio, 9(12):2149–2158. Accession ID: GSE111803 Link: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE111803 Zaporozhchenko2018: Zaporozhchenko, I. A., Morozkin, E. S., Ponomaryova, A. A., Rykova, E. Y., Cherdyntseva, N. V., Zheravin, A. A., Pashkovskaya, O. A., Pokushalov, E. A., Vlassov, V. V., and Laktionov, P. P. (2018). Profiling of 179 miRNA Expression in Blood Plasma of Lung Cancer Patients and Cancer-Free Individuals. Scientific Reports, 8(1):6348. Accession ID: E-MTAB-6304 Link: https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-6304/ The Abdollahi2019 and Boeri2011 datasets are not included as I recived them by email and I did not recieve conformation that they were OK with me publishing the datasets.