Journal name: Cancer Management and Research Article Designation: Original Research Year: 2018 Volume: 10 Cancer Management and Research Dovepress Running head verso: Wang et al Running head recto: Prognostic and diagnostic value of in colon adenocarcinoma open access to scientific and medical research DOI: http://dx.doi.org/10.2147/CMAR.S183062

Open Access Full Text Article Original Research Distinct prognostic value of dynactin subunit 4 (DCTN4) and diagnostic value of DCTN1, DCTN2, and DCTN4 in colon adenocarcinoma

Shijun Wang1 Background: Colon adenocarcinoma (COAD) is ranked as the third most commonly diagnosed Qiaoqi Wang2 cancer in both women and men, and it is the most frequently occurring malignant tumor. Dynactin Xiqian Zhang3 is a compound based on multiple subunits, including dynactin 1–6 (DCTN1–6), in most Xiwen Liao4 categories of cytoplasmic performance in eukaryotes. Nevertheless, correlations between Guixian Wang1 the DCTN family and the prognosis and diagnosis of COAD remain unidentified. Statistics for DCTN mRNA expression in patients with COAD were acquired from Long Yu5 Methods: The Cancer Genome Atlas. Kaplan–Meier analyses and a Cox regression model were applied Wei Zhang1 to determine overall survival, with computation of HRs and 95% CIs. Several online data 1 Quanbo Zhou portals were used to assess the biological process, and pathway examination was performed 1 Shengyun Hu using the Kyoto Encyclopedia of and Genomes to predict the biological functionality 1 Weitang Yuan of DCTN genes. 1Department of Colorectal and Results: We found that high expression of DCTN4 was linked with satisfactory results for overall Anal Surgery, The First Affiliated survival (P=0.042, HR=0.650, 95% CI 0.429–0.985). The expression of DCTN1, DATN2, and Hospital of Zhengzhou University, Zhengzhou, Henan Province, China; DCTN4 was closely correlated with the frequency of colon tumors (P<0.001, area under the 2Department of Medical Cosmetology, curve [AUC]=0.8811, 95% CI 0.8311–0.9312; P<0.001, AUC=0.870, 96% CI 0.833–0.9071; The Second Affiliated Hospital of and P=0.0051, AUC=0.6317, 95% CI 0.5725–0.6908, respectively). In the enrichment exami- Guangxi Medical University, Nanning, Guangxi Province, China; 3Department nation, the level of expression was related to the cell cycle, cell apoptosis, and the cell of Radiotherapy, The First Affiliated metastasis pathway. Hospital of Zhengzhou University, The expression levels of DCTN1, DCTN2, and DCTN4 could allow differentia- Henan Province, China; 4Department Conclusion: of Hepatobiliary Surgery, The First tion between cancer-bearing tissues and paracancerous tissue. These genes can be applied as Affiliated Hospital of Guangxi Medical biomarkers to predict the prognosis and diagnosis of COAD. University, Nanning, Guangxi Province, China; 5Department of Hepatobiliary Keywords: dynactin, colon adenocarcinoma, diagnosis, prognosis, biomarker Surgery, The First Affiliated Hospital of Zhengzhou University, Henan Province, China Introduction Colon adenocarcinoma (COAD) is a type of colorectal cancer (CRC) and is the most frequently occurring malignant tumor. In USA, it is ranked as the third most frequently diagnosed tumor in both males and females.1 Moreover, in 2018, the number of new cases was predicted to be 97,220, and the predicted number of deaths was 50,630.2 Correspondence: Weitang Yuan; Shijun Wang The Surveillance, Epidemiology, and End Results Program (SEER) found that the Department of Colorectal and Anal 5-year survival rate is 64.5% (https://seer.cancer.gov). The risk factors involved in this Surgery, The First Affiliated Hospital disease are old age, male gender, increased level of fat consumption, alcohol, physical of Zhengzhou University, Zhengzhou 450002, Henan Province, China inactivity, smoking, red meat, obesity, and processed food.3,4 Treatment of CRC may Tel +86 371 6796 7141 include combinations of surgery, radiotherapy, chemotherapy, and targeted therapy.5 Email [email protected]; [email protected] Diagnostic methods include colonoscopy, which is referred to as the gold standard

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Wang et al Dovepress for diagnosis and can provide a highly accurate diagnosis the (GO) functional examination and the and assess the location of the tumor5; capsule endoscopy; Kyoto Encyclopedia of Genes and Genomes (KEGG) path- computed tomography colonography; and biomarkers of way examination. The functional examination based on GO CRC such as Septin-9 (SEPT9).5–7 includes the molecular functionality (MF), biological process Dynactin is a multiple-subunit protein compound (BP), and cellular component (CC). involved in the activation of most forms of cytoplasmic A GO function analysis tool, Biological Networks Gene dynein in eukaryotes.8 Dynactin connects to cytoplasmic Ontology (BiNGO),16 was applied for predicting the func- dynein, dynein cargo adaptors, and .9 Six tionality of gene based on the results of correlation analysis. subunits of dynactin, DCTN1, DCTN2, DCTN3, DCTN4, A gene function prediction website, Gene Multiple Asso- DCTN5, and DCTN6, have been verified, and all the subunits ciation Network Integration Algorithm (GeneMANIA), was are encoded through their corresponding genes. Previous used to predict DCTN family members.17 The Search Tool research found that the DCTN family is linked with multiple for the Retrieval of Interacting Genes/ (STRING) neurodegenerative diseases.10–12 Nevertheless, after biblio- database which offers a critical evaluation and combination graphic retrieval, it was found that only a few studies stated of protein–protein interactions,18 was employed for assess- the correlation between the DCTN family and the prognosis ing the functional and physical relationships of DCTN4 and and diagnosis of COAD. correlated genes, with a collective score >0.15 being taken In this research, we accessed a public database, The to indicate statistical significance. Cancer Genome Atlas (TCGA), to assess survival-related data and DCTN family expression in patients with COAD, Co-expression matrix of the DCTN family and examined the prognostic and diagnostic value of mRNA in COAD expression levels of individual DCTN genes. Several online Pearson correlation coefficient analysis was used to identify data portals were employed for analyzing the functionality correlations between DCTN family genes in COAD. Results and signaling pathways in a bid to predict the functionality with P<0.01 were considered to be statistically significant. of DCTN genes. Characteristics of levels Materials and methods We used the Metabolic gEne RApid Visualizer (MERAV) to Data preparation make boxplots of various expression levels of DCTN family Data including mRNA expression and clinical information members in primary colon cancer-bearing tissue and normal that may be linked with COAD, including gender, age, colon tissue.19 Vertical scatterplots were produced based and tumor stage, were extracted from TCGA data portal, on the DCTN gene expression. Furthermore, the high and accessed by the University of California Santa Cruz Xena low expression level groups of DCTN genes were identified (UCSC Xena: https://xena.ucsc.edu/, retrieved June 21, according to the median values of each gene. Patients with 2018). mRNA sequencing was used in 456 patients. The expression values greater than the median values of specific expression data, which include 480 cases of cancer and 42 DCTN genes were identified as the high expression group, non-cancer mRNA sequences, were used for performing and the remaining patients were identified as the low expres- expression-associated examinations. After the cases with sion group. missing medical data and 0-day survival time had been removed, a total of 438 cases were included in the survival Diagnostic prediction examination. Receiver operating characteristics (ROC) curves were drawn to identify the prognostic importance of the DCTN Functional analysis and mRNA co- family in TCGA data portal. Standardized values of expression of the DCTN family diagnosis with P<0.05 were considered to be statistically The relevant degrees of expression of the six DCTN genes significant. in multiple different tissues were created by GTEx Portal.13 The Database for Annotation, Visualization, and Integrated Survival analysis Discovery (DAVID, v.6.8)14,15 was employed to analyze the The log-rank test, together with Kaplan–Meier survival functional enrichment, which includes two terminologies, examination, was applied to calculate the P-value and overall

5808 submit your manuscript | www.dovepress.com Cancer Management and Research 2018:10 Dovepress Dovepress Prognostic and diagnostic value of dynactin in colon adenocarcinoma survival (OS) for the DCTN gene family and clinical informa- Statistical analyses tion. Furthermore, the Cox proportional hazards regression SPSS v.25.0 software was used for statistical analyses (IBM model was applied for univariate and multivariate survival Corp., Armonk, NY, USA). In addition, GraphPad Prism examinations. HRs and 95% CIs were computed by means of v.7.0 was used for generating survival curves and vertical the Cox proportional hazards regression model after adjusting scatterplots (GraphPad Software, Inc., La Jolla, CA, USA). for clinical characteristics. The correlation plots and nomogram were produced by R v.3.5.1 (R Foundation for Statistical Computing, Vienna, Nomogram Austria). Cytoscape v.3.6.1 was employed to construct an A nomogram was employed to evaluate the relationship interactive network of the targeted genes.22 between DCTN4 and medical rank in COAD OS. Further- more, the probable utility of DCTN4 in predicting clinical Results rank was assessed. mRNA expression of DCTN genes in With regard to the clinical information and survival human non-cancer-bearing colon and analysis, after adjustment with the Cox proportional hazards regression model, only tumor stage and expression level of colon cancer tissues In human colon tissues, DCTN2, DCTN5, and DCTN6 DCTN4 were entered into the risk model. The points against were highly expressed (Figure S1B, E, and F), and DCTN1, each factor could be counted, and 1-, 5-, and 10-year survival DCTN3, and DCTN4 were expressed at a medium level rates could also be computed.20 (Figure S1A, C, and D).

Gene Set Enrichment Analysis (GSEA) DCTN family functional, pathway, and co- To investigate the mechanism by which different expres- expression enrichment analysis sion levels of DCTN4 in COAD generate different results, The biological functionality of the DCTN genes was GSEA v.3.0 (http://software.broadinstitute.org/gsea/ assessed through DAVID regarding the BP, MF, and CC msigdb/index.jsp, accessed July 10, 2018) was used for types for GO function and KEGG pathway examination analyzing dissimilarities in DCTN4 expression levels of (Figure 1A). Enrichment outcomes were examined through biological patterns in the lower expression group and BiNGO (Figure S2). Interactions between the expressed higher expression group for each gene using reference gene levels of DCTN genes are shown in Figure 1B. An exami- sets, extracted from the Molecular Signatures Database nation of co-expression at the protein level is illustrated in (MSigDB), c2 (KEGG gene sets: c2.all.v6.1.symbols. Figure 1C. These results indicated that genes in the DCTN gmt), and c5 (GO gene sets: c5.all.v6.1.symbols.gmt).21 family were correlated with substance transportation, The number of permutations was set at 1,000. Enriched together with cell cycle and protein-binding procedures results satisfying a nominal significant cut-off value of in cells. P<0.05 with a false discovery rate <0.25 were considered Correlations between the expression levels of individual to be statistically significant. DCTN genes were found through Pearson correlation coef- ficient analysis. The expression level of DCTN1 was cor- Exploring the function of DCTN4 in related with both DCTN4 and DCTN6, while the expression COAD level of DCTN2 was correlated with DCTN3 and DCTN5 Pearson correlation coefficient analysis was used to perform (all P<0.01; Figure 2A). genome-wide correlation analysis and to identify correla- tions between DCTN4 and possible survival rate associated Diagnostic value of the DCTN gene family with the COAD gene cohort of TCGA. An absolute value of Vertical scatterplots for expression levels of DCTN genes are correlation coefficient> 0.4 was taken as being highly cor- shown in Figure 2B, and each group was considered to be related. To explore the functionality of DCTN4 in COAD, the statistically significant (all P<0.05). The boxplots produced online database of DAVID, together with BiNGO, STRING, from MERAV showed that, with the exception of DCTN2, and GeneMANIA, was applied to examine the GO function the expression levels of the remaining genes in primary colon and KEGG pathway for DCTN4 and correlated genes of the tumor were higher than in normal colon tissue (Figure 3A COAD cohort in TCGA. and C–F). The expression level of DCTN2 in normal colon

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KEGG pathway A Huntington's disease Molecular function Vasopressin-regulated water reabsorption Cellular component Protein binding Biological process Motor activity

Microtubule

Spindle

Kinetochore

Dynein complex

Condensed kinetochore

Cytosol

Centrosome

Dynactin complex

Microtubule-based process

Melanosome transport

Mitotic nuclear division

G2/M transition of mitotic cell cycle

ER to Golgi vesicle-mediated transport

Antigen processing and presentation of exogenous peptide antigen via MHC class II –log10 02468101214

DCTN5 B SEC24D SAR1A C CAPZA1 SEC23A

PBX2 ATP7B DCTN4 DCTN6 CEP76 MARCKSL1

DCTN1 DCTN6 SNAP29

BICD1 DCTN2 KLHL2 DCTN1 DCTN2 DCTN5 DCTN4

GMPPA ACTR1B DCTN3

DCTN3 DCTN2 SEH1L FPGT

Co-expression ACTR1A HECTD1

ACTR10 OVOL1 AKAP10 Physical interaction Shared protein domains Experimentally determined Co-expression Pathway Co-localization

Figure 1 (A) Study of enriched GO terminology and KEGG pathways for DCTN genes assessed by DAVID; (B) DCTN gene interaction networks among selected genes generated by GeneMANIA; (C) STRING physical and functional connections of DCTN genes. Abbreviations: DAVID, Database for Explaining, Visualization, and Integrated Discovery; DCTN, dynactin; ER, endoplasmic reticulum; GeneMANIA, Gene Multiple Association Network Integration Algorithm; GO, gene ontology; KEGG, Kyoto Encyclopedia of Genes and Genomes; MHC, major histocompatibility complex; STRING, Search Tool for the Retrieval of Interacting Genes/Proteins. tissues was greater than that in the tumor-bearing colon the occurrence of colon tumors (P<0.001, area under the (Figure 3B). Furthermore, we produced ROC curves of the curve [AUC]=0.8811, 95% CI=0.8311–0.9312; P<0.001, estimated expression levels of DCTN family in tumor and AUC=0.870, 96% CI=0.833–0.9071; and P=0.0051, paired colon tissues (Figure 4). The expression levels of AUC=0.6317, 95% CI=0.5725–0.6908, respectively; DCTN1, DATN2, and DCTN4 were closely correlated with ­Figure 4A, B, and D, respectively).

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Dovepress Prognostic and diagnostic value of dynactin in colon adenocarcinoma

<0.001 6

High DCTN6 High

5

Low DCTN Low <0.001 5

PP

High DCTN High

Low DCTN Low

<0.001 4

High DCTN4 High

3 Low DCTN Low

<0.001 3

PP

High DCTN High

Low DCTN Low

<0.001 2

High DCTN2 High

1 Low DCTN Low

<0.001 1

PP High DCTN High

9 8 7 7 0

14 13 12 11 10

Expression level (log2) level Expression Low DCTN Low B 1 0. 8 0. 6 0. 4 0. 2 0 −0.2 −0.4 −0.6 −0.8 −1 gene family expression levels in TC GA . DCTN6 DCTN 1 DCTN 5 −0.04 DCTN4 1 0.34* DCTN3 P < 0.001; ( B ) scatterplots for 0.04 0.06 DCTN2 1 DCTN1 0.48* 0.09 0.31* −0.03 −0.24* gene expression levels, * 0 1 −0.05 DCTN DCTN6 0.67* −0.4* DCTN5 1 −0.01 DCTN4 0 DCTN 3 , dynactin; TC GA The Cancer G enome A tlas. 1 DCTN DCTN 2 1 ( A ) Pearson’s correlation coefficients for A DCTN Figure 2 Abbreviations:

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A B C

3000 500 2000 2500 400

Tissue 2000 Tissue 1500 Tissue 300 Normal tissue Normal tissue Normal tissue Primary tumor Primary tumor Primary tumor Expression Expression Expression 1500 200 1000

1000 100

500 Colon Colon Colon

D E F 1200 600

500 1500 900

400 Tissue Tissue Tissue 600 Normal tissue Normal tissue 1000 Normal tissue Primary tumor Primary tumor Primary tumor 300 Expression Expression Expression

300 200 500

100 0 Colon Colon Colon

Figure 3 MERAV boxplots of expression of DCTN family in normal tissues and tumor-bearing tissues. Note: Boxplots are shown for the expression levels of (A) DCTN1; (B) DCTN2; (C) DCTN3; (D) DCTN4; (E) DCTN5; and (F) DCTN6. Abbreviations: DCTN, dynactin; MERAV, Metabolic gEne RApid Visualizer.

Survival analysis ­(Figure 7A–I). In the GSEA of KEGG pathways, the expres- The univariable survival analysis indicated that, with regard sion level of the gene was linked with the cell cycle, cell to clinical information, tumor stage was the only factor that apoptosis, and the cell metastasis pathway. The GO function was linked with OS, and preliminary stages were correlated enriched examination produced no significant outcomes. The significantly with favorable OS (P<0.001, HR=0.323, 95% remaining results are presented in Tables S1 and S2. CI=0.210–0.498; Table 1). The Kaplan–Meier curves of the Correlations between DCTN4 and possible survival asso- DCTN gene family are shown in Figure 5A–F. The tumor ciated with the COAD gene cohort in TCGA are presented in phase was included in the Cox proportional hazards regres- Figure 8. The outcomes of GO function and KEGG pathway sion model for multivariate survival examination; higher examination performed by DAVID among these genes are expression levels of DCTN4 correlated significantly with presented in Figure 9. The co-functional examination con- satisfactory OS results (adjusted P=0.042, HR=0.650, 95% ducted by means of BiNGO among genes associated with CI=0.429–0.985; Table 2; Figure 5D), and the results were DCTN4, based on the results of correlation analysis, and consistent with the outcomes of univariate survival examina- DCTN4 is presented in Figure 10. The items shown in red tion (P=0.009, HR=0.581, 95% CI=0.386–0.874; Table 2). were consistent with the results of the DAVID examination. The nomogram for scoring risk includes the expression The results of co-expression examination by GeneMA- level of DCTN4 and tumor stage to predict results and the NIA are presented in Figure 11. The integration of protein– 1-, 5-, and 10-year related survival percentage (Figure 6). protein co-expression examination by STRING is presented in Figure 12. These genes were correlated with cell cycle, Function of DCTN4 in COAD protein ubiquitination, protein binding, protein transport, and The relative difference in DCTN4 expression level of some cancer-related procedures including nuclear factor-κB COAD in TCGA records was assessed by means of GSEA (NF-κB) signaling pathways and cellular adhesion.

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AB 100 100 DCTN1 DCTN2

80 80 ) ) 60 60

40 40 Sensitivity (% Sensitivity (%

20 20

P<0.0001 P<0.0001 0 AUC (95% CI)=0.8811 (0.8311–0.9312) 0 AUC (95% CI)=0.87 (0.833–0.9071)

020406080 100 020406080 100 100% – specificity (%) 100% – specificity (%)

C D 100 100 DCTN3 DCTN4 80 80 ) ) 60 60

40 40 Sensitivity (% Sensitivity (%

20 20

P=0.3071 P=0.0051 0 AUC (95% CI)=0.548 (0.487–0.6091) 0 AUC (95% CI)=0.6317 (0.5725–0.6908)

020406080 100 020406080 100 100% – specificity (%) 100% – specificity (%)

EF 100 100 DCTN5 DCTN6 80 80 ) ) 60 60

40 40 Sensitivity (% Sensitivity (%

20 20

P=0.1027 P=0.1866 0 AUC (95% CI)=0.5767 (0.4986–0.6548) 0 AUC (95% CI)=0.5621 (0.5007–0.6235)

020406080 100 020406080 100 100% – specificity (%) 100% – specificity (%)

Figure 4 ROCs of six DCTN genes, showing differences between COAD tissue and adjacent normal colon tissue. Note: ROCs of six prognostic differentially expressed miRNAs: (A) DCTN1; (B) DCTN2; (C) DCTN3; (D) DCTN4; (E) DCTN5; and (F) DCTN6. Abbreviations: COAD, colon adenocarcinoma; DCTN, dynactin; ROC, receiver operating characteristics.

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Table 1 Demographic and clinical data for 438 COAD patients Variable Patients No. of MST HR (95% CI) Log-rank (n=438) events (%) (days) P-value Gender 0.545 Male 234 54 (23.1) 2,475 Ref. Female 204 44 (22.6) N/A 1.131 (0.759–1.686) Age (years) 0.114 ≥65 168 29 (17.3) 2,475 Ref. <65 268 116 (25.4) N/A 1.420 (0.919–2.194) Tumor stage <0.001 Advanced 187 62 (33.2) 1,711 Ref. Early 240 31 (12.9) 3,042 0.323 (0.210–0.498) Missing 11 Tumor stage <0.001 IV 61 31 (51.8) 858 Ref. I 73 4 (5.5) N/A 0.089 (0.031–0.251) II 167 27 (16.2) 2,821 0.198 (0.118–0.335) III 126 31 (24.6) N/A 0.360 (0.218–0.596) Missing Abbreviations: COAD, colon adenocarcinoma; MST, median survival time; N/A, not available.

Discussion to be associated with multiple cancers or cancer cell lines,28 In the current study, we investigated the prognostic and diag- including lung cancer29 and Spitz tumors.30 DCTN2 was nostic values of the DCTN gene family based on the TCGA observed to be over expressed in SJSA-1 osteosarcoma database. Higher expression of DCTN4 was found to be cor- cells.31 Nevertheless, the correlation between DCTN4 and related with favorable OS in COAD, and the expression levels cancer was not stated. Here, we have employed statistics of DCTN1, DCTN2, and DCTM4 may be used to predict the from TCGA on expression and medical data in COAD to occurrence of colon cancer. In addition, we investigated the investigate correlations between DCTN gene family expres- GO function analysis, KEGG pathway, and protein–protein sion levels and prognosis and to identify biomarkers that can relationships among DCTN4 and correlated genes to predict be used for prognosis and diagnosis in patients with COAD. the function of DCTN4. We observed that DCTN4 had a positive correlation with Dynactin is a multiple-subunit protein compound several pathways as follows. The eukaryotic initiation factor involved in the activation of most forms of cytoplasmic (EIF) pathway was correlated with cell apoptosis,32,33 necropto- dynein in eukaryotes.8 Dynactin connects to cytoplasmic sis,34,35 cellular senescence,36 proteoglycans in cancer,37 and cho- dynein, dynein cargo adaptors, and microtubules.9 The exis- line metabolism in cancer.38,39 The cell cycle phase was observed tence of six subunits of dynactin, DCTN1, DCTN2, DCTN3, to be associated with the tumor owing to stability of the genome DCTN4, DCTN5, and DCTN6, has been verified, and all and uncontrolled cellular growth process. Nevertheless, the of them are encoded through their corresponding genes. detailed mechanisms of molecules that link dysfunctionality DCTN1 is considered the largest subunit of dynactin,23 and in such pathways to the beginning of specific tumors are not DCTN1 has been implicated in many neurodegenerative stated in the majority of cases.40 In our functional assessment diseases.10–12 DCTN2 connects with DCTN1 and DCTN3 performed by GO and KEGG, we observed that the function to form a complex subunit.23 DCTN4 was found to be asso- of DCTN4 was significantly enriched in multiple cell cycle ciated with Wilson’s disease24 and chronic Pseudomonas processes, including cell cycle S phase and G2/M change in aeruginosa infection.25 the mitotic cell cycle. DCTN4 and correlated genes were found In addition to its dynactin functions,8,26 the DCTN gene to be linked with NF-κB signaling, which played a crucial role family plays a crucial role in many cancers. Some research in initiating human cancer, cancer progression, metastasis, and on this subject has been published. Our previous research resistance.41–43 Cell–cell adhesion, as found on BP examination, found that DCTN1, DCTN2, and DCTN5 were upregulated is an essential cellular process and may result in cancer.44,45 All in cutaneous melanoma, while DCTN6 was downregulated the results discussed herein were essential aspects in the process and linked with favorable OS.27 DCTN1 has been observed of occurrence, progression, and prognosis in COAD.

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AB 100 100 Low DCTN1 Low DCTN2 l 80 High DCTN1 l 80 High DCTN2 HR=0.734 (0.492–1.096) HR=0.783 (0.525–1.169) Log-rank P=0.131 Log-rank P=0.232 60 60

40 40

Percent surviva 20 Percent surviva 20

0 0

0 1000 2000 3000 4000 5000 0 1000 2000 3000 4000 5000 Overall survival (days) Overall survival (days)

CD 100 100 Low DCTN3 Low DCTN4 l 80 High DCTN3 l 80 High DCTN4 HR=1.097 (0.737–1.632) HR=0.581 (0.386–0.874) Log-rank P=0.649 Log-rank P=0.009 60 60

40 40

Percent surviva 20 Percent surviva 20

0 0

0 1000 2000 3000 4000 5000 0 1000 2000 3000 4000 5000 Overall survival (days) Overall survival (days)

EF 100 100 Low DCTN5 Low DCTN6

l High DCTN5 l High DCTN6 80 80 HR=1.011 (0.677–1.508) HR=0.733 (0.492–1.093) Log-rank P=0.958 Log-rank P=0.128 60 60

40 40

Percent surviva 20 Percent surviva 20

0 0

0 1000 2000 3000 4000 5000 0 1000 2000 3000 4000 5000 Overall survival (days) Overall survival (days)

Figure 5 Prognostic graphs of DCTN expression for overall survival. Note: Kaplan–Meier survival curves for complete COAD patients according to expression of (A) DCTN1; (B) DCTN2; (C) DCTN3; (D) DCTN4; (E) DCTN5; and (F) DCTN6 (n=438). Abbreviations: COAD, colon adenocarcinoma; DCTN, dynactin.

The functionality of the DCTN4 subunit is yet not In the present research, we observed that only a higher clear, although its nonappearance does not have a signifi- expression level of DCTN4 was correlated with favorable cant impact on the stabilization of dysfunction.46 In colon OS, out of all the DCTN family mRNA expression levels. tumors, dysfunction of several factors may have an impact We also constructed a nomogram, showing that the contribu- on the Wnt signaling pathway, which increases the signaling tion of tumor stage was increased with advancing stage, and performance.47,48 Our KEGG analysis showed that a higher a higher expression level of DCTN4 had a lower influence expression level of DCTN4 was correlated with cell metasta- on time-related survival percentage. Comparing these two sis, together with cancer relapse and the cell cycle, which may possible factors associated with risk, the role of tumor stage be a part of the pathway associated with cancer occurrence. was much greater than that of DCTN4 expression. By apply- Particularly in the colon tumor recurrence pathway, DCTN4 ing this model, we could forecast the time-related survival may be an indispensable factor in patients with COAD. percentage. The 1-, 5-, and 10-year survival rates were much

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Table 2 Prognostic survival analysis according to high or low expression of DCTN family genes Gene Patients No. of MST (days) Crude HR Crude Adjusted HRa Adjusted (n=438) events (%) (95% CI) P-value (95% CI) P valuea DCTN1 0.131 0.446 Low 219 43 (19.6) 3,042 Ref. Ref. High 219 55 (25.1) 2,134 0.734 (0.492–1.096) 0.851 (0.563–1.288) DCTN2 0.231 0.340 Low 219 56 (25.6) 2,475 Ref. Ref. High 219 42 (19.2) N/A 0.783 (0.525–1.169) 1.222 (0.810–1.844) DCTN3 0.649 0.594 Low 219 49 (22.4) 2,821 Ref. Ref. High 219 49 (22.4) 2,475 1.097 (0.737–1.632) 1.118 (0.741–1.686) DCTN4 0.009 0.042 Low 219 61 (25.1) 1,910 Ref. Ref. High 219 37 (51.5) N/A 0.581 (0.386–0.874) 0.650 (0.429–0.985) DCTN5 0.958 0.701 Low 219 51 (23.3) 3,042 Ref. Ref. High 219 47 (21.5) 2,532 1.011 (0.677–1.508) 0.922 (0.611–1.393) DCTN6 0.128 0.764 Low 219 54 (24.7) 1,910 Ref. Ref. High 219 44 (20.1) 2,821 0.733 (0.492–1.093) 0.938 (0.618–1.424) Notes: aAdjusted for tumor stage. Bold figures indicate statistically significance. Abbreviations: DCTN, dynactin; MST, median survival time.

0102030405060708090 100 Points

II IV Tumor stage I III

Low expression DCTN4 High expression

Total points 0102030405060708090 100 110 120 130 140

1−year survival 0.95 0.9 0.85 0.8 0.75 0.7 0.6

5−year survival 0.9 0.85 0.8 0.75 0.7 0.6 0.5

10−year survival 0.85 0.8 0.75 0.7 0.6 0.5

Figure 6 Nomogram for the relations hip between medical data and risk score. Abbreviation: DCTN, dynactin. better for patients with lower total points than for those with and adenomatous polyposis coli (APC).50 In the present higher total points. research, the ROC curves indicated that the expression A number of traditional biomarkers have been used levels of DCTN1, DCTN2, and DCTN4 can be used to to try to detect the frequency of COAD, including distinguish adjacent normal tissues from colon tumor- metastasis-associated in colon cancer-1 (MACC1)49 bearing tissues.

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ABC

NES=1.777 NOM p-val=0.012 NES=1.768 NES=1.810 FDR q-val=0.156 NOM p-val=0.002 NOM p-val=0.006 FDR q-val=0.160 FDR q-val=0.134

D EF

NES=1.860 NES=1.762 NES=1.671 NOM p-val=0.018 NOM p-val=0.020 NOM p-val=0.010 FDR q-val=0.019 FDR q-val=0.163 FDR q-val=0.226

GHI

NES=2.122 NES=1.770 NES=2.049 NOM p-val<0.001 NOM p-val=0.019 NOM p-val<0.001 FDR q-val=0.060 FDR q-val=0.159 FDR q-val=0.069

Figure 7 GSEA outcomes achieved for KEGG pathway analysis for higher and lower levels of expression of DCTN4, using gene set c2. Note: (A) Metastasis; (B) cancer relapse tumor sample; (C) colon cancer recurrence; (D) metastasis; (E) EIF pathway; (F) metastasis; (G) inhibited invasion; (H) oncogenesis; (I) cell cycle S. Abbreviations: DCTN, dynactin; EIF, eukaryotic initiation factor; ES, enrichment score; FDR, false discovery rate; GSEA, Gene Set Enrichment Analysis; KEGG, Kyoto Encyclopedia of Genes and Genomes; NES, normalized enrichment score; NOM, nominal.

This research has several limitations. First, further study index, and pathological diagnosis. Third, the relevant patient with a larger sample size is necessary to improve the consis- data were extracted from one source; thus, the results need tency of our results. Second, more clinical information will further validation for use in other groups. be needed in further studies, such as smoking and alcohol Despite these limitations, this is the first study to show history, hereditary non-polyposis CRC, size of the primary that upregulated DCTN4 in COAD is correlated with a satis- tumor, radical resection position, family history, body mass factory prognosis. This gene may be applied as a biomarker

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GTF2BGRPELGPR1802 GTPBP1GTF2H0 1 DR1 DNAJB9 GTPBP8 DNAJB14 HSD17B4 DNAJA2 HSPA13 DLEU1 ICE2 DIS3 FBXW11FBXO8 ING3 FEM1CFCHO2 FBXO3FBXO28 DIMT1 FYTTD1 FBXL5 ITGB3BP GIN1 FASTKD3 DHX29 KATNBL1 GLRX3 FASTKD2 DESI2 GMFB FAM200B KIAA1191 LNPKLMBRD1LIN9 DCUN1D1 GNPAT LSM11LRRC40 LIN7C LARS ECT2 MRPL35 LARP1B KIAA1586 GPALPP1 MRPL39 LANCL1 ECHDC1 DCK GPN3 MRPL42 LAMTOR3 DTD2 KIF3A MRPL47 KYAT3 CYB5R4 IDE DDX59 KLHL9 MRPL50 KRR1 CUL2 RBBP4RB1RARS2 ITM2B MRPS22 RBM22RBM18 RARSNOC3L EXOC6 CTDSPL2 KPNA4 RBM27 NHLRC2 CTBS LZTFL1 RBM7 NEK7 COG6 MRPS27 RBMX NECAP1 ETNK1 MRPS30 MRPL30 MRPS35 RCHY1 NEBL ETFRF1 CLN5 CSNK1A1 RCN2 NDUFS4 NAE1 MTRR MRPS36 SDHD NDUFB5 ETF1 CEPT1 CRYZL1 MTPN SEC23IP SAMD4B RPS6KA4 NDUFA5 ERLEC1 NDFIP2 SART1 RHBDD3 CRIPT RSL24D1 SELENOF MTMR6 CEP57L1 MYNN SCAF1 RANGAP1 ERGIC2 PANK3 SAR1B SENP8 SMAD5 SLU7 SLC39A10 MARVELD2 CEP57 CRBN SCYL1 SMARCAD1 RHOT1 PPP1R12C PRDX3 SEPSECS MAPK9 ERCC8 SMNDC1 RFK PEX13 SCYL2 CEP120 COX7A2L SELENOO POLR3H PREPL SERP1 SNX14 SELENOTRSBN1RNASEH2B RFESD MAPK8 EPS15 SPRED1 PRRC1 SPCS3 CENPQ PFDN1 SFXN1 SNX2 SREK1IP1 PPP1R2 REEP5 MAP4K3 COX11 PRIM2 SETD1A PLEKHM2 ENPP4 NDFIP1 MFAP3 SKIV2L2 SRFBP1 POLK MANEA PI4K2B STARD4 CDK7 COPS4 PRKCI SNX3 NMD3 METTL9 PCNP ELMOD2 SRP19 PHAX SKP1 SH3GL1 PHRF1 LZIC STXBP3 OCIAD1 NUS1 NUP54 CCDC59 PIBF1 PWWP2A SNX6 PAPD4 RYK NUP35 METTL14 PCGF5 EIF5A2 COPS2 SLC10A7 SRSF10 PGGT1B LYSMD3 TAF7 SACM1L NSA2 CCDC125 PIGK SIPA1 DMWD PCNX3 COPB1 PYROXD1 SLC25A36 SPAST SSR1 EGLN2 DGKZ PDS5APCBD2 LYRM2 EIF4A2 PMS1 SCAMP1 EHBP1L1 DGCR2 NEPRO METAP2 TATDN3 CBFB PLEKHA3 RAB10 SLC25A40 EHD1 DAPK3 LYPLAL1 EIF3E COMMD8 STAM2 PDCD2 SLC39A13TMA16 SCFD1 ESD DCLRE1A NDUFAF4 PAWR PACS2 TBK1 SLC25A46 EML3 FAM204A COMMD3 CHST12 LIPT1 C18orf21 PLGRKT RAB14 RINT1 MED7 EIF2A COMMD2 STARD3NL SCOC MIER1 CNOT2 NCOA4 TMBIM4 PDCD10 PARPBP TDRD3 SLC30A5 FBXL19 CEP170B KPNA3 BTF3L4 PLRG1 RAB18 SLC9A3R2 MINDY3 RNF2 RNF14 CNIH1 NCDN EIF1B COMMD10 NUF2 SLC30A6 TBC1D23 SLC30A9 MZT1 ISCA1 TFB2M G6PD RPAP2 RAPGEF6 CCS BTF3 RAB28 TMED2 RWDD4 PAQR3 EFCAB7 POC1B RIOK2 MMADHC TMEM182 RSRC1 CHUK FPGT CNOT7 TBCE IPO11 SNRNP70 UTP15 NUDT21 MYO9B TGDS RAB33B SLC33AIGHMBP21 RPF1 TMEM184C RSPRY1 MICU2 CCM2 HNRNPLL ECD BTBD1 POC5 TBPL1 TMED5 MOB1A CFAP36 PAPOLG INTS7 CNOT6 THAP6 TMEM267 RPRD1A BROX RAB3IP VEZT NUDCD2 EAF1 POGLUT1 TCAIM SYVN1 RMI1SLC35AINPPL5 1 CASKIN2HNRNPK MOB2 IKZF5 CMTR2 MOB4 SRP9 MGST2 CEP44 FOXN2 UBE2E1 TMEM33 GNPDA2 PAIP2 TMEM135 RAB4A TFAM DCTN4 HSPA9 DYNC2LI1 BMT2 POLR2M VPS26A NSUN3 CLDND1 SLC38AINTS9 1 C17orf62 HMMR MOCS2 CENPK TOM1L1 THAP2 TAB1 TMPO GMCL1 MKL1 HSPA4 BLZF1 RABL3 UBE2K TMEM161B MFF PAIP1 DUSP11 PPHLN1 RMND1 FOPNL CGGBP1 VTA1 NPM1 TNPO1IPO13 TMX1 GLMN BRF1 HBS1L TRIM23 RAD17 THAP5 MRPL1 CDK1 HSD17B12 DTWD2 BLOC1S5 PPID UBE2N TOMM70 GDI2 PAFAH1B2 CFAP97 TAF6L TMEM167A GABPA G3BP1 MEN1 THAP9 WDR41 IRF3 BAP1 MRS2 FBXL3 TRIM59 SDE2 TOMM20 NT5DC1 CDC73 HACD2 DPH3 BET1 PPIL3 RNF13 FNIP1 CETN3 THUMPD2 UBE2W TMEM168 G2E3 PACRGL FBXL17 TRMT11 SRSF3 XPO1 JMJD8 UBXN2A FRS2 CDC5L B4GALT2 MBLAC2 CCNG1 AZI2 TAOK2 MED15 PPIL4 UBE2D1 GPBP1 C5orf24 TIAL1 UBXN4 CDC42SE2 FASTKD1 SSR3 UBLCP1 KIAA0930 ATXN7L3 OSTC CCNC TTC1 YAF2 UCHL5 CDC23CDC25C MAT2B ATE1 PPIP5K2 TIPRL TMED7 UBE2D2 GORAB FNDC3A FANCL C5orf15 TESK1 LEMD2 ATG2A MBD3 TXNDC9 STT3B CCDC126 ASF1A TRMT10A UBTD2 ZNF24 UBE2D3 LIMK1 ARHGAP45 GOLT1B LYRM7 OSBPL8 FAM96A PPP1CB C4orf46 LZTR1 AP5B1 ARAP1 UBQLN1 STX12 TRMT10C TMEM106B ZFP1 GOLPH3L FGFR1OP2 FAM8A1 CASC4 ARMT1 TMEM104 UFM1 ZNF277 LCORL ORC4 MAP3K11 PPP1CC ZFP2 GLUD1 C3orf38 STX7 TRUB1 FAM60A CAPZA2 UFL1 ZNF280D ZFR FBXO38 GGPS1 INSIG2 ARL14EP USP16 TMEM128 CD46 OLA1 PPP2CA TSN TMEM184B MAP3K10 FAM35A C2orf49 SUCO ZNF354A TMEM14A CD164 GTF3C3 CAPZA1 UIMC1 CCT8 ANKRA2 TSNAX ZFYVE16 ZNF383 GFM2 NSL1 FAM175B PPP2R2A SVIP CAPRIN1 C21orf91 TRAF2 ZMYM1 ZNF441 DEPDC1B NAP1L1 AP1B1 USP33 TTC33 ZNF561 CCSAP CCT4 FAM172A ANAPC10 PPP3CB SWT1 ZMYM6 MED28 CAPN7 C1orf27 TWF1 VAC14 ANKRD13D FAM149B1 WDR36 ZNF136 MED21 AK6 ZNF148 MDH1 PPP3R1 TADA1 TXNL1 CCNT1 FAM114A2 CANX C17orf75 XRCC5 VPS37C AMPD2 AGGF1 TYW5 FAF2 TAF9 ZBTB22 AKT1 CAND1 PPP4R3B C12orf29 YEATS4 UBA3 ZDHHC8 ABCF3 AGAP3 CSNK1G3 AGFG1 TANK CAMLG UBA5 CNOT8 PPP6C C11orf57 YIPF4 TBC1D15 UBE2B CKAP2 CAAP1 AFF4 PPWD1 YME1L1 CCNI ARRDC3 YIPF5 TRAPPC13 ZBED8 CCNH C1D ADD3 ZBTB6 CALM2 TRDMT1 ZCCHC10 C9orf85 ATP6V1G1 PRIMPOL YWHAQ ZCCHC7 BMI1 ACTR6 ARPP19 TRIM13 ZCCHC9ZFAND1BCAS2BCLAFBLOC1S1 6 ATP6V1A ZBTB11 ACTR3 PRKAA1 TRIQK ATL2 ARPC3 ZCCHC4 UGGT2 ATG5 ACTR10 PRKRA UHMK1 ATG4C ARMC1 ZDHHC20 USO1 ATG12 AC008560.1 PSMA1 USP15 ATF1 ARL8B ZFAND6 VAMP4VDAC1ARSKASNSD1ATAD1 ABI1 PSMC6 ZNF33B ABHD18 ARL6 ZNF627 ABHD13 PTCD2 ZNF675 ABHD10 ARL5B PTER ZNF799 ABCE1 ARL5A ZNF816ZRANB2 7-MaAASDHPPr T PTGES3 ZZZ3 10-Sep 5-Mar ARL1 RNGTT ARFIP1 RPAP3 API5 SIKE1 AP3S1 SLC30A7 AP3M1 SMIM15 AP3B1 SMIM3SRP72 ALG6 AMD1ANAPC13 Negative correlation gene Positive correlation gene

Figure 8 Pearson’s correlations among DCTN4 and possible associated COAD gene cohort of TCGA. Note: An absolute value of the correlation coefficient> 0.4 was considered to be highly correlated. Abbreviations: COAD, colon adenocarcinoma; DCTN, dynactin; TCGA, The Cancer Genome Atlas.

for prognosis in COAD patients. In addition, expression of level of DCTN4 expression was significantly correlated with DCTN1, DCTN2, and DCTN4 can be employed as prognostic a favorable prognosis for patients with COAD and could biomarkers in patients with COAD. serve as a prognostic biomarker for patients with COAD. In the current research work, we also examined the possible Conclusion mechanism of DCTN4 in COAD OS by means of GSEA and The present research found that expression of DCTN1, genome-wide co-expression examination and established a DCTN2, and DCTN4 was downregulated among COAD nomogram composed of DCTN4 and tumor stage in a bid tumor and paracancerous tissue and may have possible to predict OS in COAD. Nevertheless, all of these outcomes diagnostic value for COAD. We also observed that a higher require validation in future research.

5818 submit your manuscript | www.dovepress.com Cancer Management and Research 2018:10 Dovepress Dovepress Prognostic and diagnostic value of dynactin in colon adenocarcinoma 5 –Log10 –Log10 .5 44 , dynactin; G O, gene s e .5 33 Basal transcription factor mRNA surveillance pathway Dopaminergic synaps .5 ntegrated Discovery; DCTN I ntegrated 22 Golgi membrane Lysosomal membrane Cyclin/CDK-positive transcription elongation factor complex DNA-directed RNA polymerase II, holoenzyme Endoplasmic reticulum .5 F, nuclear factor; R IG - I -like N F, nuclear factor; receptor, retinoic acid-inducible C 11 e RIG-I-like receptor signaling pathway Cell cycl Hepatitis .5 0123456 Nucleus 00 s e e C Centrosome m Protein complex Golgi membrane Nuclear envelope NAFL D Cell cycl CCR4-NOT complex Hepatitis Lysosomal membrane Endoplasmic reticulum P < 0.001. Circadian rhythm RNA degradation Centrosome Nucleus Nuclear envelope CCR4-NOT complex Protein complex Dopaminergic synaps Basal transcription factor mRNA surveillance pathway D, Database for A nnotation, Visualization, and D A V I D, Database

Protein processing in endoplasmic reticulum RNA degradation NAFL D Circadian rhythm DNA-directed RNA polymerase II, holoenzyme RIG-I-like receptor signaling pathway Protein processing in endoplasmic reticulu B D Cyclin/CDK-positive transcription elongation factor complex D ) K EGG outcomes. * 0 4 –Log10 –Log10 82 .5 e 61 C ) MF outcomes; ( 33 41 .5 21 22 and the linked CO A D gene cohort of TC GA obtained using V I D. B ) CC outcomes; ( 01 DCTN4 .5 t e 81 11 Protein transpor Regulation of ubiquitin protein ligase activity involved in mitotic cell cycl mRNA processing Mitotic nuclear division Mitotic cell cycl Poly(A) RNA binding Cadherin binding involved in cell–cell adhesion activity Enzyme activator activity Ribosomal small subunit binding A ) BP outcomes; ( .5 D, nonalcoholic fatty liver disease; MF, molecular functionality; NA F L D, nonalcoholic protein kinase; mitogen-activated G enomes; M A PK, 00 t e e 0246 Mitotic cell cycl Protein transpor mRNA processing Cell–cell adhesion Mitotic nuclear division RNA binding Protein binding Stress-activated MAPK cascade G2/M transition of mitotic cell cycl e Poly(A) RNA binding Protein kinase activity I-kappaB kinase/NF-kappaB signaling Negative regulation of gene expression Enzyme activator activity Protein binding RNA binding Protein serine/threonine phosphatase activity RNA polymerase II carboxy-terminal domain kinase activity Polynucleotide 5'-phosphatase activity Ribosomal small subunit binding BP, biological process; CC, cellular component; CDK, cyclin-dependent kinase; CO A D, colon adenocarcinoma; CC, cellular component; BP, biological process; Polynucleotide 5'-phosphatase activity Cell–cell adhesion Stress-activated MAPK cascade G2/M transition of mitotic cell cycl e I-kappaB kinase/NF-kappaB signaling Negative regulation of gene expression Protein serine/threonine phosphatase activity Cadherin binding involved in cell–cell adhesion A nalysis of G O terms that are enriched and K EGG pathways for C A Regulation of ubiquitin protein ligase activity involved in mitotic cell cycl RNA polymerase II carboxy-terminal domain kinase activity Figure 9 gene- I -like receptor; TC GA , The Cancer G enome A tlas. ncyclopedia of G enes and K EGG , E ncyclopedia Kyoto ontology; Notes: Outcomes of G O analysis functional enrichment: ( Abbreviations:

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positive regulation of protein ubiquitination positive regulation of ubiquitin-protein A ligase activity regulation of protein ubiquitination

regulation of ubiquitin-protein ligase activity positive regulation of protein modification processregulation of protein modification process positive regulation of ligase activity posttranscriptional regulation of gene expression negative regulation of proteinprotein modification processrocesror s regulation of gene expression regulation of ligase activity positivepo regulation of cellular protein positive regulation of protein metabolic metabolic process process regulation of macromolecule regulation of translation proteasomal ubiquitin-dependent protein regulation of cellular proteinbiosyntheticteteineini metabolictbla processi catabolic process positive regulation of catalytic activity process regulationtion of proteinp metabolic process ubiquitin-dependent protein catabolic regulationregule a of macromolecule metabolicbolicboli positive regulation of macromolecule process process negativenegativn gativve regulationre of cellular protein metabolic process metabolicmetaab process

regulation of catalytic activity negative regulation of protein metabolic procesregulationregulregulaattitso of biosynthetic procescessess regulation of cellular biosynthetic proteasomal protein catabolic process regulation of primary metabolic process positive regulation of cellular metabolic process positive regulation of molecular function process negativeve regulationregguulation ofo macromoleculeromoleculem modification-dependent protein metabolicmeeetabolet process catabolic process positive regulation of metabolic process zinc ion transport regulation of metabolic procesproccese s regulation of cellular metabolicnegativega procesregulations of cellular metabolic process proteolysis involved in cellular protein catabolic process regulation of molecular function negative regulationti of metabolic process

modification-dependent macromolecule positive regulation of biological process transition metal ion transport positivepos regulationg of cellular process catabolic process

negative regulation of cellular process proteolysis negativee regulation of biological procesrocess regulation of biological process cellular protein catabolic procesproteins catabolic process metal ion transport

protein K48-linked ubiquitination protein folding protein polyubiquitination regulation of cellular process cellular macromoleculemacromoleculemac catabolic catabolic process protein modification by small protein protein metabolic procesocesprocesssss s biological regulation conjugation protein modification by small protein catabolic process cation transport cellular protein metabolic process protein K11-linked ubiquitination conjugation or removal

protein modification process interspecies interaction between protein ubiquitination protein modification by small protein organisms macromolecule modification macromolecule metabolic process cellular catabolic process regulation of cell cycle protein monoubiquitination removal primaryprimap mary metabolicmetab procesocess ion transport post-translational protein modification metabolic process cellular macromoleculemoleculle e metabolicmetme multi-organism process protein autoubiquitination process cotranslational protein targeting to establishment of protein localization macromoleculemacromoleculeeeccu biosyntheticb processrocess membrane histone ubiquitination biosynthetic process protein deubiquitination gene expression mRNA metabolic process protein targeting to membrane nucleobase, nucleoside, nucleotide and establishment of localizationcell cyclecy checkpoint protein transport nucleic acid metabolic process nitrogenni g compoundc p metabolicme process cellularcellluu metabolic process transport cellular nitrogen compoundundd metabolicmmeta RNA metabolic process biological_process process localization histone modification signalssig transductiond protein localization mRNA processing RNA processing cellular macromolecule biosynthetic SRP-dependent cotranslational protein signaling process process macromolecule localization intracellular protein transport protein targeting targeting to membrane protein targeting to ER histone deubiquitination nucleic acid metabolic process cellular biosynthetic process vesicle-mediated transport signal transmission establishmente of localizationGolgi vesicleon in cell transport cellularcellular proteinp localization protein localization in organelleprotein localization in endoplasmic reticulum transcription cellular process cellular localization intracellular transport DNA integrity checkpoint RNA biosynthetic process covalent chromatin modification cellular component biogenesis signaling cellular macromolecule localization

cellularcellulacellllu aar componentcom organization organelle organization responsererees to stimulus protein targeting to vacuole DNA damage checkpoint vacuolar transport chromatin modification chromosome organizationGolgi organization cell cycle process chromatin organization intracellular signal transduction cell cycle cellularcellu component assembly nuclear transport protein targeting to transcription, DNA-dependent protein complex biogenesis signaling pathway cellular response to stimulusimulus lysosomal transport

macromolecular complex subunit organization response to stress

DNA damage response, signal mitotic cell cycle transduction intracellular signaling pathway nucleocytoplasmic transport transcription from RNA polymerase II protein complex assemblmacromoleculary complex assembly small GTPase mediatedediaateda signal transcription initiation transductionn cellular response to stress

response to DNA damage stimulus transcription initiation from RNA polymerase II promoter intracellular receptor mediated signaling pathway

steroid hormone receptor signaling pathway

BCtranslation initiation factor activity ubiquitin binding

cytoplasmic part

translation factor activity, nucleic acid 7S RNA binding binding small conjugating protein binding RING-like zinc finger domain binding ribosome binding

organelle RNA binding membrane-bounded organelle proteinp domain specific binding intracellular non-membrane-bounded organelle nucleic acid bindinindingg protein binding organellar small ribosomal subunismallt ribosomal subunitnitt membrane-enclosed lumen ribonucleoproteinribonucleeoop binding

Golgi membrane centrosome protein transporter activity endomembrane system intracellularintrant non-membrane-bounded transcription factor binding organelleo part organelle substrate-specific transporter activity unfolded proteinprotein binding organelle lumen cytoskeleton organelle membrane microtubule cytoskeleton cell lipid binding mitochondrial small ribosomalorganellarorganeeella subunitar ribosome transporter activity binding membrane intracellular organelle transcriptiontrans cofactor activity ribosomalGolgi subunitunit apparatus part phospholipid binding cytoskeletal part mitochondrial ribosome microtubule organizingearly center endosome membrane transcription coactivator activity ribosome molecular_function nucleotide binding ribonucleotide binding ATP binding intracellular organelle lumen endosomal part phosphoinositide binding mitochondrial lumen membrane mitochondrial part transcription regulator activity nucleoside binding intracellular membrane-bounded transcription activator activity mitochondrial matrix organelle endosome early endosome ribonucleoprotein complex adenyla ribonucleotide binding purine ribonucleotide binding phosphatidylinositol-3,4,5-trisphosphate purine nucleotide bindingngn membrane part binding cellular_component nuclear lumen RNA polymerase II transcription factortor catalytic activity cytosol activity adenyl nucleotide binding coated membrane purine nucleoside binding nuclear part spliceosomalspp complex intracellular organelle part signal recognitionperinuclear particlecl regione of cytoplasm guanyl ribonucleotide binding intracellular part guanyl nucleotide binding membrane coat nucleoplasm

ligase activity macromolecular complex protein complex GDP binding methyltransferasemethyth compleomplexmplex GTP binding histone acetyltransferase complex ubiquitin ligase complex signals recognition particle, endoplasmic SAGA-type complex reticulum targeting STAGA complex nucleoplasm part

ligase activity, forming carbon-nitrogen bonds

transcriptionDNA-directedDNA-dir factore comple RNAhistonehistonx polymerase methyltransferase II, complex holoenzyme cullin-RING ubiquitin ligase complex nucleus nuclear body cell part acid-amino acid ligase activity

nuclear speck

holo TFIIH complex small conjugating protein ligase activity MLL1 complex Cajal body ubiquitin-protein ligase activity

Figure 10 GO analysis of functional enrichment by BiNGO for all the correlated genes. Note: (A) BP outcomes; (B) CC outcomes; and (C) MF outcomes of GO analysis of functional enrichment by BiNGO. Abbreviations: BiNGO, Biological Networks Gene Ontology; BP, biological process; CC, cellular component; DCTN, dynactin; ER, endoplasmic reticulum; GO, gene ontology; MF, molecular function; MLL, myeloid/lymphoid leukemia; SRP, signal recognition particle; TFIIH, transcription factor II H.

5820 submit your manuscript | www.dovepress.com Cancer Management and Research 2018:10 Dovepress Dovepress Prognostic and diagnostic value of dynactin in colon adenocarcinoma

DCTN4

Co-expression

Figure 11 Gene contact networks between DCTN4 and potential-linked COAD gene cohort of TCGA generated by GeneMANIA. Abbreviations: COAD, colon adenocarcinoma; DCTN, dynactin; GeneMANIA, Gene Multiple Connection Network Integration Algorithm; TCGA, The Cancer Genome Atlas.

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DTWD2 SREK1IP1 KIAA1430 AGFG1 MAPK9 ZFP1 ZNF561 FASTKD1 RPS6KA4C5orf54 ZNF675 ARL5B CLN5 TRIQK C4orf46 ARSK LZIC ZNF816 ZNF33B PACRGL PPP1R2 SLC39A10 ZBTB22 SDE2 NSL1 MFAP3 MARVELD2 ZCCHC10CASKIN2 LYRM2 ZNF799 NUS1 ING3 IKZF5 TOM1L1 NT5DC1 GLUD1 C17orf62 ZNF627 PPIL3 AP3M1 TAF6L GNPDA2 POGLUT1 CEP57L1 NEBL ZNF383 MED28 MYNN FAM175B G2E3 ZBTB6 ZFP2 AP1B1 PPP1R12C MAP3K11 CHST12PDYNC2LI1 AWR LIN9 TAB1 KLHL9 FBXL19 ZNF354A BRF1 ZNF441 PANK3 PEX13 MYO9B IPO13 RANGAP1 C17orf75 STARD4 FAM200B PAIP2 EGLN2 SYVN1IPO11 TIAL1 ECENPP4D SLC30A6 VAMP4 PPP3CB PPP6C KIAA0930MOB2 ZFAND6 HSD17B4 AKT1 REEP5 TGDS DEPDC1B RB1 DIS3 NDFIP1 IDE TMEM33 SETD1A C3orf17 ARRDC3 CNOT7 UBE2D2 OCIAD1 MAPK8 PRKCIATG2A NARG2 PPIL4PI4K2B THUMPD2 RMI1 PPP2R2A IGHMBP2 SRFBP1 RAB28 ECT2 INPPL1 PRRC1 CTDSPL2 HMMR FBXW11 SCAF1 CASC4 SEC23IP RAD1DUSP17 1 STX12 SART1 TBPL1 FAM204A MRS2 INTS1 FBXO28 CKAP2 TMPO RPRD1A PHAX GLMN FAM114A2 ERCC8 PREPL FBXO8 BAP1 SNX3 NEK7 CUL2 RINT1 SLU7 FYTTD1 PARPBP METTL9 MED15 FAF2 COX11 CBFB PTPLBDCK RPKPNAAP2 4 NUF2 G6PD PIGK RCHY1 ARL5A TMA16 TMEM184C LANCL1TIPRL RBBP4 GNPAT CDC25C MAP4K3 SLC35A5 ITM2B DESI2 C1orf27 CAAP1 TNPO1 UBE2K SLC25A36 CENPK TMEM184B ATG4C BET1 XRCC5 UBXN4 GGPS1 GABPA CSNK1A1 ARPP1FOPN9 L THAP6 SMARCAD1 UBLCP1 CDK1 MGST2 SLC30A5 ARL1 CENPQ POLK DHX29 SLC39A13 ZNF280D TRDMT1 CDC23VTA1 C5orf43 CNOT6 ATP6V1A GTF3C3 CCDC59 ITGB3BP THAP5 PPHLN1 AGGF1 UFM1 PMS1 ASF1A CAPRIN1 SFXN1 API5 COG6 LMBRD1 MAT2B BTBD1 SERP1 RFESD CCM2 SLC33A1 GMFB SAR1B RARS2 TMEM161B RBM27 TMX1 ATL2 ACTR10 TFAM LARS TBCE KIAA1704 CUX1 GOLT1B NUDT21 C6orf211 STAM2 ZRANB2 ARMC1 SSR1 SCOC PAQR3 CRYZL1 CHUK BMI1 HBS1L PAPOLG METTL14 ATAD1 TSNAX NCDN ALG6 PDCD2 UHMK1 TAF7 RPAP3 UCHL5 TRMT11 MRPS30GTPBP10 CD46 GTF2BXPO1 RIOK2 ZNF24 CSNK1G3 CDK7 LARP1B PACS2 CEP44 YIPF5 LAMTOR3 COPB1 ESD ORC4 METAP2 HMHA1 UBE2N ANAPC10 CCT8 NUP35 ELMOD2 PWWP2A CAND1 SLC25A46 CCNC CAPN7 VAC14 USO1 TMED5USP16 SRSF10 ZCCHC9 ETNK1 SRP9 MRPS35 AMD1 RNF13 C5orf44SRP72PPP2CA ABCE1 G3BP1 ARPC3 SLC30A7 KRR1 RARS GOLPH3L TMBIM4 MOB4 YME1L1 GPN3 OSTC COMMD3 LYSMD3 KPNA3EIF2A PDS5A SMEK2 SNX2 PSMA1OLA1 PTCD2 ZNF148 MMADHC YEATS4 ARFIP1 TMED7 SKIV2L2 PRKAA1PIBF1 ZNF136 TBK1 PSMC6 VDAC1 RSPRY1 ZZZ3 TFB2M UTP15 EHD1 RAB18 PPP1CC NOC3L ABCF3 SAMD4B TMEM106B UBA3 SPCS3 BROX EXOC6 CDC5L DDX59 RHOT1TBC1D15STXBP3 SCFD1 COMMD8 EIF3E MRPL42 MDH1 FPGT PPP1CB ACTR6 CNIH MAP3K10 CEP120 NAE1 MRPL30 SLC30A9NUP54 TOMM20 NPM1 CNOT2 SPAST CETN3 WDR36 MRPL39 GPR180 STX7 LRRC40 ETF1 MRPS22 UBXN2A SEPSECS GPBP1 VPS26A PCNP RSL24DCOPS1 4 LCORL PPWD1 AASDHPPT POLR3H SACM1L NMD3 C12orf29UBA5 GMCL1 DR1 EFHA1 COMMD10DIMT1 TRMT10A TBC1D23 SCYL2 TRMT10C YAF2 ZMYM6 PAPD4 DNAJB14 TXNDC9 EIF4A2 UBE2W CCNH RPF1 SRP19 C4orf29 USP33 CCT4 FASTKD2 AP3B1 TMEM14A SNX6 FBXL3 POC1B NAP1L1 FAM8A1 GTF2H1 PDCD10 ASNSD1 ECHDC1 ERGIC2 GFM2 COX7A2L PLEKHM2 PPIP5K2 ZBTB11 ARL8B PTGES3 NSA2 NDUFB5 ADD3 CAPZA2 BCLAF1 NUDCD2 ZDHHC20 ZFYVE16 SMNDC1 CCNG1SRSF3 YWHAQ PRDX3 GLRX3 SH3GL1 RNF2 FCHO2 SUCO USP15 TAF9 COPS2 TRUB1 ATE1 CYB5R4 TOMM70A PCGF5 ERLEC1 MRPL1 ATP6V1G1 PPID FNDC3A PGGT1B ABHD13 UFL1 TMEM167ANSUN3 HSPA4 CDC73 ZFR ACTR3 TMED2 NDUFAF4 FAM172A LZTFL1 LYRM7 TTC33 RCN2 MRPL50 FNIP1 MRPL35 FBXL5 MTMR6 NDUFS4 CRIPT DAPK3 BCAS2 CRBN BTF3 FOXN2 CD164 ATF1 FBXO38 HSPAZF9AND1 RWDD4 DLEU1 OSBPL8 RNASEH2B TRIM23 CNOT8 SSR3 TANK EPS15 HSPA13PLRG1 SKP1 MRPL47 C7orf60 NCOA4 WDR41 LIN7C MED7 CCNT1 RAB33B GDI2 AFF4 ANKRA2 FASTKD3ZRBMX NF277 RBM7 TXNL1 KIAA1191 ATXN7L3 MIER1 FGFR1OP2 UBE2D3SDHD DNAJA2 NDUFA5 C1D DCTNRSBN14 CANX DCLRE1A YIPF4 UBQLN1 ZDHHC8 CEPT1CGGBP1 EAF1 KATNBL1 UGGT2 CEP57 HNRNPK UBE2D1 PRKRA CALMAP3S2 1 LEMD2 SWT1 PYROXD1 BTF3L4 GORAB FBXO3 CAPZA1 DMWD TWF1 DNAJB9 SNRNP70 RMND1 LIPT1 GIN1 RSRC1 GRPEL2 BLOC1S5 LYPLAL1 TMEM182 DCUN1D1 EIF1B BLOC1S6 ARL14EP ABHD10 TADA1 TMEM168 MED2STT31 B MTRR CDC42SE2 EIF5A2 C9orf85 PCNXL3 GTPBP8 CCNI FAM96A TDRD3 FANCL RAB4AMRPS36 TAOK2 DGCR2 UBE2B ZCCHC7 UIMC1 RNF14 RNGTT TYW5 RBM22 PAFAH1B2 AZI2 C5orf15 PPP3R1 ISCA1 CAMLG MFF CCS TSN MZT1 ATG12 PFDN1 CCBL2 SNX14 SVIP ABI1 CCDC104 HNRPLL AMPD2 TTC1 RAPGEF6 ATG5 TMEM135 ARL6 JMJD8 EHBP1L1 C3orf38 PAIP1 TATDN3 MEN1 MBD3 TRIM13 KIAA0284 MOCS2 MTPN POC5 RAB10 RFK SLC38A9 ZMYM1 EFCAB7 RBM18 LZTR1 PTER MOB1A RYK TRAF2 FAM35A SMAD5 SLC9A3R2 STARD3NL ARAP1 FTSJD1 CLDND1 INTS7 MBLAC2 PLGRKT NDFIP2 RHBDD3 SPRED1 PLEKHA3 MANEA INSIG2 FAM149B1 KIF3A ANAPC13 THAP9 ANKRD13DC5orf28 C2orf49 PCBD2 TMEM128 SLC10A7 BLZF1 MRPS27 RABL3 SCYL1 LSM11 FAM60A C21orf91 CCSAP HSD17B12 FEM1C C11orf57 VPS37C POLR2M FRS2 SIPA1 AGAP3 CCDC126 UBE2E1 ZCCHC4 CCDC111 DTD2 TRIM59 THAP2 B4GALT2 IRF3 C5orf24 LIMK1TMEM104 SLC25A40 NECAP1 TCAIMTSENP8 ESK1 RAB14 KIAA1586 CTBS SIKE1 NHLRC2 MKL1 CCDC125 EML3 UBTD2 DPH3 COMMD2 DGKZ PHRF1 VEZT C18orf21 AP5B1 RAB3IP FBXL17 SMIM3

Protein homology Co-expression

Figure 12 STRING connections with functional and physical DCTN4 and correlated genes. Abbreviations: DCTN, dynactin; STRING, The Search Tool for the Retrieval of Interacting Genes/Proteins.

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