The Identification of Zinc-Finger Protein 433 as a Possible Prognostic Biomarker for Clear-Cell Renal Cell Carcinoma
Abstract
:1. Introduction
2. Materials and Methods
2.1. Gene and Protein Expression Analysis
2.1.1. UALCAN Analysis
2.1.2. TNM Plotter
2.1.3. TIMER2.0
2.1.4. Human Protein Atlas
2.2. Overall Survival Analysis
2.3. Methylation Analysis
2.4. Gene Ontology and Pathway Analysis
2.5. Statistical Analysis
3. Results
3.1. ZNF433 mRNA and Protein Expression in Normal and Clear-Cell Renal Cell Carcinoma
3.2. ZNF433 mRNA Expression in Association with the Clinicopathological Features of Clear-Cell Renal Cell Carcinoma
3.3. Overall Survival of Patients with Clear-Cell and Papillary Renal Cell Carcinomas as a Function of ZNF433 Expression
3.4. Effect of CpG Methylation on ZNF433 Gene Expression
3.5. Effect of BAP1, KDM5C, MTOR, PBRM1, SETD2, and VHL Mutations on ZNF433 mRNA Expression
3.6. ZNF433 Pathway Enrichment, Target Gene Expression, and Target Gene Ontology
3.7. Pan-Cancer Analysis of ZNF433 Target Gene Expression
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Clinicopathological Features | N | Statistics |
---|---|---|
Gender | N.S. | |
Male | 385 | |
Female | 188 | |
Histological Grade | p < 0.001 | |
Normal | 72 | |
1 | 14 | |
2 | 229 | |
3 | 206 | |
4 | 76 | |
Pathological Stage | p < 0.001 | |
Normal | 72 | |
1 | 267 | |
2 | 57 | |
3 | 123 | |
4 | 84 | |
Metastasis | p < 0.001 | |
Normal | 72 | |
N0 | 240 | |
N1 | 16 | |
Age | N.S. | |
21–40 years | 26 | |
41–60 years | 238 | |
61–80 years | 246 | |
81+ years | 23 |
Clinicopathological Feature | Univariate Analysis HR (95% CI) p-Value | Multivariate Analysis HR (95% CI) p-Value |
---|---|---|
ZNF433 | 0.6227 (0.4593–0.8440) | 0.7390 (0.6987–1.3065) |
p = 0.0023 | p = 0.0597 | |
Gender | 0.9508 (0.7003–1.2910) | 0.9711 (0.7094–1.3292) |
p = 0.7466 | p = 0.8547 | |
Age | 1.7589 (1.2979–2.3835) | 1.5889 (1.1612–2.1742) |
p = 0.0003 | p = 0.0038 | |
Stage | 3.8179 (2.7869–5.2303) | 3.3766 (2.4441–4.6649) |
p < 0.0001 | p < 0.001 | |
Grade | 1.5172 (1.1152–2.0639) | 1.2429 (0.9088–1.6697) |
p = 0.0079 | p = 0.1734 |
Tumor | Normal | Change | Significance (p-Value) |
---|---|---|---|
BLCA.Tumor (n = 408) | BLCA.Normal (n = 19) | Upregulation | 0.016096887 |
BRCA.Tumor (n = 1093) | BRCA.Normal (n = 112) | Downregulation | 0.446186328 |
CESC.Tumor (n = 304) | CESC.Normal (n = 3) | Downregulation | 0.210693518 |
CHOL.Tumor (n = 36) | CHOL.Normal (n = 9) | Upregulation | 0.005768157 |
COAD.Tumor (n = 457) | COAD.Normal (n = 41) | Upregulation | 0.792680029 |
ESCA.Tumor (n = 184) | ESCA.Normal (n = 11) | Downregulation | 0.164913994 |
GBM.Tumor (n = 153) | GBM.Normal (n = 5) | Upregulation | 0.001122476 |
HNSC.Tumor (n = 520) | HNSC.Normal (n = 44) | Downregulation | 6.12 × 10−8 |
KICH.Tumor (n = 66) | KICH.Normal (n = 25) | Downregulation | 8.04 × 10−5 |
KIRC.Tumor (n = 533) | KIRC.Normal (n = 72) | Downregulation | 1.13 × 10−23 |
KIRP.Tumor (n = 290) | KIRP.Normal (n = 32) | Downregulation | 2.86 × 10−9 |
LIHC.Tumor (n = 371) | LIHC.Normal (n = 50) | Upregulation | 7.93 × 10−11 |
LUAD.Tumor (n = 515) | LUAD.Normal (n = 59) | Downregulation | 0.039291777 |
LUSC.Tumor (n = 501) | LUSC.Normal (n = 51) | Downregulation | 1.16 × 10−5 |
PAAD.Tumor (n = 178) | PAAD.Normal (n = 4) | Downregulation | 0.112226334 |
PCPG.Tumor (n = 179) | PCPG.Normal (n = 3) | Upregulation | 0.032947137 |
PRAD.Tumor (n = 497) | PRAD.Normal (n = 52) | Upregulation | 0.028391067 |
READ.Tumor (n = 166) | READ.Normal (n = 10) | Downregulation | 0.101167394 |
SKCM.Tumor (n = 103) | SKCM.Metast (n = 368) | Downregulation | 0.826588455 |
STAD.Tumor (n = 415) | STAD.Normal (n = 35) | Downregulation | 0.433244729 |
THCA.Tumor (n = 501) | THCA.Normal (n = 59) | Downregulation | 1.98 × 10−11 |
UCEC.Tumor (n = 545) | UCEC.Normal (n = 35) | Upregulation | 0.015728415 |
Gene Symbol | Official Name |
---|---|
ACER3 | alkaline ceramidase 3 |
ALDOA | aldolase, fructose-bisphosphate A |
ANGPTL6 | angiopoietin-like 6 |
AP1S3 | adaptor related protein complex 1 subunit sigma 3 |
ASS1P5 | argininosuccinate synthetase 1 pseudogene 5 |
AURKB | aurora kinase B |
BORCS6 | BLOC-1 related complex subunit 6 |
C6orf141 | chromosome 6 open reading frame 141 |
CCDC65 | coiled-coil domain containing 65 |
COPS3 | COP9 signalosome subunit 3 |
COQ10A | coenzyme Q10A |
CROCCP3 | CROCC pseudogene 3 |
CWC25 | CWC25 spliceosome associated protein homolog |
CYP1B1-AS1 | CYP1B1 antisense RNA 1 |
DAGLB | diacylglycerol lipase beta |
DHTKD1 | dehydrogenase E1 and transketolase domain containing 1 |
EXOSC2 | exosome component 2 |
FABP5P3 | fatty-acid-binding protein 5 pseudogene 3 |
FCHO2 | FCH and mu domain-containing endocytic adaptor 2 |
FES | FES proto-oncogene, tyrosine kinase |
FMN2 | formin 2 |
FRMD7 | FERM domain containing 7 |
GALNTL5 | polypeptide N-acetylgalactosaminyltransferase like 5 |
GIT2 | GIT ArfGAP 2 |
GLG1 | Golgi glycoprotein 1 |
GPR1-AS | GPR1 antisense RNA |
GXYLT2 | glucoside xylosyltransferase 2 |
HAPLN2 | hyaluronan and proteoglycan link protein 2 |
HEBP2 | heme binding protein 2 |
KAT8 | lysine acetyltransferase 8 |
LINC01235 | long intergenic non-protein coding RNA 1235 |
LINC01641 | long intergenic non-protein coding RNA 1641 |
LUZP1 | leucine zipper protein 1 |
MED21 | mediator complex subunit 21 |
MTFMT | mitochondrial methionyl-tRNA formyl transferase |
MTND1P14 | MT-ND1 pseudogene 14 |
MTO1 | mitochondrial tRNA translation optimization 1 |
NLE1 | notchless homolog 1 |
NOL6 | nucleolar protein 6 |
NUCB1-AS1 | NUCB1 antisense RNA 1 |
OR1X5P | olfactory receptor family 1 subfamily X member 5 pseudogene |
QSER1 | glutamine and serine rich 1 |
RN7SL93P | RNA, 7SL, cytoplasmic 93, pseudogene |
RND1 | Rho family GTPase 1 |
RNU6-1003P | RNA, U6 small nuclear 1003, pseudogene |
RNU6-166P | RNA, U6 small nuclear 166, pseudogene |
RORA | RAR related orphan receptor A |
RPL32P27 | ribosomal protein L32 pseudogene 27 |
RPL36 | ribosomal protein L36 |
RRN3P1 | RRN3 pseudogene 1 |
SDC4 | syndecan 4 |
SH2B3 | SH2B adaptor protein 3 |
SLC6A1 | solute carrier family 6-member 1 |
SNHG30 | small nucleolar RNA host gene 30 |
SPATS2L | spermatogenesis associated serine rich 2 like |
STX4 | syntaxin 4 |
SYCE2 | synaptonemal complex central element protein 2 |
TMEM98 | transmembrane protein 98 |
TNFRSF10B | TNF receptor superfamily member 10b |
TNFRSF12A | TNF receptor superfamily member 12A |
TRAV15 | T cell receptor alpha variable 15 (pseudogene) |
TRIM15 | tripartite motif containing 15 |
TTC1 | tetratricopeptide repeat domain 1 |
TTLL13P | tubulin tyrosine ligase like 13, pseudogene |
WNT8A | Wnt family member 8A |
ZNF675 | zinc-finger protein 675 |
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Heyliger, S.O.; Soliman, K.F.A.; Saulsbury, M.D.; Reams, R.R. The Identification of Zinc-Finger Protein 433 as a Possible Prognostic Biomarker for Clear-Cell Renal Cell Carcinoma. Biomolecules 2021, 11, 1193. https://doi.org/10.3390/biom11081193
Heyliger SO, Soliman KFA, Saulsbury MD, Reams RR. The Identification of Zinc-Finger Protein 433 as a Possible Prognostic Biomarker for Clear-Cell Renal Cell Carcinoma. Biomolecules. 2021; 11(8):1193. https://doi.org/10.3390/biom11081193
Chicago/Turabian StyleHeyliger, Simone O., Karam F. A. Soliman, Marilyn D. Saulsbury, and Romonia Renee Reams. 2021. "The Identification of Zinc-Finger Protein 433 as a Possible Prognostic Biomarker for Clear-Cell Renal Cell Carcinoma" Biomolecules 11, no. 8: 1193. https://doi.org/10.3390/biom11081193
APA StyleHeyliger, S. O., Soliman, K. F. A., Saulsbury, M. D., & Reams, R. R. (2021). The Identification of Zinc-Finger Protein 433 as a Possible Prognostic Biomarker for Clear-Cell Renal Cell Carcinoma. Biomolecules, 11(8), 1193. https://doi.org/10.3390/biom11081193