Integrated bioinformatics analysis of potential pathway biomarkers using abnormal proteins in clubfoot

Introduction

As a common developmental malformation of newborns, clubfoot affects approximately 2% of newborns (Wang et al., 2019). If not actively and timely treated, this deformity will accompany the child for a lifetime, which will not only affect the appearance of the child, including walking difficulties or even a disability, but also cause serious adverse effects on the mental health of the child. Therefore, timely and active treatments are urgently needed. The treatment of clubfoot includes surgical and nonsurgical treatments. Surgical releases, such as muscle balance and anterior tibial tendon transposition, may cause many problems, such as large trauma complications, which seriously affect the healthy development of children (Smith et al., 2014). The number of extensive surgical cases of clubfoot has declined by 60% from 1996 to 2006 in the United States (Zionts et al., 2010). In contrast, the Ponseti method has received increasing attention in the treatment of clubfoot and has become the most commonly used method. Although the success rate of Ponseti’s first correction is satisfactory after a long period of development, there are still many problems and challenges, such as having a recurrence of deformity, having a poor compliance, and determining the best time to stop wearing braces (Miller et al., 2016; Thacker et al., 2005).

Clubfoot is associated with neuromuscular lesions, heredity abnormalities, skeletal dysplasia, soft tissue contracture, vascular abnormalities, ECM abnormalities, and intrauterine growth retardation (Chesney, Barker & Maffulli, 2007; Eckhardt et al., 2019; Miedzybrodzka, 2003; Ošt’ádal et al., 2015; Poon, Li & Alman, 2009; Sodre et al., 1990; Wang et al., 2013a; Wang et al., 2013b). In addition, smoking and viral infections in pregnant women are also closely related to congenital clubfoot (Palma et al., 2013; Robertson Jr & Corbett, 1997). Although the direct cause of congenital clubfoot remains to be unified, these findings provide an important opportunity and basis for the treatments of clubfoot. Several studies have revealed that botulinum toxin injection can relieve muscle or soft tissue contracture and may replace percutaneous tendoachilles tenotomy in the treatment of clubfoot (Alvarez et al., 2009; Howren, Jamieson & Alvarez, 2015). Based on the progress of pathogenesis, appropriate drug treatment may improve patient compliance and ultimately improve the efficacy of the Ponseti method. In addition, familial occurrence and inter- and intraphenotypic variability of clubfoot is well documented (Basit & Khoshhal, 2018). Several genes were identified as susceptible genes in clubfoot, such as the HOX family, CASP family, PITX-TXB4 pathway, troponin (TN) family, GLI3, T-box and MTHFR genes (Hecht et al., 2007; Shrimpton et al., 2004; Shyy et al., 2009; Weymouth et al., 2016; Zhang et al., 2016). However, these studies do not further explore abnormally active signaling pathways and potential upstream and downstream regulatory networks. Therefore, the aim of the present investigation is to explore the abnormal pathways and their interactions using integrated bioinformatics analysis in clubfoot. We expect the results of this study will provide an update on the etiopathogenetic mechanism of idiopathic clubfoot.

Materials and Methods

Inclusion of abnormal proteins

Two widely used databases, PubMed and Science Direct, were used for literature retrieval. Keywords were “(clubfoot or clubfeet or congenital talipes equinovarus) and (etiology or embryology or etiopathogenesis or genomics or genetics or pathology or pathophysiology)”. The search date was up to May 7, 2019. A total of 1,057 articles were found in PubMed, and 657 articles were found in Science Direct. After eliminating duplicate articles, a total of 1,093 studies were retrieved. By reading the title and abstract, 1,015 articles were eliminated following the inclusion and exclusion criteria as described below. Inclusion criteria included clinical or preclinical studies written in English that were focused on the etiology of clubfeet. Investigations with a focus on secondary/syndromic clubfoot, such as distal arthrogryposis, myelomeningocele, and moebius syndrome, were excluded. We performed a full text assessment of the remaining 78 articles. A total of 47 articles were excluded because the study topic was not clubfoot, genetic information was not mentioned or full text of the study was not available. Finally, 8 articles were included in the present study. A total of 30 proteins that are shown in Table 1 were used in this investigation after assessing the protein. The process of the inclusion of abnormal proteins was shown in Fig. 1.

Table 1:

Protein information.

Entry ID	Entry name	Protein names	Gene names	References
Q9BXN1	ASPN_HUMAN	Asporin	ASPN	Ošt’ádal et al. (2015)
P21810	PGS1_HUMAN	Biglycan	BGN	Ošt’ádal et al. (2015)
Q8IUL8	CILP2_HUMAN	Cartilage intermediate layer protein 2, CILP-2	CILP2	Eckhardt et al. (2019)
P35222	CTNB1_HUMAN	Catenin beta-1 (Beta-catenin)	CTNNB1	Poon, Li & Alman (2009)
P02461	CO3A1_HUMAN	Collagen alpha-1(III) chain	COL3A1	Eckhardt et al. (2019)
P20908	CO5A1_HUMAN	Collagen alpha-1(V) chain	COL5A1	Eckhardt et al. (2019)
P12109	CO6A1_HUMAN	Collagen alpha-1(VI) chain	COL6A1	Eckhardt et al. (2019)
Q99715	COCA1_HUMAN	Collagen alpha-1(XII) chain	COL12A1	Eckhardt et al. (2019)
Q05707	COEA1_HUMAN	Collagen alpha-1(XIV) chain (Undulin)	COL14A1	Eckhardt et al. (2019)
P08123	CO1A2_HUMAN	Collagen alpha-2(I) chain	COL1A2	Eckhardt et al. (2019)
P12110	CO6A2_HUMAN	Collagen alpha-2(VI) chain	COL6A2	Eckhardt et al. (2019)
P12111	CO6A3_HUMAN	Collagen alpha-3(VI) chain	COL6A3	Eckhardt et al. (2019)
P20849	CO9A1_HUMAN	Collagen alpha-1(IX) chain	COL9A1	Wang et al. (2013a) and Wang et al. (2013b)
O94907	DKK1_HUMAN	Dickkopf-related protein 1, Dickkopf-1	DKK1	Poon, Li & Alman (2009)
Q06828	FMOD_HUMAN	Fibromodulin	FMOD	Eckhardt et al. (2019)
P02751	FINC_HUMAN	Fibronectin (Cold-insoluble globulin, CIG)	FN1	Ošt’ádal et al. (2015)
Q14192	FHL2_HUMAN	Four and a half LIM domains protein	FHL2	Wang et al. (2008)
P35453	HXD13_HUMAN	Homeobox protein Hox-D13 (Homeobox protein Hox-4I)	HOXD13	Wang et al. (2008)
P51884	LUM_HUMAN	Lumican	LUM	Ošt’ádal et al. (2015)
Q16853	AOC3_HUMAN	Membrane primary amine oxidase	AOC3	Ošt’ádal et al. (2015)
P20774	MIME_HUMAN	Mimecan (Osteoglycin)	OGN	Ošt’ádal et al. (2015)
Q15063	POSTN_HUMAN	Periostin (Osteoblast-specific factor 2)	POSTN	Ošt’ádal et al. (2015)
P51888	PRELP_HUMAN	Prolargin	PRELP	Ošt’ádal et al. (2015)
Q7Z7G0	TARSH_HUMAN	Target of Nesh-SH3	ABI3BP	Ošt’ádal et al. (2015)
P24821	TENA_HUMAN	Tenascin, TN (Cytotactin)	TNC	Eckhardt et al. (2019) and Ošt’ádal et al. (2015)
Q15582	BGH3_HUMAN	TGF-β-induced protein ig-h3	TGFBI	Eckhardt et al. (2019)
P48436	SOX9_HUMAN	Transcription factor SOX-9	SOX9	Wang et al. (2013a) and Wang et al. (2013b)
P10071	GLI3_HUMAN	Transcriptional activator GLI3	GLI3	Cao et al. (2009)
P01137	TGFB1_HUMAN	TGF-β-1 proprotein	TGFB1	Wang et al. (2013a) and Wang et al. (2013b)
P13611	CSPG2_HUMAN	Versican core protein	VCAN	Eckhardt et al. (2019) and Ošt’ádal et al. (2015)

DOI: 10.7717/peerj.8422/table-1

Results

Results of the enrichment analysis by g:Profiler and Reactome

To visually observe the enrichment information of these candidate proteins, g: Profiler and Reactome were performed for the bioinformatics analysis. A large number of terms were enriched by g:Profiler in the GO, KEGG, REAC, WP and HP databases (Fig. 2A). A large number of signaling pathways were enriched by Reactome (Fig. 2B). Additionally, there were extensive interactions among these signaling pathways (Fig. 2B).

To clarify the categories of these pathways, we summarized these pathways enriched by REAC. Signal transduction, disease, metabolism, gene expression (transcription), and immune system were the top 5 pathways and their percentages were as high as 65% (Fig. 3A). Among the 30 proteins, the top 10 proteins with the widest participation, such as P35222, P01137, P02751 and P08123, were mainly ECM proteins or proteins that interact with the ECM (Figs. 3B and 3C). We continued to summarize the top 10 pathways and found that these pathways were mainly focused on the ECM, metabolism and cell communication (Fig. 3D).

Results of the signaling pathway enrichment analysis

Through the Reactome enrichment analysis, a large number of pathways were enriched (Figs. 2 and 3). To further analyze these potential pathways, signaling pathway enrichment analysis was carried out using g:Profiler in the REAC, WP, KEGG and HP. A total of 32, 11, 7 and 30 pathways were enriched by g:Profiler, respectively (Figs. 4A–4D). Classification analysis revealed that these pathways were mainly concentrated in ECM, disease and metabolic pathways (Fig. 4E). The proportion of the top three was as high as 78%. In addition, human phenotype ontology enrichment analysis results revealed that these abnormal proteins were mainly expressed in the lower appendages, such as muscle, ankle, foot, joint, skin and connective tissue, and their proportion was more than 50% (Fig. 4F). Similar, similar results were found in KEGG and REAC enrichment analyses using NetworkAnalyst and WebGestalt (Fig. S1).

Results of the GO enrichment analysis

GO enrichment analysis was further performed to explore the BP, MF and CC induced by these proteins. A total of 69, 9 and 24 GO terms were enriched by g:Profiler in BP, MF and CC, respectively (Figs. 5A–5C). Classification analysis revealed that GO: BP was mainly concentrated in embryo or organ development, and its combined percentage was over 80% (Fig. 5E). Among these pathways, skeletal development was dominant. ECM function, growth factor binding, cell adhesion, heparin binding and protein binding were the main pathways in MF, and their percentages were as high as 85% (Fig. 5F). Additionally, ECM and membrane were the main CC, and their percentages were almost 60% (Fig. 5G). In addition, GO enrichment analysis results analyzed by NetworkAnalyst were consistent with those from g:Profiler (Fig. S2).

Results of PPIs and gene regulatory networks analysis

The NetworkAnalyst analysis was performed to explore protein-protein interactions and gene regulatory networks for genes that code these candidate proteins. These genes interact extensively with predictive genes (Fig. 6A). A total of 2,630 PPIs were enriched by NetworkAnalyst. There are 1,263 interactions that were related to the top 10 genes and these interactions account for 48% of the total. The top genes were FN1, CTNNB1, FHL2, TGFB1 and COL1A2 (Fig. 6B). Among these genes, FN1 and CTNNB1 were dominant, and the percentage of PPIs induced by these two genes was almost 39%.

TF-gene interactions were also enriched by NetworkAnalyst. A total of 692 TF-gene interactions were enriched (Fig. 6C). The top genes were TGFB1, FN1, SOX9, AOC3 and HOXD13 (Fig. 6D). Additionally, the interactions among these 10 genes were as high as 43% of the total.

Gene-miRNA interactome analysis results revealed that 409 interactomes were identified between these genes and predictive miRNAs (Fig. 6E). The top genes were FHL2, PRELP, CTNNB1, SOX9 and COL12A1 (Fig. 6F). Top miRNAs were hsa-mir-124-3p, hsa-mir-26b-5p, hsa-mir-335-5p, hsa-mir-1-3p and hsa-mir-5698. The interactomes between the top 10 genes and the top 10 miRNAs accounted for 39% and 5% of the total, respectively.

A large number of TF-miRNA coregulatory interactions were enriched (Fig. 6G). Transcription factors, such as SOX9, CTNNB1, GLI3, FHL2, TGFBI and HOXD13, cooperated with hsa-miR-29a, hsa-miR-101, hsa-miR-520d-5p, hsa-miR-29b and hsa-miR-568 to regulate these candidate genes (Fig. 6G). The top 10 genes were SOX9, CTNNB1, GLI3, FHL2, TGFB1, TGFBI, VCAN, TNC, COL12A1 and COL5A1 (Fig. 6H).

Combining the four interactions mentioned above, 19 genes were involved in the top interactions (Fig. 6I). SOX9, CCNNB1, VCAN, TGFB1, FHL2 and COL12A1 widely participated in the top-ranking interactions (Fig. 6J).

Discussion

In the present investigation, a large number of signaling pathways were enriched in the GO, KEGG, REAC, WP and HP databases using g:Profiler, NetworkAnalyst and WebGestalt analyses of clubfoot. Among them, pathways in embryo or organ development, ECM, metabolism, immune system, cell cycle, cell responses to external stimuli, and apoptosis or programmed cell death were the top pathways. A wide range of interactions existed among these enriched signaling pathways. In addition, there were also extensive regulations between the upstream and downstream of genes encoding these proteins.

There were 452 enriched pathways identified by REAC enrichment analysis. Among them, signal transduction, disease, metabolism, gene expression (transcription), immune system, developmental biology, cell cycle, ECM and hemostasis were advantageous pathways. Additionally, signaling pathways in DNA repair, PCD, cell response to external stimuli, cell–cell communication, molecular transport and chromatin organization were enriched. In the process of cell biological activities, numerous changes occurred in cells, such as signal transduction, gene expression, cell cycle, DNA repair, molecular transport and metabolism. Abnormal changes in these biological processes may alter cell fate, cell–cell communication, and cell response to external stimuli or even cause immune system changes.

Select soft tissues in clubfoot are contracted, resulting in stiffness. Extracellular matrix proteins, such as asporin, collagen types III, V, and VI, versican, tenascin-C, and TGF-beta induced protein, are highly expressed in contracted tissues clubfoot (Eckhardt et al., 2019; Ošt’ádal et al., 2015). Additionally, the expression levels of growth factors TGF-beta and platelet-derived growth factor are high and a blockade of growth factors led to decreased collagen expression, proliferation, and chemotaxis (Li et al., 2001). These proteins seem to be promising targets for future investigations and treatments of this disease. Indeed, the muscle contraction strategy, such as botulinum toxin injection, can relieve muscle or soft tissue contracture and thus improve and alleviate clubfoot symptoms (Howren, Jamieson & Alvarez, 2015; Shrimpton et al., 2004). ECM-associated pathways were enriched and included collagen chain trimerization, collagen formation and degradation, and ECM proteoglycans. TGF-beta receptor signaling was also enriched. These findings support the idea that these ECM proteins are promising targets for the treatment of clubfoot.

Abnormal biological development, such as muscle, neurological, skeletal and vascular abnormalities, has been previously identified and confirmed (Basit & Khoshhal, 2018; Eckhardt et al., 2019; Herceg et al., 2006; Hester et al., 2009; Lovell & Morcuende, 2007; Ošt’ádal et al., 2015). The HOX and TBX families governed limb identity, and fibroblast growth factor participated in the formation of limb muscles (Ohuchi & Noji, 1999; Wang et al., 2008). Additionally, gene-gene interactions between CASP SNPS and variants in HOXA, HOXD, and insulin-like growth factor binding protein affect muscle and limb development (Ester et al., 2010). Apoptosis and programmed cell death associated pathways and activation of HOX gene pathways, such as activation of HOX genes during differentiation, and activation of anterior HOX genes in hindbrain development during early embryogenesis, were enriched in the REAC database. A myogenesis pathway was also found.

ROBO family genes regulate axonal guidance and cell migration. ROBO1 and ROBO2 receptors regulate the proliferation and transition of primary to intermediate neuronal progenitors (Borrell et al., 2012), while the interaction of ROBO4 with SLIT3 is involved in the proliferation, motility and chemotaxis of endothelial cells, and accelerates the formation of blood vessels (Zhang et al., 2009). We found that the regulation of commissural axon pathfinding by SLIT, ROBO, netrin-1 signaling and pathways with signaling by ROBO receptors, semaphorin interactions, neurotransmitter release cycle were enriched. These results support that activation and inactivation of developmental signaling pathways initiate embryonic and organ development. Abnormalities in any link may cause deformities.

Epidemiological data confirmed that smoking by any parent or the presence of any household smoking increased the risk of clubfoot in Peru (Palma et al., 2013). Maternal diabetes also showed a significant association with clubfoot (Parker et al., 2009). In mice, maternal smoking or diabetes increased mitochondrial damage and oxidative stresses (Stangenberg et al., 2015). In addition, maternal diabetes also increased hypoxia-inducible factor 1 α expression in utero (Moazzen et al., 2015). Robertson Jr & Corbett (1997) confirmed that clubfoot was caused by an intrauterine enterovirus through allowing anterior horn cell lesions. The adverse in utero environment caused by the external or internal environment may increase oxidative stress and thus induce cell damage in utero. We found that the signaling pathways involved in the regulation of gene expression by hypoxia-inducible factor, reactive oxygen species detoxification, cell response to hypoxia, cell response to heat stress, cell response to stress, oxidative stress-induced senescence, cellular senescence, and cellular responses to external stimuli were enriched in the REAC database. In addition, these external stimuli activate the immune system. We also found that interleukin family signaling, MAP kinase activation, toll-like receptor family cascade, adaptive immune system, and innate immune system were enriched. These data indicate that abnormal changes in the immune system and cell response to external stimuli may play key roles in clubfoot.

In the enrichment analysis, we also found that several molecular transport pathways were enriched by enrichment analysis, and induced plasma lipoprotein assembly, remodeling, and clearance, iron uptake and transport, small molecules transport, binding and uptake of ligands by scavenger receptors, lysosome vesicle biogenesis, vesicle-mediated transport, trans-Golgi network vesicle budding, and membrane trafficking. Molecular transport is essential for material transport, signal transduction and neurotransmitter transporters and modulates the cell response to an external force (Hu & Papoian, 2013). Disorders induced by abnormal molecular transport are serious and even fatal for cells. Based on these results, we proposed that molecular transport abnormalities may play a large role in clubfoot.

Metabolism of proteins, RNAs or other molecules plays a key role in the basic functions of cells (Esteban-Martínez, Sierra-Filardi & Boya, 2017). Pathways in these metabolic processes were found in the enrichment analyses, and induced regulation of IGF transport and uptake by IGFBPs, activation of genes by ATF4 in response to endoplasmic reticulum stress, synthesis, secretion, and inactivation of GLP-1, metabolism of nitric oxide, activation and regulation of eNOS, metabolism of carbohydrates, and regulation of lipid metabolism by PPAR α. A previous study indicated that lipid droplets and glycogen increased and the number of mitochondria decreased in chondrocytes from the biopsied iliac crest cartilage of joint contracture patients (Nogami et al., 1983). These data suggested that glucose metabolism, lipid metabolism and mitochondrial oxidative stress were associated with multiple joint contractures. In the present work, glucose metabolism regulated by IGF or GLP, lipid metabolism regulated by PPAR, and oxidative stress regulated by NOS were found in the REAC database. These data suggest that metabolic abnormalities may play a significant role in clubfoot.

All candidate papers were obtained from PubMed and Science Direct. Almost all of these differentially expressed proteins were carefully and strictly selected from clinical trials. Clubfoot is abnormal in both bone and muscle. Most of the samples are from bone, and few are from muscle, therefore selection bias cannot be avoided. Through strict screening criteria, candidate proteins from different tissues were adopted for subsequent bioinformatics analysis, and the selection bias was possibly minimized. Although the adjusted p value method was performed, there may be some false positives in using these candidate proteins for bioinformatics analysis because these proteins were not collected from the same investigation. Although we proposed that cell or immune responses to external stimuli, abnormal molecular transport and metabolism are new potential etiopathogenetic mechanisms of clubfoot, direct experimental evidence is needed. We are carrying out preclinical and clinical studies to confirm these enrichment pathways and proposed hypotheses.

Conclusions

In summary, a large number of signaling pathways were enriched using REAC, KEGG and WP enrichment analyses by g:Profiler, NetworkAnalyst and WebGestalt. Among them, signal transduction, disease, metabolism, gene expression (transcription), immune system, developmental biology, cell cycle, and ECM were the top functions. GO enrichment analysis also revealed pathways in embryo or organ development, and ECM proteins were dominant. PPIs and GRNs analysis results indicated that extensive and complex interactions occur in these proteins, enrichment pathways, and TF-miRNA coregulatory networks. Transcription factors such as SOX9, CTNNB1, GLI3, FHL2, TGFBI and HOXD13, cooperated with hsa-miR-29a, hsa-miR-101, hsa-miR-520d-5p, hsa-miR-29b and hsa-miR-568 and regulated these candidate proteins. In addition to supporting the proposed hypotheses, such as ECM abnormalities, fetal movement reduction, genetic abnormalities, muscle abnormalities, neurological abnormalities, skeletal abnormalities, uterine compression and vascular abnormalities, we propose that cellular or immune responses to external stimuli, and abnormal molecular transport or metabolism are new potential etiological mechanisms of clubfoot.

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