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Article: Comprehensive Analysis of the Associations of LOXL1-4 with Prognosis and Immune Infiltration in Breast Cancer.

He, Lifang / Lin, Yun / Huang, Peizhi / Pan, Hongchao

Alternative therapies in health and medicine

2024

Abstract: Objective: Invasive breast cancer (BRCA) poses a major challenge to women's health due to its high incidence and poor prognosis. Dysregulated Lysine oxidase-like (LOXL) family genes are implicated in tumor progression across malignancies. Understanding ... ...

Abstract	Objective: Invasive breast cancer (BRCA) poses a major challenge to women's health due to its high incidence and poor prognosis. Dysregulated Lysine oxidase-like (LOXL) family genes are implicated in tumor progression across malignancies. Understanding the role of Lysine oxidase-like (LOXL) family genes in BRCA is crucial for advancing treatment strategies. Methods: TIMER, Oncomine, TNMplot, TCGA, GTEx and GEPIA datasets were used to investigate LOXL1-4 expression in breast cancer. The UALCAN and HPA datasets were utilized to detect the protein levels of LOXL1-4 in BRCA. Kaplan-Meier Plotter was used to analyze the prognostic values of LOXL1-4 in BRCA patients. Gene ontology (GO) and KEGG pathway enrichment analyses, conducted through DAVID 6.8 and R, revealed potential biological functions. TIMER was used to explore the link between LOXL1-4 expression and tumor immune infiltration. The cBioPortal dataset was used to analyze LOXL1-4 alterations and CNV-survival links in breast cancer. GSCA was used to assess LOXL1-4's correlations with immune infiltration. LOXL1-4's links to the eight immune checkpoint genes were analyzed using R's pheatmap. Results: Our study revealed that aberrant expression of LOXL1/2/4 in BRCA significantly affects relapse-free survival (RFS), overall survival (OS), and distant metastasis-free survival (DMFS), particularly highlighting the prognostic importance of LOXL4. LOXL1-4 displayed substantial relationships with the tumor immune microenvironment and immune cell infiltration. Furthermore, copy number variations (CNVs) of LOXL1-4 are significantly associated with immune infiltration in BRCA, particularly LOXL2 CNV, which significantly impacts OS and progression-free survival (PFS). Conclusion: The correlation between LOXL1-4 expression, prognosis, and immune infiltration in BRCA underscores their potential as biomarkers for prognosis and targets for immunotherapy.
Language	English
Publishing date	2024-03-22
Publishing country	United States
Document type	Journal Article
ZDB-ID	1225073-9
ISSN	1078-6791
ISSN	1078-6791
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Zs.A 4504: Show issues

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Article ; Online: The therapeutic potential of dietary intervention: based on the mechanism of a tryptophan derivative-indole propionic acid on metabolic disorders.

Niu, Ben / Pan, Tong / Xiao, Yue / Wang, Hongchao / Zhu, Jinlin / Tian, Fengwei / Lu, Wenwei / Chen, Wei

Critical reviews in food science and nutrition

2024 , Page(s) 1–20

Abstract: Tryptophan (TRP) contributes to individual immune homeostasis and good ... ...

Abstract	Tryptophan (TRP) contributes to individual immune homeostasis and good condition
Language	English
Publishing date	2024-01-08
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	1037504-1
ISSN	1549-7852 ; 1040-8398
ISSN (online)	1549-7852
ISSN	1040-8398
DOI	10.1080/10408398.2023.2299744
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Zs.A 1459: Show issues

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Article ; Online: A Novel Immune-Related Signature to Predict Prognosis and Immune Infiltration of Cervical Cancer.

Lin, Yun / Zhang, Rendong / Pan, Hongchao / Li, Yaochen

Medical science monitor : international medical journal of experimental and clinical research

2023 Volume 29, Page(s) e938660

Abstract: BACKGROUND Cervical cancer is one of the most common malignances among women globally. This study aimed to construct a novel immune-related signature to predict the prognosis and immune infiltration of cervical cancer. MATERIAL AND METHODS Transcriptomic ...

Abstract	BACKGROUND Cervical cancer is one of the most common malignances among women globally. This study aimed to construct a novel immune-related signature to predict the prognosis and immune infiltration of cervical cancer. MATERIAL AND METHODS Transcriptomic profiles and corresponding clinical information of cervical cancer patients were obtained from The Cancer Genome Atlas (TCGA) database and GEO database. The hub immune-related genes were screened and selected using Cox regression analysis and LASSO regression analysis. A novel signature was established based on the expression levels and corresponding coefficients of the selected hub immune-related genes. Kaplan-Meier survival curve and ROC curve illustrated the prognostic value of this novel signature in cervical cancer. The predictive accuracy and stability of this novel signature were confirmed in the validation cohort, internal testing set and external testing set. Then, a nomogram was constructed to predict individual survival probability of cervical cancer patient. The association between the risk scores of novel signature and immune infiltration was investigated through single-sample gene set enrichment analysis (ssGSEA). RESULTS Ten hub immune-related genes (TFRC, SPP1, CAMP, CSF2, TUBB3, ZAP70, CHIT1, LEPR, DLL4, and DES) were selected to construct a novel signature. The risk score of this novel signature could be an independent prognostic factor in cervical cancer, which divided patients into high-risk and low-risk groups. The patients in high-risk groups showed significantly worse overall survival rates than those in low-risk groups in all training and validation cohorts (all P<0.05). A nomogram model was constructed based on the risk score of the novel signature and other clinical characteristics, which achieved the highest clinical net benefit across the entire range of reasonable threshold probabilities (concordance index=0.813). Furthermore, gene enrichment analysis revealed that the novel signature was closely related with immunology. The novel signature was negatively correlated with the infiltration of most immune cell types, especially T cell subsets (P<0.001). CONCLUSIONS The novel signature could comprehensively predict the prognosis and immune infiltration of cervical cancer. It may provide new insights for the precise treatment in cervical cancer.
MeSH term(s)	Humans ; Female ; Uterine Cervical Neoplasms/genetics ; Prognosis ; Nomograms ; Risk Factors ; Databases, Factual
Language	English
Publishing date	2023-03-28
Publishing country	United States
Document type	Journal Article
ZDB-ID	1439041-3
ISSN	1643-3750 ; 1234-1010
ISSN (online)	1643-3750
ISSN	1234-1010
DOI	10.12659/MSM.938660
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Zs.A 4924: Show issues

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Article: IGFBP5, as a Prognostic Indicator Promotes Tumor Progression and Correlates with Immune Microenvironment in Glioma.

Lin, Jiediao / Huang, Guowei / Zeng, Qianru / Zhang, Rendong / Lin, Yun / Li, Yaochen / Huang, Baohua / Pan, Hongchao

Journal of Cancer

2024 Volume 15, Issue 1, Page(s) 232–250

Abstract: Background: ...

Abstract	Background:
Language	English
Publishing date	2024-01-01
Publishing country	Australia
Document type	Journal Article
ZDB-ID	2573318-7
ISSN	1837-9664
ISSN	1837-9664
DOI	10.7150/jca.87733
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Article: Effects of in ovo feeding of chlorogenic acid on antioxidant capacity of postnatal broilers.

Pan, Yali / Lin, Hai / Jiao, Hongchao / Zhao, Jingpeng / Wang, Xiaojuan

Frontiers in physiology

2023 Volume 14, Page(s) 1091520

Abstract: In this study, chlorogenic acid (CGA) was injected into the amniotic cavity of chicken embryos to study the effects of in ovo feeding of CGA on the antioxidant capacity of postnatal broilers. On the 17th day of embryonic age, a total of 300 healthy ... ...

Abstract	In this study, chlorogenic acid (CGA) was injected into the amniotic cavity of chicken embryos to study the effects of in ovo feeding of CGA on the antioxidant capacity of postnatal broilers. On the 17th day of embryonic age, a total of 300 healthy broiler fertile eggs with similar weights were randomly subjected to five groups as follows; in ovo injection with 0.5 ml CGA at 4 mg/egg (4CGA) or 7 mg/egg (7CGA) or 10 mg/egg (10CGA), or sham-injection with saline (positive control, PC) or no injection (negative control, NC). Each group had six replicates of ten embryos. Six healthy chicks with similar body weights hatched from each replicate were selected and reared until heat stress treatment (35°C ± 1°C, 8 h/d) at 28-42 days of age. The results showed that there was no significant difference in the hatching rate between the groups (
Language	English
Publishing date	2023-01-16
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2564217-0
ISSN	1664-042X
ISSN	1664-042X
DOI	10.3389/fphys.2023.1091520
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Article ; Online: Mn

Li, Hongchao / Yuan, Na / Qian, Jieshu / Pan, Bingcai

Environmental science & technology

2022 Volume 56, Issue 7, Page(s) 4498–4506

Abstract: The environmentally benign Mn oxides play a crucial role in the transformation of organic contaminants, either through catalytically decomposing oxidants, e.g., peroxymonosulfate (PMS), or through directly oxidizing the target pollutants. Because of ... ...

Abstract	The environmentally benign Mn oxides play a crucial role in the transformation of organic contaminants, either through catalytically decomposing oxidants, e.g., peroxymonosulfate (PMS), or through directly oxidizing the target pollutants. Because of their dual roles and the complex surface chemical reactions, the mechanism involved in Mn oxide-catalyzed PMS activation processes remains obscure. Here, we clearly elucidate the mechanism involved in the Mn
MeSH term(s)	Electrons ; Environmental Pollutants ; Oxidation-Reduction ; Oxides ; Peroxides
Chemical Substances	Environmental Pollutants ; Oxides ; Peroxides ; peroxymonosulfate (22047-43-4)
Language	English
Publishing date	2022-03-17
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1520-5851
ISSN (online)	1520-5851
DOI	10.1021/acs.est.1c08790
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Effects of Varied Sulfamethazine Dosage and Exposure Durations on Offspring Mice.

Wang, Hongchao / Dang, Danting / Zhu, Leilei / Pan, Mingluo / Zhu, Jinlin / Lu, Wenwei / Lu, Shourong / Zhao, Jianxin

Microorganisms

2024 Volume 12, Issue 2

Abstract: The development of antibiotics was a turning point in the history of medicine; however, their misuse and overuse have contributed to the current global epidemic of antibiotic resistance. According to epidemiological studies, early antibiotic exposure ... ...

Abstract	The development of antibiotics was a turning point in the history of medicine; however, their misuse and overuse have contributed to the current global epidemic of antibiotic resistance. According to epidemiological studies, early antibiotic exposure increases the risk of immunological and metabolic disorders. This study investigated the effects of exposure to different doses of sulfamethazine (SMZ) on offspring mice and compared the effects of exposure to SMZ on offspring mice in prenatal and early postnatal periods and continuous periods. Furthermore, the effects of SMZ exposure on the gut microbiota of offspring mice were analyzed using metagenome. According to the results, continuous exposure to high-dose SMZ caused weight gain in mice. IL-6, IL-17A, and IL-10 levels in the female offspring significantly increased after high-dose SMZ exposure. In addition, there was a significant gender difference in the impact of SMZ exposure on the gut microbiota of offspring: Continuous high-dose SMZ exposure significantly decreased the relative abundance of
Language	English
Publishing date	2024-02-13
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2720891-6
ISSN	2076-2607
ISSN	2076-2607
DOI	10.3390/microorganisms12020381
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Article ; Online: Indole metabolites and colorectal cancer: Gut microbial tryptophan metabolism, host gut microbiome biomarkers, and potential intervention mechanisms.

Liu, Yufei / Pei, Zhangming / Pan, Tong / Wang, Hongchao / Chen, Wei / Lu, Wenwei

Microbiological research

2023 Volume 272, Page(s) 127392

Abstract: Tryptophan (Trp) functions in host-disease interactions. Its metabolism is a multi-pathway process. Indole and its derivatives are Trp metabolites unique to the human gut microbiota. Changes in Trp metabolism have also been detected in colorectal cancer ( ...

Abstract	Tryptophan (Trp) functions in host-disease interactions. Its metabolism is a multi-pathway process. Indole and its derivatives are Trp metabolites unique to the human gut microbiota. Changes in Trp metabolism have also been detected in colorectal cancer (CRC). Here, combined with the existing CRC biomarkers, we ascribed it to the altered bacteria having the indole-producing ability by making a genomic prediction. We also reviewed the anti-inflammatory and possible anti-cancer mechanisms of indoles, including their effects on tumor cells, the ability to repair the gut barrier, regulation of the host immune system, and provide resistance against oxidative stress. Indole and its derivatives, along with related bacteria, could be targeted as auxiliary strategies to restrain cancer development in the future.
MeSH term(s)	Humans ; Gastrointestinal Microbiome/physiology ; Tryptophan/metabolism ; Indoles/metabolism ; Biomarkers ; Bacteria/genetics ; Bacteria/metabolism ; Colorectal Neoplasms
Chemical Substances	Tryptophan (8DUH1N11BX) ; indole (8724FJW4M5) ; Indoles ; Biomarkers
Language	English
Publishing date	2023-04-25
Publishing country	Germany
Document type	Journal Article ; Review
ZDB-ID	1189614-0
ISSN	1618-0623 ; 0944-5013
ISSN (online)	1618-0623
ISSN	0944-5013
DOI	10.1016/j.micres.2023.127392
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Article: A Comprehensive Comparative Analysis of Deep Learning Based Feature Representations for Molecular Taste Prediction.

Song, Yu / Chang, Sihao / Tian, Jing / Pan, Weihua / Feng, Lu / Ji, Hongchao

Foods (Basel, Switzerland)

2023 Volume 12, Issue 18

Abstract: Taste determination in small molecules is critical in food chemistry but traditional experimental methods can be time-consuming. Consequently, computational techniques have emerged as valuable tools for this task. In this study, we explore taste ... ...

Abstract	Taste determination in small molecules is critical in food chemistry but traditional experimental methods can be time-consuming. Consequently, computational techniques have emerged as valuable tools for this task. In this study, we explore taste prediction using various molecular feature representations and assess the performance of different machine learning algorithms on a dataset comprising 2601 molecules. The results reveal that GNN-based models outperform other approaches in taste prediction. Moreover, consensus models that combine diverse molecular representations demonstrate improved performance. Among these, the molecular fingerprints + GNN consensus model emerges as the top performer, highlighting the complementary strengths of GNNs and molecular fingerprints. These findings have significant implications for food chemistry research and related fields. By leveraging these computational approaches, taste prediction can be expedited, leading to advancements in understanding the relationship between molecular structure and taste perception in various food components and related compounds.
Language	English
Publishing date	2023-09-09
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2704223-6
ISSN	2304-8158
ISSN	2304-8158
DOI	10.3390/foods12183386
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Extracellular vesicles in plant-microbe interactions: Recent advances and future directions.

Zhang, Junsong / Pan, Liying / Xu, Wenjie / Yang, Hongchao / He, Fuge / Ma, Jianfeng / Bai, Linlin / Zhang, Qingchen / Zhou, Qingfeng / Gao, Hang

Plant science : an international journal of experimental plant biology

2024 Volume 341, Page(s) 111999

Abstract: Extracellular vesicles (EVs) are membrane-enclosed nanoparticles that have a crucial role in mediating intercellular communication in mammals by facilitating the transport of proteins and small RNAs. However, the study of plant EVs has been limited for a ...

Abstract	Extracellular vesicles (EVs) are membrane-enclosed nanoparticles that have a crucial role in mediating intercellular communication in mammals by facilitating the transport of proteins and small RNAs. However, the study of plant EVs has been limited for a long time due to insufficient isolation and detection methods. Recent research has shown that both plants and plant pathogens can release EVs, which contain various bioactive molecules like proteins, metabolites, lipids, and small RNAs. These EVs play essential roles in plant-microbe interactions by transferring these bioactive molecules across different kingdoms. Additionally, it has been discovered that EVs may contribute to symbiotic communication between plants and pathogens. This review provides a comprehensive summary of the pivotal roles played by EVs in mediating interactions between plants and microbes, including pathogenic fungi, bacteria, viruses, and symbiotic pathogens. We highlight the potential of EVs in transferring immune signals between plant cells and facilitating the exchange of active substances between different species.
MeSH term(s)	Animals ; Extracellular Vesicles/metabolism ; RNA ; Cell Communication ; Plants ; Symbiosis ; Mammals
Chemical Substances	RNA (63231-63-0)
Language	English
Publishing date	2024-02-01
Publishing country	Ireland
Document type	Journal Article ; Review
ZDB-ID	742010-9
ISSN	1873-2259 ; 0168-9452
ISSN (online)	1873-2259
ISSN	0168-9452
DOI	10.1016/j.plantsci.2024.111999
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