Identification and Immune Characteristics Study of Pyroptosis‑Related Genes in Endometriosis

Endometriosis (EMT) is a prevalent gynecological disorder characterized by pain and infertility associated with the menstrual cycle. Pyroptosis, an emerging cell death mechanism, has been implicated in the pathogenesis of diverse diseases, highlighting its pivotal role in disease progression. Therefore, our study aimed to investigate the impact of pyroptosis in EMT using a comprehensive bioinformatics approach. We initially obtained two datasets from the Gene Expression Omnibus database and performed differential expression analysis to identify pyroptosis-related genes (PRGs) that were differentially expressed between EMT and non-EMT samples. Subsequently, several machine learning algorithms, namely least absolute shrinkage selection operator regression, support vector machine-recursive feature elimination, and random forest algorithms were used to identify a hub gene to construct an effective diagnostic model for EMT. Receiver operating characteristic curve analysis, nomogram, calibration curve, and decision curve analysis were applied to validate the performance of the model. Based on the selected hub gene, differential expression analysis between high- and low-expression groups was conducted to explore the functions and signaling pathways related to it. Additionally, the correlation between the hub gene and immune cells was investigated to gain insights into the immune microenvironment of EMT. Finally, a pyroptosis-related competing endogenous RNA network was constructed to elucidate the regulatory interactions of the hub gene. Our study revealed the potential contribution of a specific PRG to the pathogenesis of EMT, providing a novel perspective for clinical diagnosis and treatment of EMT. Data Availability The datasets presented in this study can be found on the GEO website (https://www.ncbi.nlm.nih.gov/geo/).

Baranov VS, Ivaschenko TE, Liehr T, Yarmolinskaya MI (2015) Systems genetics view of endometriosis: a common complex disorder. Eur J Obstet Gynecol Reprod Biol 185:59–65. https://doi.org/10.1016/j.ejogrb.2014.11.036 Bertschi D, McKinnon BD, Evers J, Bersinger NA, Mueller MD (2013) Enhanced inflammatory activity of endometriotic lesions from the rectovaginal septum. Mediat Inflamm 2013:450950. https://doi.org/10.1155/2013/450950 Cui L, Chen S, Wang D, Yang Q (2021) LINC01116 promotes proliferation and migration of endometrial stromal cells by targeting FOXP1 via sponging miR-9-5p in endometriosis. J Cell Mol Med 25(4):2000–2012. https://doi.org/10.1111/jcmm.16039 Chen Y, Wang X (2020) MiRDB: an online database for prediction of functional microRNA targets. Nucleic Acids Res 48(D1):D127–D131. https://doi.org/10.1093/nar/gkz757 Dai E, Meng L, Kang R, Wang X, Tang D (2020) ESCRT-III-dependent membrane repair blocks ferroptosis. Biochem Biophys Res Commun 522(2):415–421. https://doi.org/10.1016/j.bbrc.2019.11.110 Fenghua Y, Rong S, Juan S, Guan L (2022) Effect of Mirena intrauterine device combined with GNRH-A on endometriosis, sex hormone level and carbohydrate antigen 125. Cell Mol Biol (Noisy-le-grand) 68(7):22–26. https://doi.org/10.14715/cmb/2022.68.7.4 Friedman J, Hastie T, Tibshirani R (2010) Regularization paths for generalized linear models via coordinate descent. J Stat Softw 33(1):1–22 Furió-Tarí P, Tarazona S, Gabaldón T, Enright AJ, Conesa A (2016) SpongeScan: a web for detecting microRNA binding elements in lncRNA sequences. Nucleic Acids Res 44(W1):W176–80. https://doi.org/10.1093/nar/gkw443 Guyon I, Weston J, Barnhill S, Vapnik V (2002) Gene selection for cancer classification using support vector machines. Mach Learn 46(1):389–422. https://doi.org/10.1023/A:1012487302797 Hänzelmann S, Castelo R, Guinney J (2013) GSVA: gene set variation analysis for microarray and RNA-seq data. BMC Bioinform 14:7. https://doi.org/10.1186/1471-2105-14-7 Harada T, Iwabe T, Terakawa N (2001) Role of cytokines in endometriosis. Fertil Steril 76(1):1–10. https://doi.org/10.1016/s0015-0282(01)01816-7 Hassa H, Tanir HM, Tekin B, Kirilmaz SD, Sahin Mutlu F (2009) Cytokine and immune cell levels in peritoneal fluid and peripheral blood of women with early- and late-staged endometriosis. Arch Gynecol Obstet 279(6):891–895. https://doi.org/10.1007/s00404-008-0844-8 He H, Qiu Z (2023) The importance of BUD13 in the prognosis of hepatocellular carcinoma revealed by pan-cancer analysis. Cell Mol Biol (Noisy-le-grand) 69(6):41–48. https://doi.org/10.14715/cmb/2023.69.6.7 Huan Q, Cheng SC, Du ZH, Ma HF, Li C (2021) LncRNA AFAP1-AS1 regulates proliferation and apoptosis of endometriosis through activating STAT3/TGF-β/Smad signaling via miR-424-5p. J Obstet Gynaecol Res 47(7):2394–2405. https://doi.org/10.1111/jog.14801 Irandoost E, Najibi S, Talebbeigi S, Nassiri S (2023) Focus on the role of NLRP3 inflammasome in the pathology of endometriosis: a review on molecular mechanisms and possible medical applications. Naunyn Schmiedebergs Arch Pharmacol 396(4):621–631. https://doi.org/10.1007/s00210-022-02365-6 Jin Z, Huang J, Zhu Z (2017) Baicalein reduces endometriosis by suppressing the viability of human endometrial stromal cells through the nuclear factor-κB pathway in vitro. Exp Ther Med 14(4):2992–2998. https://doi.org/10.3892/etm.2017.4860 John B, Enright AJ, Aravin A, Tuschl T, Sander C, Marks DS (2004) Human MicroRNA targets. PLoS Biol 2(11):e363. https://doi.org/10.1371/journal.pbio.0020363 Joly JH, Lowry WE, Graham NA (2021) Differential gene set enrichment analysis: a statistical approach to quantify the relative enrichment of two gene sets. Bioinformatics 36(21):5247–5254. https://doi.org/10.1093/bioinformatics/btaa658 Kimber-Trojnar Ż, Pilszyk A, Niebrzydowska M, Pilszyk Z, Ruszała M, Leszczyńska-Gorzelak B (2021) The potential of non-invasive biomarkers for early diagnosis of asymptomatic patients with endometriosis. J Clin Med. https://doi.org/10.3390/jcm10132762 Kyama CM, Debrock S, Mwenda JM, D’Hooghe TM (2003) Potential involvement of the immune system in the development of endometriosis. Reprod Biol Endocrinol 1:123. https://doi.org/10.1186/1477-7827-1-123 Lebovic DI, Mueller MD, Taylor RN (2001) Immunobiology of endometriosis. Fertil Steril 75(1):1–10. https://doi.org/10.1016/s0015-0282(00)01630-7 Li B, Duan H, Wang S, Li Y (2021) Ferroptosis resistance mechanisms in endometriosis for diagnostic model establishment. Reprod Biomed Online 43(1):127–138. https://doi.org/10.1016/j.rbmo.2021.04.002 Liang D, Zhang Y, Chen L, Shu L, He Y, Ma H, Qiao M, Wang N (2022) The effect of ENEAS application in patients with endometriosis and its influence on the level of IL-8 and MCP-1. Cell Mol Biol (Noisy-le-grand) 67(4):334–339. https://doi.org/10.14715/cmb/2021.67.4.38 Liaw, A., & Wiener, M. C. (2007). Classification and Regression by randomForest. (Ed.),^(Eds.). Liu W, Wang X (2019) Prediction of functional microRNA targets by integrative modeling of microRNA binding and target expression data. Genome Biol 20(1):18. https://doi.org/10.1186/s13059-019-1629-z Martin FJ, Amode MR, Aneja A, Austine-Orimoloye O, Azov AG, Barnes I, Becker A, Bennett R, Berry A, Bhai J, Bhurji SK, Bignell A, Boddu S, Branco Lins PR, Brooks L, Ramaraju SB, Charkhchi M, Cockburn A, Da Rin Fiorretto L, Davidson C, Dodiya K, Donaldson S, El Houdaigui B, El Naboulsi T, Fatima R, Giron CG, Genez T, Ghattaoraya GS, Martinez JG, Guijarro C, Hardy M, Hollis Z, Hourlier T, Hunt T, Kay M, Kaykala V, Le T, Lemos D, Marques-Coelho D, Marugán JC, Merino GA, Mirabueno LP, Mushtaq A, Hossain SN, Ogeh DN, Sakthivel MP, Parker A, Perry M, Piližota I, Prosovetskaia I, Pérez-Silva JG, Salam AIA, Saraiva-Agostinho N, Schuilenburg H, Sheppard D, Sinha S, Sipos B, Stark W, Steed E, Sukumaran R, Sumathipala D, Suner MM, Surapaneni L, Sutinen K, Szpak M, Tricomi FF, Urbina-Gómez D, Veidenberg A, Walsh TA, Walts B, Wass E, Willhoft N, Allen J, Alvarez-Jarreta J, Chakiachvili M, Flint B, Giorgetti S, Haggerty L, Ilsley GR, Loveland JE, Moore B, Mudge JM, Tate J, Thybert D, Trevanion SJ, Winterbottom A, Frankish A, Hunt SE, Ruffier M, Cunningham F, Dyer S, Finn RD, Howe KL, Harrison PW, Yates AD, Flicek P (2023) Ensembl 2023. Nucleic Acids Res 51(D1):D933–D941. https://doi.org/10.1093/nar/gkac958 McGeary SE, Lin KS, Shi CY, Pham TM, Bisaria N, Kelley GM, Bartel DP (2019) The biochemical basis of microRNA targeting efficacy. Science 366(6472):eaav1741. https://doi.org/10.1126/science.aav1741 Miao EA, Leaf IA, Treuting PM, Mao DP, Dors M, Sarkar A, Warren SE, Wewers MD, Aderem A (2010) Caspase-1-induced pyroptosis is an innate immune effector mechanism against intracellular bacteria. Nat Immunol 11(12):1136–1142. https://doi.org/10.1038/ni.1960 Miao EA, Rajan JV, Aderem A (2011) Caspase-1-induced pyroptotic cell death. Immunol Rev 243(1):206–214. https://doi.org/10.1111/j.1600-065X.2011.01044.x Miller JE, Monsanto SP, Ahn SH, Khalaj K, Fazleabas AT, Young SL, Lessey BA, Koti M, Tayade C (2017) Interleukin-33 modulates inflammation in endometriosis. Sci Rep 7(1):17903. https://doi.org/10.1038/s41598-017-18224-x Newman AM, Liu CL, Green MR, Gentles AJ, Feng W, Xu Y, Hoang CD, Diehn M, Alizadeh AA (2015) Robust enumeration of cell subsets from tissue expression profiles. Nat Methods 12(5):453–457. https://doi.org/10.1038/nmeth.3337 Ozkan S, Arici A (2009) Advances in treatment options of endometriosis. Gynecol Obstet Invest 67(2):81–91. https://doi.org/10.1159/000163071 Rigatti, S. (2017). Random Forest. Journal of insurance medicine New York, N.Y), 47(1), 31–39 doi https://doi.org/10.17849/insm-47-01-31-39.1 Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, Smyth GK (2015) limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res 43(7):e47. https://doi.org/10.1093/nar/gkv007 Robin X, Turck N, Hainard A, Tiberti N, Lisacek F, Sanchez J-C, Müller M (2011) pROC: an open-source package for R and S+ to analyze and compare ROC curves. BMC Bioinform. https://doi.org/10.1186/1471-2105-12-77 Rocha AL, Reis FM, Petraglia F (2012) New trends for the medical treatment of endometriosis. Expert Opin Investig Drugs 21(7):905–919. https://doi.org/10.1517/13543784.2012.683783 Rühl S, Shkarina K, Demarco B, Heilig R, Santos JC, Broz P (2018) ESCRT-dependent membrane repair negatively regulates pyroptosis downstream of GSDMD activation. Science 362(6417):956–960. https://doi.org/10.1126/science.aar7607 Saunders PTK, Horne AW (2021) Endometriosis: etiology, pathobiology, and therapeutic prospects. Cell 184(11):2807–2824. https://doi.org/10.1016/j.cell.2021.04.041 Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13(11):2498–504. https://doi.org/10.1101/gr.1239303 Stelzer G, Rosen N, Plaschkes I, Zimmerman S, Twik M, Fishilevich S, Stein TI, Nudel R, Lieder I, Mazor Y, Kaplan S, Dahary D, Warshawsky D, Guan-Golan Y, Kohn A, Rappaport N, Safran M, Lancet D (2016) The geneCards suite: from gene data mining to disease genome sequence analyses. Curr Protoc Bioinformatics 54:1.30.1–1.30.33. https://doi.org/10.1002/cpbi.5 Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA 102(43):15545–50. https://doi.org/10.1073/pnas.0506580102 Vallvé-Juanico J, Houshdaran S, Giudice LC (2019) The endometrial immune environment of women with endometriosis. Hum Reprod Update 25(5):564–591. https://doi.org/10.1093/humupd/dmz018 Wang Y, Nicholes K, Shih IM (2020) The origin and pathogenesis of endometriosis. Annu Rev Pathol 15:71–95. https://doi.org/10.1146/annurev-pathmechdis-012419-032654 Wu T, Hu E, Xu S, Chen M, Guo P, Dai Z, Feng T, Zhou L, Tang W, Zhan L, Fu X, Liu S, Bo X, Yu G (2021) clusterProfiler 4.0: a universal enrichment tool for interpreting omics data. Innovation Camb 2(3):100141. https://doi.org/10.1016/j.xinn.2021.100141 Xing M, Li J (2022) Diagnostic and prognostic values of pyroptosis-related genes for the hepatocellular carcinoma. BMC Bioinform 23(1):177. https://doi.org/10.1186/s12859-022-04726-7 Yang Y, Wang M, Zhang YY, Zhao SZ, Gu S (2022) The endosomal sorting complex required for transport repairs the membrane to delay cell death. Front Oncol 12:1007446. https://doi.org/10.3389/fonc.2022.1007446 Yin W, Shen Y, Zhang L, Wang J, Yang L, Liu Q (2022) Effect of miR-223–3p on cell pyroptosis in myelodysplastic syndrome and its mechanism via regulating the expression of NLRP3. Cell Mol Biol (Noisy-le-grand) 68(2):31–41. https://doi.org/10.14715/cmb/2022.68.2.5 Yu G, Wang LG, Han Y, He QY (2012) clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS 16(5):284–287. https://doi.org/10.1089/omi.2011.0118 Zhang J, Dong L, Zhang S, Wang L (2022) Analysis of the clinical efficacy of leuprolide acetate in the treatment of obese patients with endometriosis and its role on the expression of MIF gene. Cell Mol Biol (Noisy-le-grand) 67(4):282–288. https://doi.org/10.14715/cmb/2021.67.4.31

The authors thank the GEO database for providing valuable datasets. Funding No funding was received for conducting this study. Author information Authors and Affiliations Contributions ZS and WS designed the study and wrote the original manuscript. CL and PD searched relevant literature and prepared figures. KL and YL conducted data acquisition and analysis. YW helped revise the manuscript and supervised the study. All authors approved the manuscript. Corresponding author Ethics declarations Competing interests The authors declare no competing interests. Additional information Publisher's Note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Rights and permissions Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law. About this article Cite this article Su, Z., Su, W., Li, C. et al. Identification and Immune Characteristics Study of Pyroptosis‑Related Genes in Endometriosis. Biochem Genet 62, 2810–2829 (2024). https://doi.org/10.1007/s10528-023-10583-7 Received: Accepted: Published: Version of record: Issue date: DOI: https://doi.org/10.1007/s10528-023-10583-7