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Article ; Online: Screening immune-related blood biomarkers for DKD-related HCC using machine learning.

Chen, Chao / Xie, Zhinan / Ni, Ying / He, Yuxi

2024 Volume 15, Page(s) 1339373

Abstract: Background: Diabetes mellitus is a significant health problem worldwide, often leading to diabetic kidney disease (DKD), which may also influence the occurrence of hepatocellular carcinoma (HCC). However, the relationship and diagnostic biomarkers ... ...

Abstract	Background: Diabetes mellitus is a significant health problem worldwide, often leading to diabetic kidney disease (DKD), which may also influence the occurrence of hepatocellular carcinoma (HCC). However, the relationship and diagnostic biomarkers between DKD and HCC are unclear. Methods: Using public database data, we screened DKD secretory RNAs and HCC essential genes by limma and WGCNA. Potential mechanisms, drugs, and biomarkers for DKD-associated HCC were identified using PPI, functional enrichment, cMAP, and machine learning algorithms, and a diagnostic nomogram was constructed. Then, ROC, calibration, and decision curves were used to evaluate the diagnostic performance of the nomograms. In addition, immune cell infiltration in HCC was explored using CIBERSORT. Finally, the detectability of critical genes in blood was verified by qPCR. Results: 104 DEGs associated with HCC using WGCNA were identified. 101 DEGs from DKD were predicated on secreting into the bloodstream with Exorbase datasets. PPI analysis identified three critical modules considered causative genes for DKD-associated HCC, primarily involved in inflammation and immune regulation. Using lasso and RM, four hub genes associated with DKD-associated HCC were identified, and a diagnostic nomogram confirmed by DCA curves was established. The results of immune cell infiltration showed immune dysregulation in HCC, which was associated with the expression of four essential genes. PLVAP was validated by qPCR as a possible blood-based diagnostic marker for DKD-related HCC. Conclusion: We revealed the inflammatory immune pathways of DKD-related HCC and developed a diagnostic nomogram for HCC based on PLVAP, C7, COL15A1, and MS4A6A. We confirmed with qPCR that PLVAP can be used as a blood marker to assess the risk of HCC in DKD patients.
MeSH term(s)	Humans ; Carcinoma, Hepatocellular/etiology ; Carcinoma, Hepatocellular/genetics ; Liver Neoplasms/etiology ; Liver Neoplasms/genetics ; Algorithms ; Biomarkers ; Machine Learning
Chemical Substances	Biomarkers
Language	English
Publishing date	2024-01-22
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2606827-8
ISSN	1664-3224 ; 1664-3224
ISSN (online)	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2024.1339373
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Article ; Online: Genome‑wide analysis of the MYB gene family in pumpkin.

Xu, Minyan / Fu, Jingjing / Ni, Ying / Zhang, Chenchen

PeerJ

2024 Volume 12, Page(s) e17304

Abstract: ... ...

Abstract	The
MeSH term(s)	Cucurbita/genetics ; Gene Expression Regulation, Plant ; Multigene Family/genetics ; Stress, Physiological/genetics ; Plant Proteins/genetics ; Plant Proteins/metabolism ; Plant Growth Regulators/metabolism ; Transcription Factors/genetics ; Transcription Factors/metabolism ; Genes, myb ; Promoter Regions, Genetic/genetics ; Phylogeny ; Genome-Wide Association Study ; Genome, Plant/genetics
Chemical Substances	Plant Proteins ; Plant Growth Regulators ; Transcription Factors
Language	English
Publishing date	2024-04-25
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2703241-3
ISSN	2167-8359 ; 2167-8359
ISSN (online)	2167-8359
ISSN	2167-8359
DOI	10.7717/peerj.17304
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Article ; Online: Cell-free DNA fragmentomics and second malignant neoplasm risk in patients with PTEN hamartoma tumor syndrome.

Liu, Darren / Yehia, Lamis / Dhawan, Andrew / Ni, Ying / Eng, Charis

Cell reports. Medicine

2024 Volume 5, Issue 2, Page(s) 101384

Abstract: Individuals with PTEN hamartoma tumor syndrome (PHTS) harbor pathogenic germline PTEN variants that confer a significantly increased lifetime risk of various organ-specific cancers including second primary malignant neoplasms (SMNs). Currently, there are ...

Abstract	Individuals with PTEN hamartoma tumor syndrome (PHTS) harbor pathogenic germline PTEN variants that confer a significantly increased lifetime risk of various organ-specific cancers including second primary malignant neoplasms (SMNs). Currently, there are no reliable biomarkers that can predict individual-level cancer risk. Despite the highly promising value of cell-free DNA (cfDNA) as a biomarker for underlying sporadic cancers, the utility of cfDNA in individuals with known cancer-associated germline variants and subclinical cancers remains poorly understood. We perform ultra-low-pass whole-genome sequencing (ULP-WGS) of cfDNA from plasma samples from patients with PHTS and cancer as well as those without cancer. Analysis of cfDNA reveals that patients with PHTS and SMNs have distinct cfDNA size distribution, aberrant genome-wide fragmentation, and differential fragment end motif frequencies. Our work provides evidence that cfDNA profiles may be used as a marker for SMN risk in patients with PHTS.
MeSH term(s)	Humans ; Hamartoma Syndrome, Multiple/diagnosis ; Hamartoma Syndrome, Multiple/genetics ; Hamartoma Syndrome, Multiple/complications ; PTEN Phosphohydrolase/genetics ; Neoplasms ; Germ-Line Mutation ; Cell-Free Nucleic Acids/genetics
Chemical Substances	PTEN Phosphohydrolase (EC 3.1.3.67) ; Cell-Free Nucleic Acids ; PTEN protein, human (EC 3.1.3.67)
Language	English
Publishing date	2024-01-18
Publishing country	United States
Document type	Journal Article
ISSN	2666-3791
ISSN (online)	2666-3791
DOI	10.1016/j.xcrm.2023.101384
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Article ; Online: Identification of crosstalk genes relating to ECM-receptor interaction genes in MASH and DN using bioinformatics and machine learning.

Chen, Chao / He, Yuxi / Ni, Ying / Tang, Zhanming / Zhang, Wensheng

Journal of cellular and molecular medicine

2024 Volume 28, Issue 6, Page(s) e18156

Abstract: This study aimed to identify genes shared by metabolic dysfunction-associated fatty liver disease (MASH) and diabetic nephropathy (DN) and the effect of extracellular matrix (ECM) receptor interaction genes on them. Datasets with MASH and DN were ... ...

Abstract	This study aimed to identify genes shared by metabolic dysfunction-associated fatty liver disease (MASH) and diabetic nephropathy (DN) and the effect of extracellular matrix (ECM) receptor interaction genes on them. Datasets with MASH and DN were downloaded from the Gene Expression Omnibus (GEO) database. Pearson's coefficients assessed the correlation between ECM-receptor interaction genes and cross talk genes. The coexpression network of co-expression pairs (CP) genes was integrated with its protein-protein interaction (PPI) network, and machine learning was employed to identify essential disease-representing genes. Finally, immuno-penetration analysis was performed on the MASH and DN gene datasets using the CIBERSORT algorithm to evaluate the plausibility of these genes in diseases. We found 19 key CP genes. Fos proto-oncogene (FOS), belonging to the IL-17 signalling pathway, showed greater centrality PPI network; Hyaluronan Mediated Motility Receptor (HMMR), belonging to ECM-receptor interaction genes, showed most critical in the co-expression network map of 19 CP genes; Forkhead Box C1 (FOXC1), like FOS, showed a high ability to predict disease in XGBoost analysis. Further immune infiltration showed a clear positive correlation between FOS/FOXC1 and mast cells that secrete IL-17 during inflammation. Combining the results of previous studies, we suggest a FOS/FOXC1/HMMR regulatory axis in MASH and DN may be associated with mast cells in the acting IL-17 signalling pathway. Extracellular HMMR may regulate the IL-17 pathway represented by FOS through the Mitogen-Activated Protein Kinase 1 (ERK) or PI3K-Akt-mTOR pathway. HMMR may serve as a signalling carrier between MASH and DN and could be targeted for therapeutic development.
MeSH term(s)	Humans ; Interleukin-17 ; Diabetic Nephropathies ; Phosphatidylinositol 3-Kinases ; Computational Biology ; Machine Learning
Chemical Substances	Interleukin-17 ; Phosphatidylinositol 3-Kinases (EC 2.7.1.-)
Language	English
Publishing date	2024-03-04
Publishing country	England
Document type	Journal Article
ZDB-ID	2074559-X
ISSN	1582-4934 ; 1582-4934 ; 1582-1838
ISSN (online)	1582-4934
ISSN	1582-4934 ; 1582-1838
DOI	10.1111/jcmm.18156
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Article ; Online: Causal associations between liver traits and Colorectal cancer: a Mendelian randomization study.

Ni, Ying / Wang, Wenkai / Liu, Yongming / Jiang, Yun

BMC medical genomics

2023 Volume 16, Issue 1, Page(s) 316

Abstract: Objective: This study aimed to investigate the causal associations between several liver traits (liver iron content, percent liver fat, alanine transaminase levels, and liver volume) and colorectal cancer (CRC) risk using a Mendelian randomization (MR) ... ...

Abstract	Objective: This study aimed to investigate the causal associations between several liver traits (liver iron content, percent liver fat, alanine transaminase levels, and liver volume) and colorectal cancer (CRC) risk using a Mendelian randomization (MR) approach to improve our understanding of the disease and its management. Methods: Genetic variants were used as instrumental variables, extracted from genome-wide association studies (GWAS) datasets of liver traits and CRC. The Two-Sample MR package in R was used to conduct inverse variance weighted (IVW), MR Egger, Maximum likelihood, Weighted median, and Inverse variance weighted (multiplicative random effects) MR approaches to generate overall estimates of the effect. MR analysis was conducted with Benjamini-Hochberg method-corrected P values to account for multiple testing (P < 0.013). MR-PRESSO was used to identify and remove outlier genetic variants in Mendelian randomization (MR) analysis. The MR Steiger test was used to assess the validity of the assumption that exposure causes outcomes. Leave-one-out validation, pleiotropy, and heterogeneity testing were also conducted to ensure the reliability of the results. Multivariable MR was utilized for validation of our findings using the IVW method while also adjusting for potential confounding or pleiotropy bias. Results: The MR analysis suggested a causal effect between liver volume and a reduced risk of CRC (OR 0.60; 95% CI, 0.44-0.82; P = 0.0010) but did not provide evidence for causal effects of liver iron content, percent liver fat, or liver alanine transaminase levels. The MR-PRESSO method did not identify any outliers, and the MR Steiger test confirmed that the causal direction of the analysis results was correct in the Mendelian randomization analysis. MR results were consistent with heterogeneity and pleiotropy analyses, and leave-one-out analysis demonstrated the overall values obtained were consistent with estimates obtained when all available SNPs were included in the analysis. Multivariable MR was utilized for validation of our findings using the IVW method while also adjusting for potential confounding or pleiotropy bias. Conclusion: The study provides tentative evidence for a causal role of liver volume in CRC, while genetically predicted levels of liver iron content, percent liver fat, and liver alanine transaminase levels were not associated with CRC risk. The findings may inform the development of targeted therapeutic interventions for colorectal liver metastasis (CRLM) patients, and the study highlights the importance of MR as a powerful epidemiological tool for investigating causal associations between exposures and outcomes.
MeSH term(s)	Humans ; Alanine Transaminase/analysis ; Colorectal Neoplasms/epidemiology ; Colorectal Neoplasms/genetics ; Genome-Wide Association Study ; Iron/analysis ; Liver/anatomy & histology ; Liver/chemistry ; Liver/pathology ; Mendelian Randomization Analysis ; Reproducibility of Results ; Adipose Tissue/pathology ; Organ Size ; Risk
Chemical Substances	Alanine Transaminase (EC 2.6.1.2) ; Iron (E1UOL152H7)
Language	English
Publishing date	2023-12-06
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2411865-5
ISSN	1755-8794 ; 1755-8794
ISSN (online)	1755-8794
ISSN	1755-8794
DOI	10.1186/s12920-023-01755-w
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Article ; Online: Melanoma body site distribution: Germline genetics may have a lesser role.

Decosma, Lorvens / Ni, Ying / Funchain, Pauline / Arbesman, Joshua

JAAD international

2023 Volume 11, Page(s) 220–221

Language	English
Publishing date	2023-03-28
Publishing country	United States
Document type	Journal Article
ISSN	2666-3287
ISSN (online)	2666-3287
DOI	10.1016/j.jdin.2023.03.003
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Article ; Online: The mitochondrial genome as a modifier of autism versus cancer phenotypes in

Wei, Ruipeng / Yehia, Lamis / Ni, Ying / Eng, Charis

HGG advances

2023 Volume 4, Issue 3, Page(s) 100199

Abstract: Cancer and autism spectrum disorder/developmental delay (ASD/DD) are two common clinical phenotypes in individuals with ... ...

Abstract	Cancer and autism spectrum disorder/developmental delay (ASD/DD) are two common clinical phenotypes in individuals with germline
MeSH term(s)	Humans ; Hamartoma Syndrome, Multiple/genetics ; Autistic Disorder/genetics ; Autism Spectrum Disorder/genetics ; Genome, Mitochondrial/genetics ; DNA Copy Number Variations/genetics ; Phenotype ; Thyroid Neoplasms/genetics ; DNA, Mitochondrial/genetics ; PTEN Phosphohydrolase/genetics
Chemical Substances	DNA, Mitochondrial ; PTEN protein, human (EC 3.1.3.67) ; PTEN Phosphohydrolase (EC 3.1.3.67)
Language	English
Publishing date	2023-04-24
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ISSN	2666-2477
ISSN (online)	2666-2477
DOI	10.1016/j.xhgg.2023.100199
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Article: Distribution and correlation of refractive parameters in children with different corneal curvatures in southeast China.

He, Si-Yuan / He, Ting / Xu, Meng-Yue / Ni, Ying-Jie / Hong, Chao-Yang / Shen, Ting

International journal of ophthalmology

2024 Volume 17, Issue 4, Page(s) 713–720

Abstract: Aim: To analyze the distribution of refractive status in school-age children with different corneal curvatures (CC) and the correlation between CC and refractive status.: Methods: A total of 2214 school-aged children of grade 4 in Hangzhou who were ... ...

Abstract	Aim: To analyze the distribution of refractive status in school-age children with different corneal curvatures (CC) and the correlation between CC and refractive status. Methods: A total of 2214 school-aged children of grade 4 in Hangzhou who were screened for school myopia were included. Uncorrected distance visual acuity (UCDVA), non-cycloplegic refraction, axial length (AL), horizontal and vertical corneal curvature (K Results: Both SE and AL were greater in the LCC group ( Conclusion: School-aged children in the LCC group have a lower incidence of screening myopia and longer AL. Low CC can mask SE reduction and AL growth to some extent, and the change of AL growth change more in children with low CC than high CC. Before the onset of myopia, its growth rate is even faster than that after the onset of myopia.
Language	English
Publishing date	2024-04-18
Publishing country	China
Document type	Journal Article
ZDB-ID	2663246-9
ISSN	2227-4898 ; 2222-3959
ISSN (online)	2227-4898
ISSN	2222-3959
DOI	10.18240/ijo.2024.04.16
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Article ; Online: A SCYL2 gene from Oryza sativa is involved in phytosterol accumulation and regulates plant growth and salt stress.

Xu, Minyan / Ni, Ying / Tu, Yaling / Wang, Yanping / Zhang, Zhi / Jiao, Yuhuan / Zhang, Xin

Plant science : an international journal of experimental plant biology

2024 Volume 343, Page(s) 112062

Abstract: Rice is a crucial food for humans due to its high nutritional value. Phytosterols, essential components of the plant membrane lipid bilayer, play a vital role in plant growth and contribute significantly to lipid-lowering, antitumor, and immunomodulation ...

Abstract	Rice is a crucial food for humans due to its high nutritional value. Phytosterols, essential components of the plant membrane lipid bilayer, play a vital role in plant growth and contribute significantly to lipid-lowering, antitumor, and immunomodulation processes. In this study, SCY1-like protein kinases 2 (SCYL2) was found to be closely related to the accumulation of phytosterols. The levels of campesterol, stigmasterol, and β-sitosterol significantly increased in transgenic rice seeds, husks, and leaves, whereas there was a considerable reduction in scyl2 plants. Subsequent investigations revealed the crucial role of SCYL2 in plant development. Mutations in this gene led to stunted plant growth while overexpressing OsSCYL2 in Arabidopsis and rice resulted in larger leaves, taller plants, and accelerated development. When subjected to salt stress, Arabidopsis plants overexpressed OsSCYL2 showed significantly higher germination rates than wild-type plants. Similarly, transgenic rice seedlings displayed better growth than both ZH11 and mutant plants, exhibiting lower malondialdehyde (MDA) content and higher peroxidase (POD), and catalase (CAT) activities. Conversely, scyl2 plants exhibited more yellow leaves or even death. These findings suggested that OsSCYL2 proteins might be involved in phytosterols synthesis and play an important role during plant growth and development. This study provides a theoretical basis for developing functional rice.
MeSH term(s)	Humans ; Oryza/metabolism ; Arabidopsis/metabolism ; Stress, Physiological ; Salt Stress ; Plant Development ; Phytosterols/metabolism ; Plants, Genetically Modified/genetics ; Plant Proteins/genetics ; Plant Proteins/metabolism ; Gene Expression Regulation, Plant
Chemical Substances	Phytosterols ; Plant Proteins
Language	English
Publishing date	2024-03-09
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.2024.112062
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Article: Benchmarking of Nanopore R10.4 and R9.4.1 flow cells in single-cell whole-genome amplification and whole-genome shotgun sequencing.

Ni, Ying / Liu, Xudong / Simeneh, Zemenu Mengistie / Yang, Mengsu / Li, Runsheng

Computational and structural biotechnology journal

2023 Volume 21, Page(s) 2352–2364

Abstract: Third-generation sequencing can be used in human cancer genomics and epigenomic research. Oxford Nanopore Technologies (ONT) recently released R10.4 flow cell, which claimed an improved read accuracy compared to R9.4.1 flow cell. To evaluate the benefits ...

Abstract	Third-generation sequencing can be used in human cancer genomics and epigenomic research. Oxford Nanopore Technologies (ONT) recently released R10.4 flow cell, which claimed an improved read accuracy compared to R9.4.1 flow cell. To evaluate the benefits and defects of R10.4 flow cell for cancer cell profiling on MinION devices, we used the human non-small-cell lung-carcinoma cell line HCC78 to construct libraries for both single-cell whole-genome amplification (scWGA) and whole-genome shotgun sequencing. The R10.4 and R9.4.1 reads were benchmarked in terms of read accuracy, variant detection, modification calling, genome recovery rate and compared with the next generation sequencing (NGS) reads. The results highlighted that the R10.4 outperforms R9.4.1 reads, achieving a higher modal read accuracy of over 99.1%, superior variation detection, lower false-discovery rate (FDR) in methylation calling, and comparable genome recovery rate. To achieve high yields scWGA sequencing in the ONT platform as NGS, we recommended multiple displacement amplification with a modified T7 endonuclease Ⅰ cutting procedure as a promising method. In addition, we provided a possible solution to filter the likely false positive sites among the whole genome region with R10.4 by using scWGA sequencing result as a negative control. Our study is the first benchmark of whole genome single-cell sequencing using ONT R10.4 and R9.4.1 MinION flow cells by clarifying the capacity of genomic and epigenomic profiling within a single flow cell. A promising method for scWGA sequencing together with the methylation calling results can benefit researchers who work on cancer cell genomic and epigenomic profiling using third-generation sequencing.
Language	English
Publishing date	2023-03-24
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2694435-2
ISSN	2001-0370
ISSN	2001-0370
DOI	10.1016/j.csbj.2023.03.038
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