Zinc finger C3H1 domain-containing protein (ZFC3H1) evaluates the prognosis and treatment of prostate adenocarcinoma (PRAD): A study based on TCGA data

Figures & data

Table 1. TCGA datasets evaluated (data from TCGA datasets)

Types of cancer	TCGA dataset	No. of cancer tissues	No. of normal tissues
Adrenocortical carcinoma	TCGA-ACC	77	128
Bladder Urothelial Carcinoma	TCGA-BLCA	404	28
Breast invasive carcinoma	TCGA-BRCA	1085	291
Cervical squamous cell carcinoma and endocervical adenocarcinoma	TCGA-CESC	306	13
Cholangio carcinoma	TCGA-CHOL	36	9
Colon adenocarcinoma	TCGA-COAD	275	349
Lymphoid Neoplasm Diffuse Large B-cell Lymphoma	TCGA-DLBC	47	337
Esophageal carcinoma	TCGA-ESCA	182	286
Glioblastoma multiforme	TCGA-GBM	163	207
Head and Neck squamous cell carcinoma	TCGA-HNSC	519	44
Kidney Chromophobe	TCGA-KICH	66	53
Kidney renal clear cell carcinoma	TCGA-KIRC	523	100
Kidney renal papillary cell carcinoma	TCGA-KIRP	286	60
Acute Myeloid Leukemia	TCGA-LAML	173	70
Brain Lower Grade Glioma	TCGA-LGG	518	207
Liver hepatocellular carcinoma	TCGA-LIHC	369	160
Lung adenocarcinoma	TCGA-LUAD	483	347
Lung squamous cell carcinoma	TCGA-LUSC	486	338
Mesothelioma	TCGA-MESO	87	0
Ovarian serous cystadenocarcinoma	TCGA-OV	426	88
Pancreatic adenocarcinoma	TCGA-PAAD	179	171
Pheochromocytoma and Paraganglioma	TCGA-PCPG	182	3
Prostate adenocarcinoma	TCGA-PRAD	492	152
Rectum adenocarcinoma	TCGA-PEAD	92	318
Sarcoma	TCGA-SARC	262	2
Skin Cutaneous Melanoma	TCGA-SKCM	461	558
Stomach adenocarcinoma	TCGA-STAD	408	211
Testicular Germ Cell Tumors	TCGA-TGCT	137	165
Thyroid carcinoma	TCGA-THCA	512	337
Thymoma	TCGA-THYM	118	339
Uterine Corpus Endometrial Carcinoma	TCGA-UCEC	174	91
Uterine Carcinosarcoma	TCGA-UCS	57	78

Figure 1. The correlation between ZFC3H1 expression levels and overall survival of patients with PRAD. A, ZFC3H1 expression profile across all tumor samples and paired normal tissues. B, The expression level of ZFC3H1 in PRAD tissues and adjacent non-tumor tissues. C, The overall survival of human PRAD patients in relation with high or low expression levels of ZFC3H1. D. Immunohistochemical staining examined the expression of ZFC3H1 in 10 prostate cancer specimens and paracancerous.

Table 2. Prognosis adenocarcinoma-associated genes identified in The cancer genome atlas using four databases (data from TCGA datasets)

Database	Gene name
STRING	BMS1C1DCDC5LDCAF13DCP2DDX47DDX49DDX52DIS3DIS3LEMG1EXOSC1EXOSC10EXOSC2EXOSC3EXOSC4EXOSC5EXOSC6EXOSC7EXOSC8EXOSC9FBLHBS1LHEATR1HNRNPDIMP3IMP4KHSRPKRR1MPHOSPH6MPP6NOC4LNOL6NOP14NOP56PDCD11PNPT1PWP2RCC1RPL23ARPL27ARPL30RPL32RPL38RPL39RPL5RRP7ARRP9SKIV2LSKIV2L2SUPV3L1TBL3TDP2TEX10TTC37UTP11 LUTP14AUTP14BUTP15UTP18UTP3UTP6WDR3WDR36WDR43WDR46WDR61WDR75XRN1ZFC3H1ZFP36
BioGRID	ACTR1AADARANGEL2ANKHD1-EIF4EBP3ANKRD52APPBUB1BBUB3C1DC9ORF41CCDC57CCDC85BCEP70CSNK2A1CUL7DAP3DDB1DGKZDHX30DOCK8EIF2B1ERCC1ERCC4ESR2EXOSC1EXOSC5EXOSC7FBXO38FBXW8GANGOLGA2GPN3HIST1H4AHNRNPCL1HNRNPKHTTKHDRBS2KIAA1429LARP1LARP1BLENG8LGR4MAPK9MCATMIB1MKRN2MOV10MPHOSPH6MRPS11MRPS14MRPS23MRPS24MRPS25MRPS27MRPS31MRPS35MRPS5MRPS7MRPS9MTERF3MTUS2MYH13NINLNOL6PABPC4PAPOLGPCID2PPHLN1PPP1CCPPP2CAPPP2R2DPPP2R3APRMT6PTCD3RALYRBM27RBM45RNF4RPAP2SKIV2L2SLBPSMYD2SPAG5SRGNSRPK2SRRTSUFUTACC3TBC1D1TBCETHOC1TP53BP1TRIM27UNC119BUPF1VPRBPVPS26BVPS72YLPM1ZC3H18ZC3H3ZCCHC3ZDHHC17
IntAct	ACTR1AADARANGEL2ANKHD1APPBUB1BBUB3C1DCADPSCARNMT1CCDC57CCDC85BCDC5LCEP70COG6CSNK2A1CUL7DCAF1Ddb1DHX30DOCK8EIF2B1ERCC1ERCC4ESR1EXOSC1EXOSC7FBXW8FMR1GOLGA2GPN3H1-2H1-4H1-5HNRNPCL1HNRNPKHSF2BPHTTKHDRBS2LARP1LENG8MAPK9MKRN2MKRN3MOV10MPHOSPH6MRPS11MRPS14MRPS23MRPS24MRPS25MRPS31MRPS35MRPS5MRPS7MTERF3MTREXMTUS2MYBMYH13NINLNOL6NS1PABPC4PAPOLGPCID2PIBF1PPHLN1PPP2CAPPP2R2DPPP2R3APRMT6PTCD3q7ard3_yerpeRALYRBM27RBM45RPAP2RPL36SLBPSMYD2SPAG5SRGNSRRTSUFUTACC3TBC1D1TBCETHOC1TNIKTP53BP1TRIM27UNC119BUPF1VPS26BZC3H18ZC3H3ZDHHC17

Figure 2. Venn diagram of predicted target genes from three databases

Table 3. Pathway enrichment analysis of overlapping target genes (data from TCGA datasets)

Term	Description	Count	Frequency, %	Log10(P)	Log10(q)
GO:0006415	translational termination	11	13.75	−14.02	−9.86
GO:1,903,311	regulation of mRNA metabolic process	12	15	−9.73	−6.55
GO:0006397	mRNA processing	13	16.25	−8.34	−5.36
GO:0140014	mitotic nuclear division	9	11.25	−6.73	−3.87
ko03015	mRNA surveillance pathway	6	7.5	−6.62	−3.8
GO:0044770	cell cycle phase transition	12	15	−6.59	−3.78
GO:0031123	RNA 3ʹ-end processing	7	8.75	−6.56	−3.76
GO:0009896	positive regulation of catabolic process	10	12.5	−6.22	−3.49
GO:0090305	nucleic acid phosphodiester bond hydrolysis	8	10	−5.58	−3
GO:0050657	nucleic acid transport	6	7.5	−4.66	−2.19
GO:0042255	ribosome assembly	4	5	−4.47	−2.06
GO:0000226	microtubule cytoskeleton organization	9	11.25	−4.23	−1.88
GO:0045070	positive regulation of viral genome replication	3	3.75	−4.03	−1.72
GO:0043632	modification-dependent macromolecule catabolic process	9	11.25	−3.98	−1.68
GO:0044089	positive regulation of cellular component biogenesis	8	10	−3.89	−1.6
GO:0006914	autophagy	8	10	−3.81	−1.54
GO:0042769	DNA damage response, detection of DNA damage	3	3.75	−3.73	−1.5
GO:0031330	negative regulation of cellular catabolic process	5	6.25	−3.08	−0.99
GO:1,901,796	regulation of signal transduction by p53 class mediator	4	5	−2.78	−0.76
GO:0030099	myeloid cell differentiation	5	6.25	−2.15	−0.28
GO:0044839	Cell cycle G2/M phase transition	11	47.83	−15.46	−11.14
GO:0042752	Regulation of circadian rhythm	7	30.43	−10.97	−7.66
GO:0045786	Negative regulation of cell cycle	9	39.13	−8.47	−5.51
GO:0097193	Intrinsic apoptotic signaling pathway	6	26.09	−6.63	−3.91
GO:0031648	Protein destabilization	3	13.04	−4.84	−2.67

Figure 3. Protein-protein interaction network of overlapping target genes

Figure 4. The correlation between selected gene expression levels and overall survival of PRAD patients. A, The expression level of selected genes in PRAD tissues and adjacent non-tumor tissues. B, The overall survival of human patients with PRAD in relation to high or low expression levels of MPHOSPH6 and MRPS31

Figure 5. ZFC3H1 knockdown reduced PRAD cell invasive and migration capability. (a) Wound healing assay to determine the cell migration ability following transfection with the ZFC3H1 siRNA or negative siRNA. (b) Transwell assay showing the number of invaded cells following transfection with ZFC3H1 siRNA or negative siRNA. ***P < 0.001. (c) Western blotting showing the interference efficiency of ZFC3H1 siRNA

Availability of Data and Materials

The datasets used and/or analyzed during the current study are available from the corresponding author upon reasonable request.