A Hiplot-based web service for cold atmospheric plasma high-throughput data integration and analysis on breast cancer

Abstract

Incremental evidence on the effect of cold atmospheric plasma (CAP) in specifically killing transformed cells and advances in sequencing technologies at multiple omics have led to the demand of in-depth exploration on the mechanisms of action driving the potency of CAP against cancer cells at the molecular level. However, high-throughput data detailing the effect of CAP on cancer cells is lacking, let alone the corresponding database and analytical tool. Here, we sequenced the whole transcriptome, proteome, phosphorylome, acetylome, and lactylome of transformed cells in response to CAP using breast cancer cells as the disease model; and advanced our previously developed Hiplot platform by establishing a focus-driven tumor-specific module, namely CAP medicine in breast cancer (CAPmed-BC) (https://capbc.hiplot.com.cn). CAPmed-BC is the first multi-omics data resource in plasma medicine for analyzing the treatment response of breast cancer cells to CAP. It can analyze each type of omics data regarding differentially expressed biomarkers, expression landscape, gene ontology analysis, pathway interpretation, gene set enrichment analysis, and protein-protein interaction network. It can also interrogate the dynamic fluctuation, functional activity, and metabolic vulnerability of cancer cells in response to CAP by combinatorially analyzing omics at multiple carefully defined dimensions. We also built in a visualization module to support users for producing personalized graphs via adjusting parameters. We believe that CAPmed-BC will become a valuable resource for characterizing the outcome of CAP on breast cancers at the omics and molecular levels, and make considerable contributions to both plasma medicine and oncology.

Keywords

acetylome / breast cancer / cold atmospheric plasma / Hiplot / phosphorylome / proteome / whole transcriptome

References

[1] Von Woedtke, Thomas, Anke Schmidt, Sander Bekeschus, Kristian Wende, and Klaus-Dieter Weltmann. 2019. “Plasma Medicine: A Field of Applied Redox Biology.” In Vivo 33: 1011-1026. https://doi.org/10.21873/invivo.11570

[2] Takamatsu, Toshihiro, Kodai Uehara, Yota Sasaki, Hidekazu Miyahara, Yuriko Matsumura, Atsuo Iwasawa, Norihiko Ito, et al. 2014. “Investigation of Reactive Species Using Various Gas Plasmas.” RSC Advances 4: 39901-39905. https://doi.org/10.1039/c4ra05936k

[3] Keidar, Michael, Ryan Walk, Alexey Shashurin, P. Srinivasan, Anthony Sandler, S. Dasgupta, Rajani Ravi, Rafael E. Guerrero-Preston, and B. Trink. 2011. “Cold Plasma Selectivity and the Possibility of a Paradigm Shift in Cancer Therapy.” British Journal of Cancer 105: 1295-1301. https://doi.org/10.1038/bjc.2011.386

[4] Kaushik, Neha, Nizam Uddin, Geon Bo Sim, Young June Hong, Ku Youn Baik, Chung Hyeok Kim, Su Jae Lee, Nagendra Kumar Kaushik, and Eun Ha Choi. 2015. “Responses of Solid Tumor Cells in DMEM to Reactive Oxygen Species Generated by Non-Thermal Plasma and Chemically Induced ROS Systems.” Scientific Reports 5: 8587. https://doi.org/10.1038/srep08587

[5] Aggarwal, Vaishali, Hardeep Tuli, Ayşegül Varol, Falak Thakral, Mukerrem Yerer, Katrin Sak, Mehmet Varol, et al. 2019. “Role of Reactive Oxygen Species in Cancer Progression: Molecular Mechanisms and Recent Advancements.” Biomolecules 9: 735. https://doi.org/10.3390/biom9110735

[6] Park, Jeongyeon, Hyunyoung Lee, Hae June Lee, Gyoo Cheon Kim, Sung-Soo Kim, Sungbum Han, and Kiwon Song. 2019. “Non-Thermal Atmospheric Pressure Plasma Is an Excellent Tool to Activate Proliferation in Various Mesoderm-Derived Human Adult Stem Cells.” Free Radical Biology and Medicine 134: 374-384. https://doi.org/10.1016/j.freeradbiomed.2019.01.032

[7] Aikman, Brech, Andreia de Almeida, Samuel M. Meier-Menches, and Angela Casini. 2018. “Aquaporins in Cancer Development: Opportunities for Bioinorganic Chemistry to Contribute Novel Chemical Probes and Therapeutic Agents.” Metallomics 10: 696-712. https://doi.org/10.1039/c8mt00072g

[8] Rivel, Timothée, Christophe Ramseyer, and Semen Yesylevskyy. 2019. “The Asymmetry of Plasma Membranes and Their Cholesterol Content Influence the Uptake of Cisplatin.” Scientific Reports 9: 5627. https://doi.org/10.1038/s41598-019-41903-w

[9] Van der Paal, Jonas, Erik C. Neyts, Christof C. W. Verlackt, and Annemie Bogaerts. 2016. “Effect of Lipid Peroxidation on Membrane Permeability of Cancer and Normal Cells Subjected to Oxidative Stress.” Chemical Science 7: 489-498. https://doi.org/10.1039/c5sc02311d

[10] Estarabadi, Hanieh, Seyed Alireza Atyabi, Sajjad Tavakkoli, Zahra Noormohammadi, Mohamad Reza Gholami, Ali Ghiaseddin, and Shiva Irani. 2021. “Cold Atmospheric Plasma Induced Genotoxicity and Cytotoxicity in Esophageal Cancer Cells.” Molecular Biology Reports 48: 1323-1333. https://doi.org/10.1007/s11033-021-06178-3

[11] Ha, Ji-Hui, and Young-Jin Kim. 2021. “Photodynamic and Cold Atmospheric Plasma Combination Therapy Using Polymeric Nanoparticles for the Synergistic Treatment of Cervical Cancer.” International Journal of Molecular Sciences 22: 1172. https://doi.org/10.3390/ijms22031172

[12] di Giacomo, Viviana, Marwa Balaha, Morena Pinti, Maria Carmela Di Marcantonio, Ilaria Cela, Tirtha Raj Acharya, Nagendra Kumar Kaushik, et al. 2024. “Cold Atmospheric Plasma Activated Media Selectively Affects Human Head and Neck Cancer Cell Lines.” Oral Diseases 31: 401-416. https://doi.org/10.1111/odi.15120

[13] Soulat, Abolfazl, Taghi Mohsenpour, Leila Roshangar, Seyyed Yaghoub Moaddab, and Fatemeh Soulat. 2025. “Innovative Therapeutic Approach Targeting Colon Cancer Stem Cells: Transitional Cold Atmospheric Plasma.” ACS Omega 10: 12109-12121. https://doi.org/10.1021/acsomega.4c10378

[14] Liu, Jinlin, Yang Li, Ruonan Ma, Youming Chen, Jinyang Wang, Lindong Zhang, Baojin Wang, et al. 2025. “Cold Atmospheric Plasma Drives USP49/HDAC3 Axis Mediated Ferroptosis as a Novel Therapeutic Strategy in Endometrial Cancer via Reinforcing Lactylation Dependent p53 Expression.” Journal of Translational Medicine 23: 442. https://doi.org/10.1186/s12967-025-06449-8

[15] Sun, Tao, Changqing Liu, Ling Kong, Jingjing Zha, and Guohua Ni. 2024. “Cold Plasma Irradiation Inhibits Skin Cancer via Ferroptosis.” Biomedical Physics & Engineering Express 10: 065036. https://doi.org/10.1088/2057-1976/ad8200

[16] He, Yuanyuan, Fu Lu, Chenmin Jiang, Fanwu Gong, Zhengwei Wu, and Kostya Ostrikov. 2024. “Cold Atmospheric Plasma Stabilizes Mismatch Repair for Effective, Uniform Treatment of Diverse Colorectal Cancer Cell Types.” Scientific Reports 14: 15. https://doi.org/10.1038/s41598-024-54020-0

[17] Tabassum, Shazia, Muhammad Noman Khan, Nosheen Faiz, Almas, Bushra Yaseen, and Iftikhar Ahmad. 2024. “Correction: Cold Atmospheric Plasma-Activated Medium for Potential Ovarian Cancer Therapy.” Molecular Biology Reports 51(1), 065036. https://doi.org/10.1007/s11033-024-09841-7

[18] Yazdani, Zahra, Marzieh Sharifi Pasandi, Monireh Golpour, Mina Eslami, and Alireza Rafiei. 2024. “Effect of Cold Atmospheric Plasma on Changing of Biomolecular Structures Involved in Apoptosis Pathways of Melanoma Cancer.” Skin Research and Technology 30: 7. https://doi.org/10.1111/srt.13544

[19] Jung, Joon-Min, Hae-Kyeong Yoon, Su-Yeon Kim, Mi-Ra Yun, Gyeong-Hoon Kim, Woo-Jin Lee, Mi-Woo Lee, Sung-Eun Chang, and Chong-Hyun Won. 2023. “Anticancer Effect of Cold Atmospheric Plasma in Syngeneic Mouse Models of Melanoma and Colon Cancer.” Molecules 28: 4171. https://doi.org/10.3390/molecules28104171

[20] Privat-Maldonado, Angela, Ruben Verloy, Edgar Cardenas Delahoz, Abraham Lin, Steve Vanlanduit, Evelien Smits, and Annemie Bogaerts. 2022. “Cold Atmospheric Plasma Does Not Affect Stellate Cells Phenotype in Pancreatic Cancer Tissue in Ovo.” International Journal of Molecular Sciences 23: 1954. https://doi.org/10.3390/ijms23041954

[21] Wang, Yanhong, Xinyu Mang, Xuran Li, Zhengyu Cai, and Fei Tan. 2022. “Cold Atmospheric Plasma Induces Apoptosis in Human Colon and Lung Cancer Cells Through Modulating Mitochondrial Pathway.” Frontiers in Cell and Developmental Biology 10: 17. https://doi.org/10.3389/fcell.2022.915785

[22] Wang, Peiyu, Renwu Zhou, Rusen Zhou, Shuo Feng, Liqian Zhao, Wenshao Li, Jinyong Lin, et al. 2024. “Epidermal Growth Factor Potentiates EGFR(Y992/1173)-Mediated Therapeutic Response of Triple Negative Breast Cancer Cells to Cold Atmospheric Plasma-Activated Medium.” Redox Biology 69: 102976. https://doi.org/10.1016/j.redox.2023.102976

[23] Dai, Xiaofeng, Dongyan Cai, Peiyu Wang, Nan Nan, Lihui Yu, Zhifa Zhang, Renwu Zhou, et al. 2022. “Cold Atmospheric Plasmas Target Breast Cancer Stemness via Modulating AQP3-19Y Mediated AQP3-5K and FOXO1 K48-Ubiquitination.” International Journal of Biological Sciences 18: 3544-3561. https://doi.org/10.7150/ijbs.72296

[24] Wang, Peiyu, Renwu Zhou, Patrick Thomas, Liqian Zhao, Rusen Zhou, Susmita Mandal, Mohit Jolly, et al. 2021. “Epithelial-to-Mesenchymal Transition Enhances Cancer Cell Sensitivity to Cytotoxic Effects of Cold Atmospheric Plasmas in Breast and Bladder Cancer Systems.” Cancers 13: 2889. https://doi.org/10.3390/cancers13122889

[25] Xiang, Liangjian, Xiaoyu Xu, Shuo Zhang, Dongyan Cai, and Xiaofeng Dai. 2018. “Cold Atmospheric Plasma Conveys Selectivity on Triple Negative Breast Cancer Cells Both In Vitro and In Vivo.” Free Radical Biology and Medicine 124: 205-213. https://doi.org/10.1016/j.freeradbiomed.2018.06.001

[26] Shen, Li, Xinyu Lv, Yixin Li, and Xiaofeng Dai. 2025. “Spermidine Antagonizes the Anti-Cancer Effect of Cold Atmospheric Plasma and Induces Transit G0/G1 Cell Cycle Arrest of Triple Negative Breast Cancers.” Free Radical Biology and Medicine 229: 30-38. https://doi.org/10.1016/j.freeradbiomed.2025.01.024

[27] Bakhtiyari-Ramezani, Mahdiyeh, Meysam Nasiri, and Mansoureh Baniasadi. 2025. “Helium and Argon Cold Plasma Effects on the 4T1 Cancer Cells and a Triple Negative Mouse Model of Breast Cancer.” Scientific Reports 15: 10569. https://doi.org/10.1038/s41598-025-95065-z

[28] Almeida-Ferreira, Catarina, Francisca Rodrigues, Carlos Miguel Marto, Maria Filomena Botelho, and Mafalda Laranjo. 2025. “Cold Atmospheric Plasma for Breast Cancer Treatment: What Next?” Medical Gas Research 15: 110-111. https://doi.org/10.4103/mgr.MEDGASRES-D-24-00043

[29] Dezhpour, Ail, Hossein Ghafouri, Saed Jafari, and Maryam Nilkar. 2023. “Effects of Cold Atmospheric-Pressure Plasma in Combination With Doxorubicin Drug against Breast Cancer Cells In Vitro and In Vivo.” Free Radical Biology and Medicine 209: 202-210. https://doi.org/10.1016/j.freeradbiomed.2023.10.405

[30] Aggelopoulos, Christos A., Anna-Maria Christodoulou, Myrsini Tachliabouri, Stauros Meropoulis, Maria-Elpida Christopoulou, Theodoros T. Karalis, Athanasios Chatzopoulos, and Spyros S. Skandalis. 2022. “Cold Atmospheric Plasma Attenuates Breast Cancer Cell Growth Through Regulation of Cell Microenvironment Effectors.” Frontiers in Oncology 11: 16. https://doi.org/10.3389/fonc.2021.826865

[31] Almeida-Ferreira, Catarina, Rafael Silva-Teixeira, Ana Cristina Gonçalves, Carlos Miguel Marto, Ana Bela Sarmento-Ribeiro, Francisco Caramelo, Maria Filomena Botelho, and Mafalda Laranjo. 2022. “Cold Atmospheric Plasma Apoptotic and Oxidative Effects on MCF7 and HCC1806 Human Breast Cancer Cells.” International Journal of Molecular Sciences 23: 1698. https://doi.org/10.3390/ijms23031698

[32] Canady, Jerome. 2020. “Canady Helios Cold Plasma Scalpel Successfully Used by Chaim Sheba Medical Center Surgeons to Remove Inoperable Retroperitoneal cancer.” https://www.businesswire.com/news/home/20200129005667/en/.

[33] Metelmann, Hans-Robert, Christian Seebauer, Vandana Miller, Alexander Fridman, Georg Bauer, David B. Graves, Jean-Michel Pouvesle, et al. 2018. “Clinical Experience With Cold Plasma in the Treatment of Locally Advanced Head and Neck Cancer.” Clinical Plasma Medicine 9: 6-13. https://doi.org/10.1016/j.cpme.2017.09.001

[34] Canady, Jerome, Saravana R. K. Murthy, Taisen Zhuang, Steven Gitelis, Aviram Nissan, Lawan Ly, Olivia Z. Jones, et al. 2023. “The First Cold Atmospheric Plasma Phase I Clinical Trial for the Treatment of Advanced Solid Tumors: A Novel Treatment Arm for Cancer.” Cancers 15: 3688. https://doi.org/10.3390/cancers15143688

[35] Mark, Peplow. 2019. “Plasma Scalpel Takes on Cancer: A New Tool Enters a Pivotal Pilot Study.” Scientific American 321: 14. https://doi.org/10.1038/scientificamerican1219-14

[36] Dai, Xiaofeng, Zhifa Zhang, Jianying Zhang, and Kostya (Ken) Ostrikov. 2020. “Dosing: the Key to Precision Plasma Oncology.” Plasma Processes and Polymers 17: 15. https://doi.org/10.1002/ppap.201900178

[37] Yan, Dayun, Annie Talbot, Niki Nourmohammadi, Xiaoqian Cheng, Jerome Canady, Jonathan Sherman, and Michael Keidar. 2015. “Principles of Using Cold Atmospheric Plasma Stimulated Media for Cancer Treatment.” Scientific Reports 5: 18339. https://doi.org/10.1038/srep18339

[38] Siu, Alan, Olga Volotskova, Xiaoqian Cheng, Siri S. Khalsa, Ka Bian, Ferid Murad, Michael Keidar, and Jonathan H. Sherman. 2015. “Differential Effects of Cold Atmospheric Plasma in the Treatment of Malignant Glioma.” PLoS One 10: e0126313. https://doi.org/10.1371/journal.pone.0126313

[39] Wiegand, Cornelia, Sarah Fink, Oliver Beier, Kerstin Horn, Andreas Pfuch, Arnd Schimanski, Bernd Grünler, Uta-Christina Hipler, and Peter Elsner. 2016. “Dose- and Time-Dependent Cellular Effects of Cold Atmospheric Pressure Plasma Evaluated in 3D Skin Models.” Skin Pharmacology and Physiology 29: 257-265. https://doi.org/10.1159/000450889

[40] Dai, Xiaofeng, Xinyu Lv, Erik W. Thompson, and Kostya (Ken) Ostrikov. 2022. “Histone Lactylation: Epigenetic Mark of Glycolytic Switch.” Trends in Genetics 38: 124-127. https://doi.org/10.1016/j.tig.2021.09.009

[41] Li, Jianfeng, Benben Miao, Shixiang Wang, Wei Dong, Houshi Xu, Chenchen Si, Wei Wang, et al. 2022. “Hiplot: A Comprehensive and Easy-to-Use Web Service for Boosting Publication-Ready Biomedical Data Visualization.” Briefings in Bioinformatics 23: bbac261. https://doi.org/10.1093/bib/bbac261

[42] Liu, Zaoqu, Long Liu, Siyuan Weng, Hui Xu, Zhe Xing, Yuqing Ren, Xiaoyong Ge, et al. 2023. “BEST: A Web Application for Comprehensive Biomarker Exploration on Large-Scale Data in Solid Tumors.” Journal of Big Data 10: 165. https://doi.org/10.1186/s40537-023-00844-y

[43] Xu, Shuangbin, Erqiang Hu, Yantong Cai, Zijing Xie, Xiao Luo, Li Zhan, Wenli Tang, et al. 2024. “Using Clusterprofiler to Characterize Multiomics Data.” Nature Protocols 19: 3292-3320. https://doi.org/10.1038/s41596-024-01020-z

[44] Szklarczyk, Damian, Rebecca Kirsch, Mikaela Koutrouli, Katerina Nastou, Farrokh Mehryary, Radja Hachilif, Annika L. Gable, et al. 2023. “The STRING Database in 2023: Protein-Protein Association Networks and Functional Enrichment Analyses for Any Sequenced Genome of Interest.” Nucleic Acids Research 51: D638-D646. https://doi.org/10.1093/nar/gkac1000

[45] Kim, Daehwan, Geo Pertea, Cole Trapnell, Harold Pimentel, Ryan Kelley, and Steven L. Salzberg. 2013. “TopHat2: Accurate Alignment of Transcriptomes in the Presence of Insertions, Deletions and Gene Fusions.” Genome Biology 14: R36. https://doi.org/10.1186/gb-2013-14-4-r36

[46] Trapnell, Cole, Adam Roberts, Loyal Goff, Geo Pertea, Daehwan Kim, David R. Kelley, Harold Pimentel, et al. 2012. “Differential Gene and Transcript Expression Analysis of RNA-seq Experiments With TopHat and Cufflinks.” Nature Protocols 7: 562-578. https://doi.org/10.1038/nprot.2012.016

[47] Bateman, Alex, Maria-Jesus Martin, Sandra Orchard, Michele Magrane, Shadab Ahmad, Emanuele Alpi, Emily H. Bowler-Barnett, et al. 2023. “UniProt: The Universal Protein Knowledgebase in 2023.” Nucleic Acids Research 51: D523-D531. https://doi.org/10.1093/nar/gkac1052

RIGHTS & PERMISSIONS

2025 The Author(s). iMeta published by John Wiley & Sons Australia, Ltd on behalf of iMeta Science.