bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Small Tumor Antigen of Merkel Cell Polyomavirus Accomplishes Cellular Transformation by Uniquely Localizing to the Nucleus Despite the Absence of a Known Nuclear Localization Signal
Authors: Thevenin Kaira R. , Tieche Isabella S. , Benedetto Cody E. , Schrager Matt , Dye Kristine N. 
Published: November 2023

Abstract
Background: Merkel Cell Carcinoma (MCC) is an aggressive skin cancer that is three times deadlier than melanoma. In 2008, it was found that 80% of MCC cases are caused by the genomic integration of a novel polyomavirus, Merkel Cell Polyomavirus (MCPyV), and the expression of its small and truncated large tumor antigens (ST and LT-t, respectively). MCPyV belongs to a family of human polyomaviruses; however, it is the only one with a clear association to cancer.
Methods: To investigate the role and mechanisms of various polyomavirus tumor antigens in cellular transformation, Rat-2, 293A, and human foreskin fibroblasts were transduced with pLENTI MCPyV LT-t, MCPyV ST, TSPyV ST, HPyV7 ST, or empty pLENTI and assessed through multiple transformation assays, mass spectrometry, and subcellular fractionations. One-way ANOVA tests were used to assess statistical significance.
Results: Soft agar, proliferation, doubling time, glucose uptake, and serum dependence assays confirmed ST to be the dominant transforming protein of MCPyV. Furthermore, it was found that MCPyV ST is uniquely transforming, as the ST antigens of other non-oncogenic human polyomaviruses such as Trichodysplasia Spinulosa Polyomavirus (TSPyV) and Human Polyomavirus 7 (HPyV7) were not transforming when similarly assessed. Identification of structural dissimilarities between transforming and non-transforming tumor antigens revealed that the uniquely transforming domain(s) of MCPyV ST are likely located within the structurally dissimilar loops of the MCPyV ST unique region. Of all potential MCPyV ST cellular interactors, 62% are exclusively or transiently nuclear, suggesting that MCPyV ST localizes to the nucleus despite the absence of a canonical nuclear localization signal. Indeed, subcellular fractionations confirmed that MCPyV ST could achieve nuclear localization through a currently unknown, regulated mechanism independent of its small size, as HPyV7 and TSPyV ST proteins were incapable of nuclear translocation. Although nuclear localization was found to be important for several transforming properties of MCPyV ST, some properties were also performed by a cytoplasmic sequestered MCPyV ST, suggesting that MCPyV ST may perform different transforming functions in individual subcellular compartments.
Conclusions: Together, these data further elucidate the unique differences between MCPyV ST and other polyomavirus ST proteins necessary to understand MCPyV as the only known human oncogenic polyomavirus.
MicroRNA3650 Promotes Gastric Cancer Proliferation and Migration
through the PTEN/PI3K-AKT-mTOR and Hippo Pathways
Authors: Yang Xiansheng , Wen Juncai , He Qingjun , Wang Shuoshan , Ruan Qiang , Liao Quanxing , He Jinfu , Fang Shuxian , Liu Chang , Tang Hongsheng 
Published: November 2023

Background::
Gastric cancer (GC) is a malignant tumor with seriously poor outcomes.
Studies have shown that microRNAs (miRNAs) play an omnifarious regulatory effect in GC.
However, the role of miR-3650 in the progression of GC is not well known.

Methods::
In this study, miR-3650 expression and its clinical significance were determined using
clinical specimens. The biological functions of miR-3650 were determined in gastric cancer cell
lines through CCK-8, cell scratch, and transwell experiments. Bioinformatics predictions, combined
with Western blot experiments, were employed to explore its downstream molecular targets.

Results::
We observed that miR-3650 was overexpressed in GC specimens and most cell lines, i.e.,
77.8% (MKN28, SNU1, AGS, MKN45, N87, BGC823 and SGC7901). The overexpression correlated
with advanced T-stage, N-stage, M-stage, and TNM-stage. Furthermore, miR-3650 promoted
the proliferation and migration of gastric cancer cells, and its overexpression promoted the
PI3K-AKT-mTOR pathway and inhibited the PTEN and hippo pathways. The potassium ion signaling
pathway was also involved in the biological process of miR-3650 promoting cancer.

Conclusion::
Therefore, we concluded that miR-3650/PTEN/PI3K-AKT-mTOR and
miR-3650/hippo pathways are vital in the progression of GC and serve as novel targets for GC
therapy.
Bioinformatics-based Analysis and Verification of Chromatin Regulators and the Mechanism of Immune Infiltration Associated with Myocardial Infarction
Authors: Zhao Huanyi , Tang Na , Xu Liang , Li Junlong , Pi Jianbin , Chu Qingmin 
Published: November 2023

Background:
Recent studies have shown that dysfunction in chromatin regulators
(CRs) may be an important mechanism of myocardial infarction (MI). They are thus expected
to become a new target in the diagnosis and treatment of MI. However, the diagnostic value of
CRs in MI and the mechanisms are not clear.

Methods:
CRs-related differentially expressed genes (DEGs) were screened between healthy
controls and patients with MI via GSE48060, GSE60993, and GSE66360 datasets. DEGs were
further analyzed for enrichment analysis. Hub genes were screened by least absolute shrinkage
and selection operator (LASSO) regression and weighted gene co-expression network analysis
(WGCNA). GSE61144 datasets were further used to validate hub genes. RT-qPCR examined
peripheral blood mononuclear cells (PBMCs) to verify expressions of hub genes. In addition, a
correlation between hub genes and immune cell infiltration was identified by CIBERSORT
and single-sample gene set enrichment analysis (ssGSEA). Finally, we constructed a diagnostic
nomogram and ceRNA network and found possible therapeutic medicines which were
based on hub genes.

Results:
Firstly, 16 CR-related DEGs were identified. Next, Dual-specificity phosphatase 1
(DUSP1), growth arrest and DNA damage-inducible 45 (GADD45A), and transcriptional regulator
Jun dimerization protein 2 (JDP2) were selected as hub genes by LASSO and WGCNA.
Receiver operating characteristic curves in the training and test data sets verified the reliability
of hub genes. Results of RT-qPCR confirmed the upregulation of hub genes in MI. Subsequently,
the immune infiltration analysis indicated that DUSP1, GADD45A, and JDP2 were
correlated with plasmacytoid dendritic cells, natural killer cells, eosinophils, effector memory
CD4 T cells, central memory CD4 T cells, activated dendritic cells, and activated CD8 T cells.
Furthermore, a nomogram that included DUSP1, GADD45A, and JDP2 was created. The calibration
curve, decision curve analysis, and the clinical impact curve indicated that the nomogram
could predict the occurrence of MI with high efficacy. The results of the ceRNA network
suggest that hub genes may be cross-regulated by various lncRNAs and miRNAs. In addition,
10 drugs, including 2H-1-benzopyran, Nifuroxazide, and Bepridil, were predicted to be potential
therapeutic agents for MI.

Conclusion:
Our study identifies three promising genes associated with the progression of
chromatin regulators (CRs)-related myocardial infarction (MI) and immune cell infiltration, including
Dual-specificity phosphatase 1 (DUSP1), growth arrest and DNA damage-inducible 45
(GADD45A), and Jun dimerization protein 2 (JDP2), which might be worthy of further study.
Differential miRNA Profiling Reveals miR-4433a-5p as a Key Regulator of
Chronic Obstructive Pulmonary Disease Progression via PIK3R2-
mediated Phenotypic Modulation
Authors: Tao Siming , Liao Chunyan , Wang Yide , Xu Dan , Li Zheng , Li Fengsen 
Published: November 2023

Objective:
In this study, a high-throughput sequencing technology was used to screen
the differentially expressed miRNA in the patients with "fast" and "slow" progression of chronic
obstructive pulmonary disease (COPD). Moreover, the possible mechanism affecting the progression
of COPD was preliminarily analyzed based on the target genes of candidate miRNAs.

Methods:
The "fast" progressive COPD group included 6 cases, "slow" and Normal progressive
COPD groups included 5 cases each, and COPD group included 3 cases. The peripheral blood
samples were taken from the participants, followed by total RNA extraction and high throughput
miRNA sequencing. The differentially expressed miRNAs among the progressive COPD groups
were identified using bioinformatics analysis. Then, the candidate miRNAs were externally verified.
In addition, the target gene of this miRNA was identified, and its effects on cell activity,
cell cycle, apoptosis, and other biological phenotypes of COPD were analyzed.

Results:
Compared to the Normal group, a total of 35, 16, and 7 differentially expressed miRNAs
were identified in the "fast" progressive COPD, "slow" progressive COPD group, and
COPD group, respectively. The results were further confirmed using dual-luciferase reporter assay
and transfection tests with phosphoinositide- 3-kinase, regulatory subunit 2 (PIK3R2) as a
target gene of miR-4433a-5p; the result showed a negative regulatory correlation between the
miRNA and its target gene. The phenotype detection showed that the activation of the phosphatidylinositol
3 kinase (PI3K)/protein kinase B (AKT) signaling pathway might participate in the
progression of COPD by promoting the proliferation of inflammatory A549 cells and inhibiting
cellular apoptosis.

Conclusions:
MiR-4433a-5p can be used as a marker and potential therapeutic target for the
progression of COPD. As a target gene of miR-4433a-5p, PIK3R2 can affect the progression of
COPD by regulating phenotypes, such as cellular proliferation and apoptosis.
Exploring Asthma Mechanism of Belamcanda Chinensis by “Dose–effect Weighted Coefficient” Network Pharmacology and Experiment Validation
Authors: Zhang Kaiyue , Lv Jingwei , Shen Jiaming , Zhang Nanxi , Gao Xiaochen , Wang Yuelong , Li Chunnan , Sun Jiaming 
Published: November 2023

Background:
Asthma is a chronic inflammatory disease of the airways that seriously
endangers human health. Belamcanda chinensis (BC), a traditional Chinese medicine, has been
used to counteract asthma as it has been shown to possess anti-inflammatory and regulatory immunity
properties.

Objective::
The study aimed to investigate the mechanisms of action of BC in the treatment of
asthma; a “dose–effect weighted coefficient” network pharmacology method was established to
predict potential active compounds.

Methods:
Information on the components and content of BC was obtained by UPLC-QEOrbitrap-
MS spectrometry. Based on BC content, oral bioavailability, and molecular docking
binding energy, dose-effect weighting coefficients were constructed. With the degree greater than
average as the index, a protein–protein interaction (PPI) database was used to obtain the core key
targets for asthma under dose–effect weighting. GO function and KEGG pathway analyses of the
core targets were performed using DAVID software. Finally, MTT and ELISA assays were used
to assess the effects of active components on 16HBE cell proliferation.

Results:
The experimental results using the 16HBE model demonstrated BC to have a potential
protective effect on asthma. Network pharmacology showed SYK, AKT1, and ALOX5 to be the
main key targets, and Fc epsilon RI as the promising signaling pathway. Eight components, such
as tectoridin, mangiferin, luteolin, and isovitexin were the main active compounds, Finally, we
analyzed the LPS-induced 16HBE proliferation of each active ingredient. Based on the activity
verification study, all five predicted components promoted the proliferation of 16HBE cells. These
five compounds can be used as potential quality markers for asthma.

Conclusion:
This study provides a virtual and practical method for the simple and rapid screening
of active ingredients in natural products.
Transcutaneous Electrical Acupoint Stimulation Improves Postoperative Nutrition and Promotes Early Recovery of Gastrointestinal Function in Patients with Colorectal Cancer
Authors: Li Xia , Kou Zhijian , Liu Ruijuan , Zhou Zhendong , Mei Ju , Yan Wenjun 
Published: November 2023

Objective:
To investigate the effect of transcutaneous electrical acupoint stimulation
(TEAS) on the postoperative nutritional status and recovery of gastrointestinal function in colorectal
cancer patients.

Methods:
Sixty-five patients with ASA grade I-II, undergoing laparoscopic radical colorectal
cancer surgery under elective general anesthesia were selected. They were divided into two
groups according to the random number table method: the TEAS group (T group) and the sham
stimulation group (S group). Two groups of patients were given separate transcutaneous electrical
acupoint stimulation and sham stimulation for 30 min at the Hegu (LI4), Neiguan (PC6),
Zusanli (ST36), Shangjuxu (ST37), Xiajuxu (ST39), and Sanyinjiao (SP6) points. The intervention
time point from the day before surgery, 30 minutes before the start of anesthesia induction,
at the start of skin incision, and at the end of surgery to the first, second, and third postoperative
days. Changes in serum total protein (TP), albumin (ALB), prealbumin (PA), and transferrin
(TRF) were observed, postoperative recovery of gastrointestinal function, and the incidence of
postoperative complications were observed.

Results:
There was no statistical difference between the general data of the two groups; TP, ALB,
PA, and TRF in both groups decreased significantly (P<0.05) on postoperative day 1 and 3 compared
with those on preoperative day 1. TP, ALB, PA, and TRF were significantly higher in patients
in group T than in group S on postoperative days 3 and 7, and the differences were statistically
significant (P<0.05). The time to first ventilation, time to defecation, and time to liquid diet were
all significantly shorter in group T than in group S. The difference was statistically significant
(P<0.05). The incidence of postoperative nausea, vomiting, and abdominal distension was significantly
lower in group T than in group S, with a significant statistical difference (P<0.05).

Conclusion:
Transcutaneous electrical acupoint stimulation can improve postoperative serum
protein levels and promote postoperative early recovery in patients with colorectal cancer.
Ziyin Bushen Fang improves Diabetic Osteoporosis by Inhibiting Autophagy
and Oxidative Stress In vitro and In vivo
Authors: Jiang Bo , Mou Yan Jie , Zhang Xian Mei , Lu Kun , Xie Ping , Rao Yan Ling , Cong Ze Wei , Sun Qin guo 
Published: November 2023

Objective::
Diabetic osteoporosis (DOP) belongs to the group of diabetes-induced secondary
osteoporosis and is the main cause of bone fragility and fractures in many patients with
diabetes. The aim of this study was to determine whether Ziyin Bushen Fang (ZYBSF) can improve
DOP by inhibiting autophagy and oxidative stress.

background:
The aim of this experiment is to study whether Ziyin Bushen Fang (ZYBSF) can treat DOP through autophagy and oxidative stress.

Methods::
Type 1 diabetes mellitus (T1DM) was induced in rats using a high-fat high-sugar diet
combined with streptozotocin. Micro-CT scanning was used to quantitatively observe changes in
the bone microstructure in each group. Changes in the serum metabolites of DOP rats were analyzed
using UHPLC-QTOF-MS. The DOP mouse embryonic osteoblast precursor cell model
(MC3T3-E1) was induced using high glucose levels.

Results::
After ZYBSF treatment, bone microstructure significantly improved. The bone mineral
density, trabecular number, and trabecular thickness in the ZYBSF-M and ZYBSF-H groups significantly
increased. After ZYBSF treatment, the femur structure of the rats was relatively intact,
collagen fibers were significantly increased, and osteoporosis was significantly improved. A total
of 1239 metabolites were upregulated and 1527 were downregulated in the serum of T1DM and
ZYBSF-treated rats. A total of 20 metabolic pathways were identified. In cellular experiments,
ZYBSF reduced ROS levels and inhibited the protein expression of LC3II / I, Beclin-1, and p-
ERK.

Conclusion::
ZYBSF may improve DOP by inhibiting the ROS/ERK-induced autophagy signaling
pathway.
Acupuncture Increased the Number of Retrieved Oocytes in a Mouse Model of POR: The Involvement of DNA Methylation in the Oocytes
Authors: Wang Mengjing , Li Zimeng , Xiong Yueheng , Yuan Rongli , Zhu Xinyun , Chen Xin , Wang Tianyu , Li Zhi , Wu Jie 
Published: November 2023

Background:
Poor ovarian response (POR) reduces the success rate of in vitro fertilization
mainly because of fewer oocytes retrieved. Acupuncture (Ac) therapy can improve the number
of retrieved oocytes in the controlled ovarian stimulation program. The role of Ac in the corresponding
epigenetic mechanism of POR has not been studied.

Objective:
This study was conducted to determine the effect of Ac on the number of retrieved
oocytes and its role in DNA methylation in a mouse model of POR.

Methods::
Forty C57BL/6N female mice with normal estrous cycles were randomly classified into
4 groups of 10 each: control (Con) group, Ac-Con group, POR group, and Ac-POR group. Mice
in POR and Ac-POR groups received a gastric gavage of Tripterygium wilfordii polyglycoside
suspension of 50 mg/kg-1 once a day for 14 consecutive days. Ac was applied at “Shenting” (DU
24), “Guanyuan” (CV 4), “Zusanli” (ST 36), and “Shenshu” (BL 23) in the Ac-POR group for 10
min per session, once a day for 14 consecutive days. All four groups were stimulated with pregnant
mare serum gonadotropin and human chorionic gonadotropin, and the number of retrieved oocytes
and proportion of mature oocytes were recorded. The DNA methylation level in a single mouse
oocyte in each group was analyzed using single-cell genome-wide bisulfite sequencing (scBSseq),
and key pathways were identified using GO and KEGG enrichment analyses.

Results:
A dissecting microscope revealed that the Ac therapy improved the number of retrieved
oocytes compared with the POR group (p < 0.05). ScBS-seq showed that there was no significant
change in global DNA methylation levels between the POR model and control group mice. However,
differences were primarily observed in the differentially methylated regions (DMRs) of each
chromosome, and Ac decreased global DNA methylation. DMR analysis identified 13 genes that
may be associated with Ac treatment. Cdk5rap2 and Igf1r, which mediate germ cell apoptosis,
growth, and development, maybe most closely related to the Ac treatment of POR. KEGG analysis
revealed that differentially expressed genes were mainly enriched in Wnt, GnRH, and calcium
signaling pathways. The genes were closely related to the regulation of POR via Ac.

Conclusion:
The results suggest that DNA methylation in oocytes is related to the development
of POR and that the role of Ac in affecting DNA methylation in oocytes is associated with the
Wnt, GnRH, and calcium signaling pathways as well as Cdk5rap2 and Igf1r in POR mice.
Establishment and Validation of the Novel Necroptosis-related Genes for Predicting Stemness and Immunity of Hepatocellular Carcinoma via Machine-learning Algorithm
Authors: Li Yao-Ting , Zeng Xue-Zhen 
Published: November 2023

Background:
Necroptosis, a recently identified mechanism of programmed cell death,
exerts significant influence on various aspects of cancer biology, including tumor cell proliferation,
stemness, metastasis, and immunosuppression. However, the role of necroptosis-related
genes (NRGs) in Hepatocellular Carcinoma (HCC) remains elusive.

Methods:
In this study, we assessed the mutation signature, copy number variation, and expression
of 37 NRGs in HCC using the TCGA-LIHC dataset. We further validated our results using the
ICGC-LIRI-JP dataset. To construct our prognostic model, we utilized the least absolute shrinkage
and selection operator (LASSO), and evaluated the predictive efficacy of the NRGs-score using
various machine learning algorithms, including K-M curves, time-ROC curves, univariate and
multivariate Cox regression, and nomogram. In addition, we analyzed immune infiltration using
the CIBERSOFT and ssGSEA algorithms, calculated the stemness index through the one-class
logistic regression (OCLR) algorithm, and performed anti-cancer stem cells (CSCs) drug sensitivity
analysis using oncoPredict. Finally, we validated the expression of the prognostic NRGs
through qPCR both in vitro and in vivo.

Results:
About 18 out of 37 NRGs were found to be differentially expressed in HCC and correlated
with clinical outcomes. To construct a prognostic model, six signature genes (ALDH2, EZH2,
PGAM5, PLK1, SQSTM1, and TARDBP) were selected using LASSO analysis. These genes were
then employed to categorize HCC patients into two subgroups based on NRGs-score (low vs.
high). A high NRGs score was associated with a worse prognosis. Furthermore, univariate and
multivariate Cox regression analyses were performed to confirm the NRGs-score as an independent
risk factor. These analyses revealed strong associations between NRGs-score and critical factors,
such as AFP, disease stage, and tumor grade in the HCC cohort. NRGs-score effectively
predicted the 1-, 3-, and 5-year survival of HCC patients. Immune infiltration analysis further
revealed that the expression of immune checkpoint molecules was significantly enhanced in the
high NRGs-score group. Stemness analysis in the HCC cohort showed that NRGs-score was positively
correlated with mRNA stemness index, and patients with high NRGs-score were sensitive
to CSCs inhibitors. The findings from the external validation cohort provided confirmation that
the NRGs-score presented a trait with universal applicability in accurately predicting the survival
of HCC. Additionally, the six prognostic genes were consistently differentially expressed in both
the HCC cell line and the mouse HCC model.

Conclusions:
Our study demonstrated the pivotal role of NRGs in promoting stemness and immune
suppression in HCC and established a robust model which could successfully predict HCC prognosis.
The Prognostic Hub Gene POLE2 Promotes BLCA Cell Growth via the PI3K/AKT Signaling Pathway
Authors: Jiang Dongzhen , Zhang Huawei , Yin Bingde , He Minke , Lu Xuwei , He Chang 
Published: November 2023

Background::BLCA is a common urothelial malignancy characterized by a high recurrence rate. Despite its prevalence, the molecular mechanisms underlying its development remain unclear.Aims::This study aimed to explore new prognostic biomarkers and investigate the underlying mechanism of bladder cancer (BLCA).Objective::The objective of this study is to identify key prognostic biomarkers for BLCA and to elucidate their roles in the disease.Methods::We first collected the overlapping DEGs from GSE42089 and TCGA-BLCA samples for the subsequent weighted gene co-expression network analysis (WGCNA) to find a key module. Then, key module genes were analyzed by the MCODE algorithm, prognostic risk model, expression and immunohistochemical staining to identify the prognostic hub gene. Finally, the hub gene was subjected to clinical feature analysis, as well as cellular function assays.Results::In WGCNA on 1037 overlapping genes, the blue module was the key module. After a series of bioinformatics analyses, POLE2 was identified as a prognostic hub gene in BLCA from potential genes (TROAP, POLE2, ANLN, and E2F8). POLE2 level was increased in BLCA and related to different clinical features of BLCA patients. Cellular assays showed that si-POLE2 inhibited BLCA proliferation, and si-POLE2+ 740Y-P in BLCA cells up-regulated the PI3K and AKT protein levels.Conclusion::In conclusion, POLE2 was identified to be a promising prognostic biomarker as an oncogene in BLCA. It was also found that POLE2 exerts a promoting function by the PI3K/AKT signaling pathway in BLCA.