PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants

With the goal of providing a comprehensive, high-quality resource for both plant transcription factors (TFs) and their regulatory interactions with target genes, we upgraded plant TF database PlantTFDB to version 4.0 (http://planttfdb.cbi.pku.edu.cn/). In the new version, we identified 320 370 TFs from 165 species, presenting a more comprehensive genomic TF repertoires of green plants. Besides updating the pre-existing abundant functional and evolutionary annotation for identified TFs, we generated three new types of annotation which provide more directly clues to investigate functional mechanisms underlying: (i) a set of high-quality, non-redundant TF binding motifs derived from experiments; (ii) multiple types of regulatory elements identified from high-throughput sequencing data; (iii) regulatory interactions curated from literature and inferred by combining TF binding motifs and regulatory elements. In addition, we upgraded previous TF prediction server, and set up four novel tools for regulation prediction and functional enrichment analyses. Finally, we set up a novel companion portal PlantRegMap (http://plantregmap.cbi.pku.edu.cn) for users to access the regulation resource and analysis tools conveniently.

CPC2: a fast and accurate coding potential calculator based on sequence intrinsic features

With advances in next-generation sequencing technologies, numerous novel transcripts in a large number of organisms have been identified. With the goal of fast, accurate assessment of the coding ability of RNA transcripts, we upgraded the coding potential calculator CPC1 to CPC2. CPC2 runs ∼1000 times faster than CPC1 and exhibits superior accuracy compared with CPC1, especially for long non-coding transcripts. Moreover, the model of CPC2 is species-neutral, making it feasible for ever-growing non-model organism transcriptomes. A mobile-friendly web server, as well as a downloadable standalone package, is freely available at http://cpc2.cbi.pku.edu.cn.

PlantRegMap: charting functional regulatory maps in plants

With the goal of charting plant transcriptional regulatory maps (i.e. transcription factors (TFs), cis-elements and interactions between them), we have upgraded the TF-centred database PlantTFDB (http://planttfdb.cbi.pku.edu.cn/) to a plant regulatory data and analysis platform PlantRegMap (http://plantregmap.cbi.pku.edu.cn/) over the past three years. In this version, we updated the annotations for the previously collected TFs and set up a new section, ‘extended TF repertoires’ (TFext), to allow users prompt access to the TF repertoires of newly sequenced species. In addition to our regular TF updates, we are dedicated to updating the data on cis-elements and functional interactions between TFs and cis-elements. We established genome-wide conservation landscapes for 63 representative plants and then developed an algorithm, FunTFBS, to screen for functional regulatory elements and interactions by coupling the base-varied binding affinities of TFs with the evolutionary footprints on their binding sites. Using the FunTFBS algorithm and the conservation landscapes, we further identified over 20 million functional TF binding sites (TFBSs) and two million functional interactions for 21 346 TFs, charting the functional regulatory maps of these 63 plants. These resources are publicly available at PlantRegMap (http://plantregmap.cbi.pku.edu.cn/) and a cloud-based mirror (http://plantregmap.gao-lab.org/), providing the plant research community with valuable resources for decoding plant transcriptional regulatory systems.

Prognostic role of neutrophil-lymphocyte ratio in operable esophageal squamous cell carcinoma

AIM: To determine the prognostic significance of preoperative serum neutrophil-lymphocyte ratio (NLR) in esophageal squamous cell carcinoma (ESCC).

METHODS: Data from 371 eligible patients with ESCC who had undergone surgery with curative intent at our institution between October 2000 and May 2007 were retrospectively recruited for analysis. The cutoff value of NLR was 3.0 as determined by the receiver operating characteristic curve, which discriminated between survival and death; the area under the curve was 0.709, and the sensitivity and specificity were 66.1% and 69.1%, respectively, at the cutoff point. The correlation between the NLR and clinicopathological characteristics was analyzed using a χ² test. The prognostic influence of the NLR and other clinicopathological factors on cancer-specific survival (CSS) and recurrence-free survival (RFS) was studied using the Kaplan-Meier method. To evaluate the independent prognostic value of NLR, multivariate Cox regression models were applied.

RESULTS: The median age of the patients was 57.0 years, and 276/371 (74.4%) patients were male. The NLR was ≤ 3.0 in 80.1% (297/371) of the patients, and the remaining 19.9% (74/371) had an NLR > 3.0. Median postoperative follow-up was 66.0 mo [interquartile range (IQR): 49.0-76.0 mo], with a follow-up rate of 94%. Follow-up was not significantly different between patients with an NLR ≤ and > 3.0 (63.13 ± 1.64 vs 61.52 ± 3.66, P = 0.711). However, higher preoperative serum NLR was associated with significantly increased risks of higher pathological tumor status (P = 0.007). A significant, independent association between high preoperative serum NLR and poor clinical outcome was identified in a multivariate analysis for CSS (HR = 1.591; P = 0.007) and RFS (HR = 1.525; P = 0.013). Moreover, when patients were stratified by pathological tumor-node-metastasis (TNM) staging, the adverse effects of preoperative serum NLR on CSS (HR = 2.294; P = 0.008) and RFS (HR = 2.273; P = 0.008) were greatest in those patients with stage IIIA disease.

CONCLUSION: Preoperative serum NLR is a useful prognostic marker to complement TNM staging for operable ESCC patients, particularly in patients with stage IIIA disease.

MiR-629-3p-induced downregulation of SFTPC promotes cell proliferation and predicts poor survival in lung adenocarcinoma

The long-term prognosis of patients with lung cancer remains poor and thus it is imminent to further elucidate the molecular mechanism for the oncogenesis of lung cancer. In this study, we observed that surfactant protein C (SFTPC) expression was downregulated in human lung adenocarcinoma tissues and cell lines, and low SFTPC expression correlated with poor overall survival of lung adenocarcinoma patients. Moreover, we found that overexpression of SFTPC could inhibit lung cancer cell proliferation in vitro and in vivo, but downregulation of SFTPC showed the opposite results. Besides, it was observed that miR-629-3p expression was upregulated in human lung adenocarcinoma tissues and cell lines. More importantly, we found that miR-629-3p could downregulate SFTPC expression by directly binding to the SFTPC 3'-UTR and inhibit the regulatory effect of SFTPC on lung adenocarcinoma cell proliferation. In conclusion, these data suggested that miR-629-3p-meditated downregulation of SFTPC may promote lung adenocarcinoma progression.

Preoperative level of serum amyloid A is superior to C-reactive protein in the prognosis of esophageal squamous cell carcinoma

Preoperative elevations in the levels of serum amyloid A (SAA) or C-reactive protein (CRP) have been reported to be prognostic indicators in several malignancies. The aim of this study is to evaluate the serum levels of SAA and CRP in the prognosis of esophageal squamous cell carcinoma (ESCC). In total, 252 patients with ESCC who had undergone surgery with curative-intent were retrospectively recruited. The specificity, sensitivity, and prognostic value of SAA or CRP levels were measured as the area under the receiver operating characteristic (ROC) curve (AUC). The clinical value of SAA and CRP levels as prognostic indicators was evaluated using Cox's proportional hazards model. The 1-, 3-, and 5-year overall survival (OS) rates for the entire cohort of patients with ESCC were 71.0%, 61.0%, and 43.0%, respectively. The correlation between the levels of SAA and CRP was significant (r(2) = 0. 685, P < 0.001). The ROC analysis showed that the levels of CRP were associated with a significantly lower overall accuracy than were the SAA levels (AUC, 0.615 vs. 0.880; P < 0.001). For the complete cohort, the median OS was 52.0 months longer in patients with low preoperative serum levels of SAA (72.0 months) compared with patients who had high SAA levels (20.0 months, P < 0.001). The median OS among patients with low CRP levels was also longer compared with the patients who had high CRP levels (72.0 vs. 51.0 months, respectively; P < 0.001). Subgroup analyses showed that the preoperative elevated levels of SAA could find significant differences in OS for stage I, stage II, and stage III (P < 0.001, P = 0.001, and P < 0.001, respectively), whereas the increased levels of CRP could only find a difference in OS for stage II cancers. After a multivariate analysis, preoperative elevated level of SAA was found to be an independently and significant prognostic factor (P < 0.001). Our study indicates that the preoperative levels of SAA and CRP can act as prognostic factors, and that elevated levels of these proteins are associated with negative effects on the survival of patients with ESCC. SAA showed a higher prognostic value than CRP in both cohort and subgroup analysis.

DUS4L Silencing Suppresses Cell Proliferation and Promotes Apoptosis in Human Lung Adenocarcinoma Cell Line A549

Purpose

This study aims to investigate the potential role of DUS4L (dihydrouridine synthase 4 like) in lung adenocarcinoma (LUAD) and explore its associated pathways in human LUAD.

Methods

Firstly, we evaluated the relationships between clinicopathological characteristics and DUS4L expression via analysis of TCGA RNA sequencing data and other publicly available databases. Then, DUS4L was effectively silenced in LUAD cell line A549 using the lentiviral shRNA (short-hairpin RNA) transfection to assess its effects on cell proliferation, cycle and apoptosis in LUAD cells. RNA-seq technology was applied to shDUS4L and shCtrl-transfected cells to generate the corresponding gene expression profiles. Differentially expressed genes (DEGs) were identified using the DESeq2 program package. Also, DEGs were subjected to Gene Ontology (GO) and KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analysis to explore the associated molecular signaling pathways and relevant biological functions.

Results

Analysis of TCGA data revealed that DUS4L was highly upregulated in LUAD tissues which was related to clinical T and TNM stages of LUAD. The knockdown of DUS4L effectively inhibited cell proliferation and promoted apoptosis in A549 cells. Furthermore, the DEGs between the shDUS4L and shCtrl A549 cells were mainly enriched in biological processes associated with spliceosome, ribosome, RNA catabolic process, ncRNA (non-coding RNA) processing, and p53 signaling pathway.

Conclusion

Altogether, our results suggest that DUS4L is significantly associated with tumorigenesis and could be utilized as a novel biomarker and therapeutic target for LUAD.

PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants

With the goal of providing a comprehensive, high-quality resource for both plant transcription factors (TFs) and their regulatory interactions with target genes, we upgraded plant TF database PlantTFDB to version 4.0 (http://planttfdb.cbi.pku.edu.cn/). In the new version, we identified 320 370 TFs from 165 species, presenting a more comprehensive genomic TF repertoires of green plants. Besides updating the pre-existing abundant functional and evolutionary annotation for identified TFs, we generated three new types of annotation which provide more directly clues to investigate functional mechanisms underlying: (i) a set of high-quality, non-redundant TF binding motifs derived from experiments; (ii) multiple types of regulatory elements identified from high-throughput sequencing data; (iii) regulatory interactions curated from literature and inferred by combining TF binding motifs and regulatory elements. In addition, we upgraded previous TF prediction server, and set up four novel tools for regulation prediction and functional enrichment analyses. Finally, we set up a novel companion portal PlantRegMap (http://plantregmap.cbi.pku.edu.cn) for users to access the regulation resource and analysis tools conveniently.

Clinicopathological and prognostic significance of epithelial cell transforming sequence 2 expression in cancers: a systematic review and meta-analysis

Numerous studies have investigated the prognostic significance of ECT2 (epithelial cell transforming sequence 2) expression in patients with cancer. Nevertheless, conflicting results have been obtained. We thus performed a meta-analysis to systematically assess the prognostic significance of ECT2 in cancer. Electronic databases (PubMed and EMBASE) were searched for eligible studies. Hazard ratios (HR) and odds ratios (OR) with 95% confidence intervals (CIs) were used to estimate effect sizes. A total of 5,305 patients from 19 articles and 21 studies were included. The pooled results revealed that high ECT2 expression was correlated with advanced TNM stage (OR = 2.17; 95% CI: 1.42-3.32), positive lymph node metastasis (OR = 2.98; 95% CI: 2.28-3.89), distant metastasis (OR = 2.25; 95% CI: 1.03-4.92), and poor tumour differentiation (OR = 2.25; 95% CI: 1.03-4.92). More importantly, high ECT2 expression was significantly associated with poor overall survival (HR = 2.26; 95% CI, 1.84-2.78) and recurrence-free survival (HR = 1.52; 95% CI, 1.24-1.86). Our results suggested that ECT2 is a promising prognostic indicator and therapeutic target for cancer.

Non-invasive Assessment of Human Epidermal Growth Factor Receptor 2 Expression in Gastric Cancer Based on Deep Learning: A Computed Tomography-based Multicenter Study

RATIONALE AND OBJECTIVES

The expression of human epidermal growth factor receptor 2 (HER2) in gastric cancer is closely associated with its treatment outcomes and prognosis. This study aims to develop and validate a HER2 prediction model based on computed tomography (CT). Additionally, the study evaluates the robustness of the proposed model.

MATERIALS AND METHODS

This retrospective study included 1059 patients from three hospitals (A, B, and C), where patients from hospitals A and B formed the training set (720 cases), and patients from hospital C served as the external test set (339 cases). Venous-phase CT radiomic features were extracted, normalized using the Z-score method, and simplified via principal component analysis. Feature selection was performed using recursive feature elimination (RFE), analysis of variance, Relief, and the Kruskal-Wallis (KW) test, followed by modeling using Lasso-regularized logistic regression and Support Vector Machine (SVM) methods. The models were evaluated and validated using the area under the curve (AUC) and decision curve analysis to determine the best-performing model.

RESULTS

The positive proportions of HER2 expression were 8.60% (52/658) in the training set and 5.60% (19/320) in the test set. Eight distinct models were developed to predict HER2 expression. Among these, the model utilizing RFE and Lasso-regularized logistic regression (LR-Lasso) exhibited the highest predictive performance, with AUC values of 0.7874 (95% CI: 0.7346-0.8402) in the training set and 0.8033 (95% CI: 0.7288-0.8788) in the test set. Compared to other models, this model provided a greater net benefit on the decision curve analysis. These results suggest that the proposed model can be effectively applied to predict HER2 expression in patients.

CONCLUSION

The HER2 prediction model demonstrated promising performance in predicting HER2 expression in gastric cancer patients.

[Association between cord blood BPDE-DNA and neurodevelopment of children aged 0 and 2 years: A birth cohort study]

Objective: To explore the effects of mothers' exposure to polycyclic aromatic hydrocarbons during pregnancy on their children's neurobehavioral development. Methods: In November 2009 to April 2010, a total of 221 pairs of mother-newborn pairs were recruited from two cooperative hospitals in Taiyuan, and their children were followed up at age two. High performance liquid chromatography was used to determine the level of BPDE-DNA in cord blood leukocytes. The Neonatal behavioral neurological assessment (NBNA) was used to assess the neurodevelopment of newborns, and the Gesell Development Scale was used to measure neurodevelopmental indexes of 2-year-old children. NBNA includes behavior, active and passive tone, primitive reflexes and general assessment, with a total score of 40 points. The Gesell Developmental Schedules consisted of four sub-scales: motor development, adaptive behavior development, language development and personal-social behavior development. We used mean and standard deviation to describe continuous variables with normal distribution, median (interquartile range) to describe continuous variables with skewed distribution, and frequency and proportion to describe categorical variables. Restricted cubic spline models were applied to assess the dose-response relationships between maternal prenatal polycyclic aromatic hydrocarbons exposure and children's neurobehavioral development at two years old. Generalized linear models were applied to evaluate the effect of exposure to maternal prenatal polycyclic aromatic hydrocarbons exposure on children's neurobehavioral development at 0 and two years old. Results: The NBNA score was 38.0±0.8, and the scores of 2-year-old children's motor, adaptive, language and personal-social were 111.6±15.0, 110.5±14.6, 108.8±17.2 and 111.7±14.5, respectively. After adjusting for confounding factors, there is no dose-response association between the cord blood BPDE of pregnant women and neonatal NBNA scores, but there were dose-response associations between BPDE and scores of 2-year-old children's motor, adaptive, language and personal-social. A unit increase in cord blood ln (BPDE-DNA), the score of motor, adaptive, language and personal-social of 2-year-old children decreased on average by 4.54、6.29、8.41 and 7.02 points. Conclusion: Maternal exposure to polycyclic aromatic hydrocarbons during pregnancy is associated with decreased children's neurobehavioral development at two years old.

DUS4L suppresses invasion and metastasis in LUAD via modulation of PI3K/AKT and ERK/MAPK signaling through GRB2

OBJECTIVE

Limited research has focused on the role of dihydrouridine synthases (DUS) family members in human tumors. Our previous findings indicated an impact of dihydrouridine synthase 4 like (DUS4L) on cell proliferation and apoptosis in lung adenocarcinoma (LUAD) A549 cell, yet its broader functions and regulatory mechanisms in LUAD remain elusive.

METHODS

Using a LUAD tissue microarray and immunohistochemical (IHC) staining, we validated variations in DUS4L protein expression levels among LUAD patients and assessed its clinical significance. Additional experiments using short hairpin RNA (shRNA) against DUS4L (sh-DUS4L-2), LUAD cell lines, cell function assays (including wound healing, transwell migration and invasion, colony formation, and apoptosis assays), and mouse tumor xenografts were performed to examine the biological roles of DUS4L in LUAD progression. RNA sequencing, proteomic analyses, mass spectrometry, and co-immunoprecipitation experiments were conducted to identify and validate DUS4L-regulated downstream target genes and signaling pathways.

RESULTS

We identified a consistent upregulation of DUS4L in LUAD tissues. In vitro and in vivo experiments underscored the inhibitory effect of DUS4L downregulation on LUAD progression, including migration, invasion, and proliferation. Mechanistically, DUS4L was found to interact with the signaling molecule GRB2, promoting LUAD progression and metastasis by inducing epithelial-mesenchymal transition (EMT) via the PI3K/AKT and ERK/MAPK pathways.

CONCLUSION

Our results establish the functional role of DUS4L in driving the progression and metastasis of LUAD, implicating its potential as a candidate therapeutic target for LUAD.

Melittin kills A549 cells by targeting mitochondria and blocking mitophagy flux

Melittin, a naturally occurring polypeptide found in bee venom, has been recognized for its potential anti-tumor effects, particularly in the context of lung cancer. Our previous study focused on its impact on human lung adenocarcinoma cells A549, revealing that melittin induces intracellular reactive oxygen species (ROS) burst and oxidative damage, resulting in cell death. Considering the significant role of mitochondria in maintaining intracellular redox levels and ROS, we further examined the involvement of mitochondrial damage in melittin-induced apoptosis in lung cancer cells. Our findings demonstrated that melittin caused changes in mitochondrial membrane potential (MMP), triggered mitochondrial ROS burst (Figure 1), and activated the mitochondria-related apoptosis pathway Bax/Bcl-2 by directly targeting mitochondria in A549 cells (Figure 2). Further, we infected A549 cells using a lentivirus that can express melittin-Myc and confirmed that melittin can directly target binding to mitochondria, causing the biological effects described above (Figure 2). Notably, melittin induced mitochondrial damage while inhibiting autophagy, resulting in abnormal degradation of damaged mitochondria (Figure 5). To summarize, our study unveils that melittin targets mitochondria, causing mitochondrial damage, and inhibits the autophagy-lysosomal degradation pathway. This process triggers mitoROS burst and ultimately activates the mitochondria-associated Bax/Bcl-2 apoptotic signaling pathways in A549 cells.

[Parenteral magnesium sulfate exerts no central anticonvulsant action]

It was said that parenteral magnesium (MS) had a central anticonvulsant action responsible for controlling seizures in eclampsia of pregnancy. The present study was carried out to examine this statement. In conscious rabbits, MS 214 mg.kg-1 iv quickly relieved them from convulsion induced by sc pentylenetetrazol, yet spikes of high frequency in electrocorticogram burst inceasingly. Judging from electrocorticogram changes, MS 220 mg.kg-1 iv did not raise the electroshock seizure threshold. In mice, MS 430 mg.kg-1 did not significantly increase the LD50 of ip pentylenetetrazol. However, in anesthetized rats, MS 250 mg.kg-1 ip lowered the hypertensive response to angiotensin amide and norepinephrine. These results indicated that parenterally administered MS exerted no demonstrable central anticonvulsant action, and its benefits gained in the treatment of eclampsia of pregnancy might derive from its peripheral action, such as reduction of vascular response to pressor substances.

SYNGR2 serves as a prognostic biomarker and correlates with immune infiltrates in esophageal squamous cell carcinoma

BACKGROUND

Synaptogyrin-2 (SYNGR2) plays an important role in regulating membrane traffic in nonneuronal cells. However, the role of SYNGR2 in esophageal squamous cell carcinoma (ESCC) remains unclear.

METHODS

All original data were downloaded from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases and integrated via R 3.5.3. SYNGR2 expression was explored in the TCGA and GEO databases. The correlations between SYNGR2 and cancer immune characteristics were analyzed via the TIMER and TISIDB databases.

RESULTS

In general, SYNGR2 was predominantly overexpressed and had reference value in the diagnosis and prognostic estimation of ESCC. Upregulated SYNGR2 was associated with poorer overall survival, poorer disease-specific survival and T stage in ESCC. Mechanistically, we identified hub genes that included a total of 38 SYNGR2-related genes, which were tightly associated with the protein polyubiquitination pathway in ESCC patients. SYNGR2 expression was negatively related to the infiltrating levels of T helper cells. SYNGR2 methylation was positively correlated with the expression of chemokines (CCL2 and CXCL12), chemokine receptors (CCR1 and CCR2), immunoinhibitors (CXCL12 and TNFRSF4) and immunostimulators (CSF1R and PDCD1LG2) in ESCC.

CONCLUSION

SYNGR2 may be used as a biomarker for determining prognosis and immune infiltration in ESCC.

Short-term outcomes of robot-assisted versus thoracoscopic-assisted Mckeown esophagectomy

BACKGROUND

Thoracoscopic-assisted and robot-assisted Mckeown esophagectomy are currently two common surgical methods, but there is no clear statement on the advantages and disadvantages of the two.

METHODS

This study conducted a single-centre retrospective analysis of esophageal cancer patients diagnosed and treated at Lanzhou University Second Hospital from 1 February 2020 to 31 July 2022. According to the inclusion and exclusion criteria, 126 patients were finally included in the RAM group and 169 patients in the TAM group.

RESULTS

There was no significant difference between the RAM and TAM groups in the number of lymph node dissections, operative time, the length of stay in the intensive care unit after surgery, the incidence of hoarseness, postoperative pulmonary complications, surgery-related complications, use of opioids after surgery, the length of postoperative hospital stay, and 30-day mortality.

CONCLUSIONS

RAM is a minimally invasive alternative to TAM and has similar short-term oncological efficacy.

PYCR1 Promotes Esophageal Squamous Cell Carcinoma by Interacting With EGFR to Affecting the PI3K/Akt/mTOR Signaling Pathway

BACKGROUND

The expression and functional role of pyrroline-5-carboxylate reductase 1 (PYCR1) in esophageal squamous cell carcinoma (ESCC) remain poorly understood. This study aimed to elucidate the role and underlying mechanisms of PYCR1 in ESCC.

METHODS

We utilized an ESCC tissue microarray coupled with immunohistochemical staining to assess variability in PYCR1 protein expression among ESCC patients and evaluate its clinical relevance. PYCR1 was silenced in ESCC cell lines with short hairpin RNA (shRNA), followed by functional assays (colony formation, caspase 3/7 activity, methylthiazol tetrazolium, wound healing, and migration/invasion assays) to evaluate its role in ESCC progression. In vivo, mouse tumor xenograft models were used to examine PYCR1's impact on tumor growth. To identify downstream targets and pathways, we conducted coimmunoprecipitation, mass spectrometry, immunofluorescence, and proteomic analyses, validated by western blotting and rescue experiments.

RESULTS

Our findings demonstrated a consistent upregulation of PYCR1 in ESCC tissues. Both in vitro and in vivo studies revealed that PYCR1 suppression significantly inhibited ESCC progression, impacting key processes such as proliferation, apoptosis, migration, and invasion. Mechanistically, PYCR1 was shown to interact with EGFR, promoting ESCC progression and metastasis by activating the PI3K/AKT/mTOR signaling pathways, which are integral to the aggressive behavior of the disease. Rescue experiments further confirmed that EGFR overexpression effectively reversed the inhibitory effects of PYCR1 knockdown in ESCC cells.

CONCLUSION

This study highlights the critical role of PYCR1 in driving ESCC progression and metastasis, underscoring its potential as a promising therapeutic target for managing this malignancy.

Analysis and identification of potential biomarkers for dysfunctional uterine bleeding

Clinical evidence increasingly suggests that traditional treatments for dysfunctional uterine bleeding (DUB) have limited success. In this study, blood samples from 10 DUB patients and 10 healthy controls were collected for transcriptome sequencing. Then, the differentially expressed genes (DEGs) were screened and crossed with the DUB-related module genes to obtain the target genes. These target genes were analyzed for functional enrichment. Further, the biomarkers were screened by protein-protein interaction (PPI) analysis and analyzed by the gene set enrichment analysis (GSEA) and ingenuity pathway analysis (IPA). To explore the pathogenesis of DUB, immune microenvironment analyses were also performed. Potential drugs targeting these biomarkers were predicted for clinical treatment. The expression of these biomarkers was validated using quantitative real-time polymerase chain reaction (qRT-PCR). The results showed that, a total of 754 target genes were found to be related to cell proliferation and senescence. Five biomarkers-CENPE, KIF11, PIK3R1, SMC3, and SMC4-were identified, all of which were down-regulated in the DUB group, and most of these findings were confirmed by qRT-PCR. Notably, CENPE expression showed a negative association with activated NK cells and a positive association with resting NK cells. In addition, 44 potential drugs were predicted for DUB treatment. In conclusion, five DUB biomarkers were identified, enhancing understanding of gene regulation in DUB and providing a theoretical foundation for clinical diagnosis and treatment.