Construction of a Necroptosis-Related lncRNA Signature for Predicting Prognosis and Immune Response in Kidney Renal Clear Cell Carcinoma

Yue Zhang; Tongtian Zhuang; Zhenlong Xin; Changjian Sun; Deyang Li; Nan Ma; Xiaoyan Wang; Xuning Wang

doi:10.3390/cells12010066

journal article Open Access Dec 23, 2022

Construction of a Necroptosis-Related lncRNA Signature for Predicting Prognosis and Immune Response in Kidney Renal Clear Cell Carcinoma

Yue Zhang

Tongtian Zhuang Zhenlong Xin

Changjian Sun Deyang Li

Nan Ma

Xiaoyan Wang

Xuning Wang

Cells Vol. 12 No. 1 pp. 66 · MDPI AG

View at Publisher Save 10.3390/cells12010066

Abstract

Necroptosis is a new type of programmed cell death and involves the occurrence and development of various cancers. Moreover, the aberrantly expressed lncRNA can also affect tumorigenesis, migration, and invasion. However, there are few types of research on the necroptosis-related lncRNA (NRL), especially in kidney renal clear cell carcinoma (KIRC). In this study, we analyzed the sequencing data obtained from the TGCA-KIRC dataset, then applied the LASSO and COX analysis to identify 6 NRLs (AC124854.1, AL117336.1, DLGAP1-AS2, EPB41L4A-DT, HOXA-AS2, and LINC02100) to construct a risk model. Patients suffering from KIRC were divided into high- and low-risk groups according to the risk score, and the patients in the low-risk group had a longer OS. This signature can be used as an indicator to predict the prognosis of KIRC independent of other clinicopathological features. In addition, the gene set enrichment analysis showed that some tumor and immune-associated pathways were more enriched in a high-risk group. We also found significant differences between the high and low-risk groups in the infiltrating immune cells, immune functions, and expression of immune checkpoint molecules. Finally, we use the “pRRophetic” package to complete the drug sensitivity prediction, and the risk score could reflect patients’ response to 8 small molecule compounds. In general, NRLs divided KIRC into two subtypes with different risk scores. Furthermore, this signature based on the 6 NRLs could provide a promising method to predict the prognosis and immune response of KIRC patients. To some extent, our findings helped give a reference for further research between NRLs and KIRC and find more effective therapeutic drugs for KIRC.

Topics

No keywords indexed for this article. Browse by subject →

References

52

[1]

Global Cancer Statistics 2020: GLOBOCAN Estimates of Incidence and Mortality Worldwide for 36 Cancers in 185 Countries

Hyuna Sung, Jacques Ferlay, Rebecca L. Siegel et al.

CA: A Cancer Journal for Clinicians 2021 10.3322/caac.21660

[2]

Cancer statistics, 2022

Rebecca L. Siegel, Kimberly D. Miller, Hannah E. Fuchs et al.

CA: A Cancer Journal for Clinicians 2022 10.3322/caac.21708

[3]

Renal cell carcinoma

James J. Hsieh, Mark P. Purdue, Sabina Signoretti et al.

Nature Reviews Disease Primers 2017 10.1038/nrdp.2017.9

[4]

Makhov "Resistance to Systemic Therapies in Clear Cell Renal Cell Carcinoma: Mechanisms and Management Strategies" Mol. Cancer Ther. (2018) 10.1158/1535-7163.mct-17-1299

[5]

Kidney cancer: The next decade

Samra Turajlic, Charles Swanton, Chris Boshoff

Journal of Experimental Medicine 2018 10.1084/jem.20181617

[6]

Cohen "Renal-cell carcinoma" New Engl. J. Med. (2005) 10.1056/nejmra043172

[7]

Snyder "Intratumoral activation of the necroptotic pathway components RIPK1 and RIPK3 potentiates antitumor immunity" Sci. Immunol. (2019) 10.1126/sciimmunol.aaw2004

[8]

The role of necroptosis in cancer biology and therapy

Yitao Gong, Zhiyao Fan, Guopei Luo et al.

Molecular Cancer 2019 10.1186/s12943-019-1029-8

[9]

Wang "Up-Regulation of RIP3 Alleviates Prostate Cancer Progression by Activation of RIP3/MLKL Signaling Pathway and Induction of Necroptosis" Front. Oncol. (2020) 10.3389/fonc.2020.01720

[10]

Zhao "RIPK3 Suppresses the Progression of Spontaneous Intestinal Tumorigenesis" Front. Oncol. (2021) 10.3389/fonc.2021.664927

[11]

Park "RIPK3 activation induces TRIM28 derepression in cancer cells and enhances the anti-tumor microenvironment" Mol. Cancer (2021) 10.1186/s12943-021-01399-3

[12]

Zhu "Complex roles of necroptosis in cancer" J. Zhejiang Univ. Sci. B (2019) 10.1631/jzus.b1900160

[13]

Najafov "Necroptosis and Cancer" Trends Cancer (2017) 10.1016/j.trecan.2017.03.002

[14]

Stoll "Pro-necrotic molecules impact local immunosurveillance in human breast cancer" Oncoimmunology (2017) 10.1080/2162402x.2017.1299302

[15]

Seehawer "Necroptosis microenvironment directs lineage commitment in liver cancer" Nature (2018) 10.1038/s41586-018-0519-y

[16]

Liu "RIP3 promotes colitis-associated colorectal cancer by controlling tumor cell proliferation and CXCL1-induced immune suppression" Theranostics (2019) 10.7150/thno.32126

[17]

Ando, Y., Ohuchida, K., Otsubo, Y., Kibe, S., Takesue, S., Abe, T., Iwamoto, C., Shindo, K., Moriyama, T., and Nakata, K. (2020). Necroptosis in pancreatic cancer promotes cancer cell migration and invasion by release of CXCL5. PLoS ONE, 15. 10.1371/journal.pone.0228015

[18]

LNCcation: lncRNA localization and function

Mary Catherine Bridges, Amanda C. Daulagala, Antonis Kourtidis

The Journal of cell biology 2021 10.1083/jcb.202009045

[19]

Cao "lncRNA-RMRP promotes proliferation, migration and invasion of bladder cancer via miR-206" Eur. Rev. Med. Pharmacol. Sci. (2019)

[20]

Kong "LncRNA-CDC6 promotes breast cancer progression and function as ceRNA to target CDC6 by sponging microRNA-215" J. Cell. Physiol. (2019) 10.1002/jcp.27587

[21]

Zhen "LncRNA DANCR Promotes Lung Cancer by Sequestering miR-216a" Cancer Control J. Moffitt Cancer Cent. (2018) 10.1177/1073274818769849

[22]

Liu "LINC00973 is involved in cancer immune suppression through positive regulation of Siglec-15 in clear-cell renal cell carcinoma" Cancer Sci. (2020) 10.1111/cas.14611

[23]

Clinical drug response can be predicted using baseline gene expression levels and in vitro drug sensitivity in cell lines

Paul Geeleher, Nancy J Cox, R Stephanie Huang

Genome Biology 2014 10.1186/gb-2014-15-3-r47

[24]

Necroptosis and tumor progression

Jiong Yan, Peixing Wan, Swati Choksi et al.

Trends in Cancer 2022 10.1016/j.trecan.2021.09.003

[25]

Long Noncoding RNA and Cancer: A New Paradigm

Arunoday Bhan, Milad Soleimani, Subhrangsu S. Mandal

Cancer Research 2017 10.1158/0008-5472.can-16-2634

[26]

LncRNA-mediated regulation of cell signaling in cancer

W-X Peng, P Koirala, Y-Y Mo

Oncogene 2017 10.1038/onc.2017.184

[27]

Luo "A Necroptosis-Related lncRNA-Based Signature to Predict Prognosis and Probe Molecular Characteristics of Stomach Adenocarcinoma" Front. Genet. (2022) 10.3389/fgene.2022.833928

[28]

Chen "Necroptosis-related lncRNA to establish novel prognostic signature and predict the immunotherapy response in breast cancer" J. Clin. Lab. Anal. (2022) 10.1002/jcla.24302

[29]

Hu "Identification and Verification of Necroptosis-Related Gene Signature and Associated Regulatory Axis in Breast Cancer" Front. Genet. (2022) 10.3389/fgene.2022.842218

[30]

Lu "A Novel Necroptosis-Related lncRNA Signature Predicts the Prognosis of Lung Adenocarcinoma" Front. Genet. (2022) 10.3389/fgene.2022.862741

[31]

Huang "Construction of a necroptosis-related lncRNA signature to predict the prognosis and immune microenvironment of head and neck squamous cell carcinoma" J. Clin. Lab. Anal. (2022) 10.1002/jcla.24480

[32]

Liu "Comprehensive Analysis of Necroptosis-Related Long Noncoding RNA Immune Infiltration and Prediction of Prognosis in Patients with Colon Cancer" Front. Mol. Biosci. (2022) 10.3389/fmolb.2022.811269

[33]

Frank "Pyroptosis versus necroptosis: Similarities, differences, and crosstalk" Cell Death Differ. (2019) 10.1038/s41418-018-0212-6

[34]

Vince "The intersection of cell death and inflammasome activation" Cell. Mol. Life Sci. (2016) 10.1007/s00018-016-2205-2

[35]

Saxena "NOD-Like Receptors: Master Regulators of Inflammation and Cancer" Front. Immunol. (2014) 10.3389/fimmu.2014.00327

[36]

Liu "NOD-like receptor signaling in inflammation-associated cancers: From functions to targeted therapies" Phytomedicine (2019) 10.1016/j.phymed.2019.152925

[37]

Liu "LncRNA SNHG16 promotes migration and invasion through suppression of CDKN1A in clear cell renal cell carcinoma" Eur. Rev. Med. Pharmacol. Sci. (2020)

[38]

Wang "LncRNA MAGI2-AS3 inhibits tumor progression and angiogenesis by regulating ACY1 via interacting with transcription factor HEY1 in clear cell renal cell carcinoma" Cancer Gene Ther. (2021) 10.1038/s41417-021-00339-z

[39]

Toll-like Receptor 3-mediated Necrosis via TRIF, RIP3, and MLKL

William J. Kaiser, Haripriya Sridharan, Chunzi Huang et al.

Journal of Biological Chemistry 2013 10.1074/jbc.m113.462341

[40]

Lou "EZH2 Regulates Intestinal Inflammation and Necroptosis Through the JNK Signaling Pathway in Intestinal Epithelial Cells" Dig. Dis. Sci. (2019) 10.1007/s10620-019-05705-4

[41]

McComb "Type-I interferon signaling through ISGF3 complex is required for sustained Rip3 activation and necroptosis in macrophages" Proc. Natl. Acad. Sci. USA (2014) 10.1073/pnas.1407068111

[42]

Bakhoum "Chromosomal instability drives metastasis through a cytosolic DNA response" Nature (2018) 10.1038/nature25432

[43]

Yoo "Cytokine expression and cancer detection" Med. Sci. Monit. Int. Med. J. Exp. Clin. Res. (2009)

[44]

Yao "Cytokine Regulation of Metastasis and Tumorigenicity" Adv Cancer Res. (2016) 10.1016/bs.acr.2016.05.005

[45]

Domingues "Tumor infiltrating immune cells in gliomas and meningiomas" Brain Behav. Immun. (2016) 10.1016/j.bbi.2015.07.019

[46]

Interplay of somatic alterations and immune infiltration modulates response to PD-1 blockade in advanced clear cell renal cell carcinoma

David A. Braun, Yue Hou, Ziad Bakouny et al.

Nature Medicine 2020 10.1038/s41591-020-0839-y

[47]

Su "Immune classification of clear cell renal cell carcinoma" Sci. Rep. (2021) 10.1038/s41598-021-83767-z

[48]

Cicalese "Editorial: Follicular Helper T Cells in Immunity and Autoimmunity" Front Immunol. (2020) 10.3389/fimmu.2020.01042

[49]

Zhao "TREM1 fosters an immunosuppressive tumor microenvironment in papillary thyroid cancer" Endocr. Relat. Cancer (2022) 10.1530/erc-21-0297

[50]

Cao "Co-stimulatory and co-inhibitory pathways in cancer immunotherapy" Adv. Cancer Res. (2019) 10.1016/bs.acr.2019.03.003

Showing 50 of 52 references

Metrics

6

Citations

52

References

Details

Published: Dec 23, 2022
Vol/Issue: 12(1)
Pages: 66
License: View

Authors

Y

Yue Zhang

Department of Clinical Laboratory, The Air Force Hospital of Northern Theater PLA, Shenyang 110042, China

T

Tongtian Zhuang

Department of Dermatology, The Air Force Hospital of Northern Theater PLA, Shenyang 110042, China

Z

Zhenlong Xin

Department of Disease Control and Prevention, The Air Force Hospital of Northern Theater PLA, Shenyang 110042, China

C

Changjian Sun

Department of Clinical Laboratory, The Air Force Hospital of Northern Theater PLA, Shenyang 110042, China

D

Deyang Li

Department of Clinical Laboratory, The Air Force Hospital of Northern Theater PLA, Shenyang 110042, China

N

Nan Ma

Department of Clinical Laboratory, The Air Force Hospital of Northern Theater PLA, Shenyang 110042, China

X

Xiaoyan Wang

Department of Clinical Laboratory, The Air Force Hospital of Northern Theater PLA, Shenyang 110042, China

X

Xuning Wang

Department of General Surgery, The Air Force Hospital of Northern Theater PLA, Shenyang 110042, China

Cite This Article

Yue Zhang, Tongtian Zhuang, Zhenlong Xin, et al. (2022). Construction of a Necroptosis-Related lncRNA Signature for Predicting Prognosis and Immune Response in Kidney Renal Clear Cell Carcinoma. Cells, 12(1), 66. https://doi.org/10.3390/cells12010066

Construction of a Necroptosis-Related lncRNA Signature for Predicting Prognosis and Immune Response in Kidney Renal Clear Cell Carcinoma

You May Also Like