Role of downregulated miR-133a-3p expression in bladder cancer: a bioinformatics study

Figures & data

Figure 1 The experimental design of the paper.

Note: The flowchart illustrates that we validated miR-133a-3p expression in BC and the underlying molecular basis via systematic review and bioinformatics study.
Abbreviations: BC, bladder cancer; GO, gene ontology; GEO, Gene expression Omnibus; PPI, protein-protein interaction; KEGG, Kyoto Encyclopedia of Genes and Genomes.

Figure 2 The flow chart.

Notes: The flow chart describes the process of selection of literature studies in detail. A total of six studies were included.

Table 1 The basic information and data of the included studies

First author	ID	Year	Country	Ethnicity	Sample size		Male		Specimen	Experiment type	Platform	Control M	Control SD	Exp M	Exp SD
					Control	Case	Control	Case
Pignot et al^Citation36	PMID: 23169479	2013	France	European	7/11	14/152	NA	0.83	Tissue	PCR		158.6/1.00*		0.86/0.01*
Yoshino et al^Citation37	PMID: 21304530	2011	Japan	Asian	5/10	11/23	NA	0.81	Tissue	miRNA expression signatures and PCR	TaqMan LDA Human microRNA Panel v2.0	1.17E–01		2.48E–03
Song et al^Citation32	PMID: 21133599	2010	China	Asian	25	25	0.6	0.6	Tissue	Microarray and PCR		479.04		15.42
Han et al^Citation38	PMID: 21464941	2011	China	Asian	9	9	9	9	Tissues	MiR sequencing	Illumina Cluster Station and Genome Analyze (Illumina)	1,067.726		14.5754
Zhu et al^Citation39	PMID: 22140553	2011	China	Asian	9	9	9	9	Tissues	Digital gene expression sequencing	Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA)	18.30194	10.2901	1.677944	2.326551
Ichimi et al^Citation33	PMID: 19378336	2009	Japan	Asian	31	104	0.87	0.71	Tissue	miRNA expression signatures and PCR	GeneSpring GX V7.3.1	0.96	0.196	0.048	0.016
Ratert et al^Citation70	GSE36121	2014	Germany	European	8	16	8	14	Tissue	Non-coding RNA profiling by array	GPL8227	−0.69125	0.896317	−10.2781	1.643765
Xu et al^Citation71	GSE39093	2015	China	Asian	10	10	10	10	Tissue	Non-coding RNA profiling by array	GPL8786	20.38886	4.839885	17.16362	5.542755
Meiri et al^Citation72	GSE20414	2012	Israel	Asian	2	2	NA	NA	Tissue	Non-coding RNA profiling by array	GPL10067	12.73932	0.324303	9.07	2.008183
Lu et al^Citation24	GSE2564	2012	USA	American	2	7	NA	NA	Tissue	Non-coding RNA profiling by array	GPL1986	5.865	1.223295	5.76	0.861762

Note:

* Samples with larger size.

Abbreviations: Exp, experiment; miRNA, microRNA; NA, not available.

Figure 3 The pattern of miR-133a-3p expression in BC tissues and normal tissues.

Note: MiR-133a-3p expression was remarkably lower in BC tissues than in normal tissues from Zhu et al’s study³⁹ (A) and GSE36121 (B).
Abbreviation: BC, bladder cancer.

Figure 4 The forest plot of meta-analysis.

Notes: The pooled SMD of −3.64 (−6.99 to −0.29) with great heterogeneity (I²=97.0%, P<0.001) suggested that miR-133a-3p expression was significantly lower in BC tissues than in normal tissues. Weights are from random effect analysis.
Abbreviations: SMD, standard mean difference; BC, bladder cancer; 95% CI, 95% confidence interval.

Figure 5 The sensitivity analysis.

Note: The sensitivity analysis revealed that no study exerted significant influence on the overall pooling result.
Abbreviation: CI, confidence interval.

Figure 6 The publication bias.

Note: The symmetrical funnel plot indicates that no publication bias was detected.
Abbreviation: SMD, standard mean difference.

Figure 7 The SROC curve.

Note: An AUC value of 0.8418 from SROC curve revealed that miR-133a-3p was of significant diagnostic value for BC.
Abbreviations: SROC, summary receiver operating characteristic; AUC, area under curve; BC, bladder cancer.

Table 2 Subgroup analysis

Subgroup	I^2	SMD	95% CI
Ethnicity
Asian	97.90%	−3.79	(−8.29, 0.71)
Non-Asian	95.70%	−3.32	(−9.70, 3.05)
Experiment type
Non-coding RNA profiling by array	89.60%	−2.36	(−5.02, 0.30)
Other experiment types	98.60%	−5.96	(−13.27, 1.35)

Notes: Non-Asian subgroup contained European and American; other experiment types contained digital gene expression sequencing and miRNA expression signatures and PCR.

Abbreviations: SMD, standard mean difference; 95% CI, 95% confidential interval; miRNA, microRNA; PCR, polymerase chain reaction.

Figure 8 The PPI network of the target genes of miR-133a-3p.

Notes: A total of 75 nodes and 110 edges constituted the network, from which 10 hub genes were identified according to the value of degree. Nodes with different colors represent query proteins and first shell of interactors.
Abbreviation: PPI, protein-protein network.

Figure 9 Expression of hub genes in BC and normal tissues from GEPIA.

Notes: Expression of the hub genes were detected in 404 BC tissues (T) and 28 normal tissues (N) from GEPIA. Four of the genes, PAK2 (A), UBE2I (B), CDK16 (C) and CSK (D), were overexpressed in BC tissues than in normal tissues. Axis units are Log2(TPM+1).
Abbreviations: BC, bladder cancer; GEPIA, Gene Expression Profiling Interactive Analysis.

Table 3 GO enrichment analysis of the target genes of miR-133a-3p

Category	Term		Count	%	P-value
GOTERM_BP_DIRECT	GO:0006509	Membrane protein ectodomain proteolysis	6	0.007358532	9.84E–05
GOTERM_BP_DIRECT	GO:0032964	Collagen biosynthetic process	3	0.003679266	0.004966407
GOTERM_BP_DIRECT	GO:0006979	Response to oxidative stress	7	0.008584954	0.007494953
GOTERM_BP_DIRECT	GO:0031623	Receptor internalization	5	0.00613211	0.009738182
GOTERM_BP_DIRECT	GO:0007264	Small GTPase mediated signal transduction	13	0.015943486	0.010401849
GOTERM_BP_DIRECT	GO:0046777	Protein autophosphorylation	9	0.011037798	0.015688851
GOTERM_BP_DIRECT	GO:0048280	Vesicle fusion with Golgi apparatus	3	0.003679266	0.016393286
GOTERM_BP_DIRECT	GO:0045931	Positive regulation of mitotic cell cycle	4	0.004905688	0.01978581
GOTERM_BP_DIRECT	GO:0032456	Endocytic recycling	4	0.004905688	0.022591642
GOTERM_BP_DIRECT	GO:0030217	T cell differentiation	4	0.004905688	0.02560231
GOTERM_BP_DIRECT	GO:2000036	Regulation of stem cell population maintenance	3	0.003679266	0.027032891
GOTERM_BP_DIRECT	GO:0051292	Nuclear pore complex assembly	3	0.003679266	0.027032891
GOTERM_BP_DIRECT	GO:0000910	Cytokinesis	4	0.004905688	0.032235851
GOTERM_BP_DIRECT	GO:0030048	Actin filament-based movement	3	0.003679266	0.0331441
GOTERM_BP_DIRECT	GO:0072659	Protein localization to plasma membrane	5	0.00613211	0.034128257
GOTERM_BP_DIRECT	GO:0015031	Protein transport	6	0.007358532	0.037343901
GOTERM_BP_DIRECT	GO:2001241	Positive regulation of extrinsic apoptotic signaling pathway in absence of ligand	3	0.003679266	0.039735772
GOTERM_BP_DIRECT	GO:0030330	DNA damage response, signal transduction by p53 class mediator	3	0.003679266	0.046774564
GOTERM_BP_DIRECT	GO:0071560	Cellular response to transforming growth factor beta stimulus	4	0.004905688	0.047906842
GOTERM_CC_DIRECT	GO:0070062	Extracellular exosome	96	0.117736515	1.58E–06
GOTERM_CC_DIRECT	GO:0005925	Focal adhesion	23	0.028207707	3.54E–05
GOTERM_CC_DIRECT	GO:0005829	Cytosol	42	0.051509726	0.002077235
GOTERM_CC_DIRECT	GO:0043209	Myelin sheath	10	0.01226422	0.006631547
GOTERM_CC_DIRECT	GO:0016020	Membrane	37	0.045377615	0.008847182
GOTERM_CC_DIRECT	GO:0001931	Uropod	3	0.003679266	0.015496611
GOTERM_CC_DIRECT	GO:0005654	Nucleoplasm	50	0.061321102	0.016133224
GOTERM_CC_DIRECT	GO:0001726	Ruffle	6	0.007358532	0.017212833
GOTERM_CC_DIRECT	GO:0030175	Filopodium	5	0.00613211	0.020498143
GOTERM_CC_DIRECT	GO:0019898	Extrinsic component of membrane	6	0.007358532	0.0245113
GOTERM_CC_DIRECT	GO:0005739	Mitochondrion	33	0.040471927	0.025783112
GOTERM_CC_DIRECT	GO:0005902	Microvillus	5	0.00613211	0.026546689
GOTERM_CC_DIRECT	GO:0005802	Trans-Golgi network	8	0.009811376	0.02787919
GOTERM_CC_DIRECT	GO:0016324	Apical plasma membrane	10	0.01226422	0.028054824
GOTERM_CC_DIRECT	GO:0005794	Golgi apparatus	22	0.026981285	0.029322169
GOTERM_CC_DIRECT	GO:0005884	Actin filament	5	0.00613211	0.038776107
GOTERM_MF_DIRECT	GO:0005524	ATP binding	52	0.063773946	0.001227934
GOTERM_MF_DIRECT	GO:0000981	RNA polymerase II transcription factor activity, sequence-specific DNA binding	12	0.014717064	0.004972384
GOTERM_MF_DIRECT	GO:0004674	Protein serine/threonine kinase activity	14	0.017169909	0.007071712
GOTERM_MF_DIRECT	GO:004482	2poly(A) RNA binding	34	0.041698349	0.021519286
GOTERM_MF_DIRECT	GO:000154	Beta-amyloid binding	4	0.004905688	0.024757557

Abbreviation: GO, gene ontology.

Table 4 KEGG pathway analysis of the target genes of miR-133a-3p

Category	ID	Term	Count	%	P-value
KEGG_PATHWAY	hsa04144	Endocytosis	19	0.023302019	4.84E–04
KEGG_PATHWAY	hsa04152	AMPK signaling pathway	12	0.014717064	8.00E–04
KEGG_PATHWAY	hsa05205	Proteoglycans in cancer	14	0.017169909	0.005393183
KEGG_PATHWAY	hsa05100	Bacterial invasion of epithelial cells	8	0.009811376	0.007318134
KEGG_PATHWAY	hsa04071	Sphingolipid signaling pathway	10	0.01226422	0.008048532
KEGG_PATHWAY	hsa04810	Regulation of actin cytoskeleton	14	0.017169909	0.008355754
KEGG_PATHWAY	hsa00510	N-glycan biosynthesis	6	0.007358532	0.013382535
KEGG_PATHWAY	hsa00230	Purine metabolism	12	0.014717064	0.013384166
KEGG_PATHWAY	hsa04520	Adherens junction	7	0.008584954	0.016781642
KEGG_PATHWAY	hsa04530	Tight junction	10	0.01226422	0.018114206
KEGG_PATHWAY	hsa04261	Adrenergic signaling in cardiomyocytes	10	0.01226422	0.026173267
KEGG_PATHWAY	hsa05131	Shigellosis	6	0.007358532	0.03783327
KEGG_PATHWAY	hsa03015	mRNA surveillance pathway	7	0.008584954	0.048738091

Abbreviation: KEGG, Kyoto Encyclopedia of Genes and Genomes.

Figure S1 The GO maps for BP of target genes of miR-133a-3p.

Notes: There are 69 nodes and 101 arrows in the map. GO terms of BP are represented by nodes, and the relationships between the terms are manifested by arrows. The depth of color indicates the significance of the corresponding term.

Abbreviations: GO, Gene Ontology; BP, biological process.

Figure S2 The GO maps for CC of target genes of miR-133a-3p.

Notes: There are 75 nodes and 130 arrows in the map. GO terms of CC are represented by nodes, and the relationships between the terms are manifested by arrows. The depth of color indicates the significance of the corresponding term.

Abbreviations: GO, Gene Ontology; CC, cellular component.

Figure S3 The GO maps for MF of target genes of miR-133a-3p.

Notes: There are 36 nodes and 41 arrows in the map. GO terms of MF are represented by nodes, and the relationships between the terms are manifested by arrows. The depth of color indicates the significance of the corresponding term.

Abbreviations: GO, Gene Ontology; MF, molecular functions.

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