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Article ; Online: Risk Assessment of Liver Metastasis in Pancreatic Cancer Patients Using Multiple Models Based on Machine Learning

Qinggang Li / Lu Bai / Jiyuan Xing / Xiaorui Liu / Dan Liu / Xiaobo Hu

Disease Markers, Vol

A Large Population-Based Study

2022 Volume 2022

Abstract: Background. A more accurate prediction of liver metastasis (LM) in pancreatic cancer (PC) would help improve clinical therapeutic effects and follow-up strategies for the management of this disease. This study was to assess various prediction models to ... ...

Abstract	Background. A more accurate prediction of liver metastasis (LM) in pancreatic cancer (PC) would help improve clinical therapeutic effects and follow-up strategies for the management of this disease. This study was to assess various prediction models to evaluate the risk of LM based on machine learning algorithms. Methods. We retrospectively reviewed clinicopathological characteristics of PC patients from the Surveillance, Epidemiology, and End Results database from 2010 to 2018. The logistic regression, extreme gradient boosting, support vector, random forest (RF), and deep neural network machine algorithms were used to establish models to predict the risk of LM in PC patients. Specificity, sensitivity, and receiver operating characteristic (ROC) curves were used to determine the discriminatory capacity of the prediction models. Results. A total of 47,919 PC patients were identified; 15,909 (33.2%) of which developed LM. After iterative filtering, a total of nine features were included to establish the risk model for LM based on machine learning. The RF showed the most promising results in the prediction of complications among the models (ROC 0.871 for training and 0.832 for test sets). In risk stratification analysis, the LM rate and 5-year cancer-specific survival (CSS) in the high-risk group were worse than those in the intermediate- and low-risk groups. Surgery, radiotherapy, and chemotherapy were found to significantly improve the CSS in the high- and intermediate-risk groups. Conclusion. In this study, the RF model constructed could accurately predict the risk of LM in PC patients, which has the potential to provide clinicians with more personalized clinical decision-making recommendations.
Keywords	Medicine (General) ; R5-920
Subject code	610
Language	English
Publishing date	2022-01-01T00:00:00Z
Publisher	Hindawi Limited
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Establishment of PLAFMCi007-A, an induced pluripotent stem cell line, from peripheral blood mononuclear cells (PBMCs) of a healthy adult woman

Meihan Shi / Shunlai Shang / Yunzhao Yang / Qinggang Li / Xue-Yuan Bai

Stem Cell Research, Vol 61, Iss , Pp 102760- (2022)

2022

Abstract: Induced pluripotent stem cell (iPSC) lines for studies investigating many diseases can be established from peripheral blood mononuclear cells; here, an iPSC line was established from CD34+ cells isolated from the peripheral blood of a healthy woman. The ... ...

Abstract	Induced pluripotent stem cell (iPSC) lines for studies investigating many diseases can be established from peripheral blood mononuclear cells; here, an iPSC line was established from CD34+ cells isolated from the peripheral blood of a healthy woman. The cells were electrotransfected with three different recombinant plasmids to generate a normal-karyotype iPSC line that expresses characteristic surface markers and other pluripotent stem cell genes and can differentiate into all three germ layers in vivo. These newly established iPSC lines, a normal human cell line, can serve as a control line in studies investigating the pathogenesis of various diseases and meet the conditions for organoid studies.
Keywords	Biology (General) ; QH301-705.5
Language	English
Publishing date	2022-05-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Identification of candidate genes that specifically regulate subcutaneous and intramuscular fat deposition using transcriptomic and proteomic profiles in Dingyuan pigs

Pan Zhang / Qinggang Li / Yijing Wu / Yawen Zhang / Bo Zhang / Hao Zhang

Scientific Reports, Vol 12, Iss 1, Pp 1-

2022 Volume 13

Abstract: Abstract Subcutaneous fat and intramuscular fat (IMF) deposition are closely related to meat production and pork quality. Dingyuan pig, as a native pig breed in China, low selection leads to obvious genetic and phenotypic differences in the population. ... ...

Abstract	Abstract Subcutaneous fat and intramuscular fat (IMF) deposition are closely related to meat production and pork quality. Dingyuan pig, as a native pig breed in China, low selection leads to obvious genetic and phenotypic differences in the population. Individuals with extreme fat content in the population are ideal models for studying the mechanism of fat deposition. In this study, we used RNA-Seq and tandem mass tags-based (TMT) proteomics to analyze the key pathways and genes that specifically regulate subcutaneous fat and IMF deposition in Dingyuan pigs. We identified 191 differentially expressed genes (DEGs) and 61 differentially abundant proteins (DAPs) in the high and low back fat thickness (HBF, LBF) groups, 85 DEGs and 12 DAPs were obtained in the high and low intramuscular fat (HIMF, LIMF) groups. The functional analysis showed that the DEGs and DAPs in the backfat groups were mainly involved in carbohydrates, amino acids, and fatty acids metabolism, whereas the IMF groups were involved in the insulin pathway, longevity, and some disease-related pathways. We found 40 candidate genes that might tissue-specifically lipids deposition for subcutaneous and intramuscular fat. Our research provides theoretical reference materials for the improvement of fat deposition traits of local pig breeds in my country.
Keywords	Medicine ; R ; Science ; Q
Subject code	630
Language	English
Publishing date	2022-02-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Generation of induced pluripotent stem cells from peripheral blood mononuclear cells obtained from an adult with autosomal recessive polycystic kidney disease

Mingyang Sun / Jian Li / Shunlai Shang / Xueyuan Bai / Guangyan Cai / Qinggang Li

Stem Cell Research, Vol 61, Iss , Pp 102772- (2022)

2022

Abstract: Autosomal recessive polycystic kidney disease is a hereditary fibrocystic disease that involves the kidneys and biliary tract. Its major histological presentations are the fusiform dilatation of renal collecting ducts and the malformation of the ... ...

Abstract	Autosomal recessive polycystic kidney disease is a hereditary fibrocystic disease that involves the kidneys and biliary tract. Its major histological presentations are the fusiform dilatation of renal collecting ducts and the malformation of the hepatobiliary ductal plate. We isolated peripheral blood mononuclear cells from a 21-year-old adult female patient carrying a homozygous p.L2665P mutation in the PKHD1 gene and used nonintegrated exogenous in vitro differentiation vectors for reprogramming to obtain human induced pluripotent stem cells. The induced pluripotent stem cells thus established had a normal karyotype, expressed markers of pluripotency, and could differentiate into three germ layers in the body.
Keywords	Biology (General) ; QH301-705.5
Language	English
Publishing date	2022-05-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Establishment of the induced pluripotent stem cell line PLAFMCi006-A from peripheral blood mononuclear cells of polycystic kidney disease patients with PKD2 gene mutation

Yuxiang Ma / Shunlai Shang / Meihan Shi / Yunzhao Yang / Qinggang Li / Xue-Yuan Bai

Stem Cell Research, Vol 60, Iss , Pp 102681- (2022)

2022

Abstract: Polycystic kidney disease (PKD) caused by PKD2 mutation is an important type of autosomal dominant PKD. In this study, peripheral blood mononuclear cells from a patient with PKD2 polycystic kidney disease were reprogrammed to obtain induced pluripotent ... ...

Abstract	Polycystic kidney disease (PKD) caused by PKD2 mutation is an important type of autosomal dominant PKD. In this study, peripheral blood mononuclear cells from a patient with PKD2 polycystic kidney disease were reprogrammed to obtain induced pluripotent stem cells (iPSCs). After stable amplification, the pluripotency of the iPSCs was determined by identifying their cell-surface markers, their expression of pluripotency-related genes, and their ability to form teratomas with three germ layers in vivo. The establishment of the iPSC line could provide a basis for a kidney-like organ model of human PKD caused by PKD2 mutation for use in studying the pathogenesis of PKD along with relevant screening and testing intervention drugs.
Keywords	Biology (General) ; QH301-705.5
Language	English
Publishing date	2022-04-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Transcriptomic analysis of B cells suggests that CD70 and LY9 may be novel features in patients with systemic lupus erythematosus

Qun Liu / Yiyao Deng / Xiaomin Liu / Ying Zheng / Qinggang Li / Guangyan Cai / Zhe Feng / Xiangmei Chen

Heliyon, Vol 9, Iss 5, Pp e15684- (2023)

2023

Abstract: Dysfunction of B-cell subsets is critical in the development of systemic lupus erythematosus (SLE). There is a great diversity of B-lineage cells, and their features and functions in SLE need to be clarified. In this study, we analyzed single-cell RNA ... ...

Abstract	Dysfunction of B-cell subsets is critical in the development of systemic lupus erythematosus (SLE). There is a great diversity of B-lineage cells, and their features and functions in SLE need to be clarified. In this study, we analyzed single-cell RNA sequencing (scRNA-seq) data from peripheral blood mononuclear cells (PBMCs) and bulk transcriptomic data of isolated B-cell subsets from patients with SLE and healthy controls (HCs). We preformed scRNA-seq analysis focused on the diversity of B-cell subsets and identified a subset of antigen-presenting B cells in SLE patients that highly expressed ITGAX. A list of marker genes of each B-cell subset in patients with SLE was also identified. Comparison of bulk transcriptomic data of isolated B-cell subpopulations between SLE patients and HCs revealed the upregulated differentially expressed genes (DEGs) for each B-cell subpopulation in SLE. Common genes identified using these two methods were considered to be upregulated marker genes of B cells in SLE. The scRNA-seq data of SLE patients and HCs revealed that CD70 and LY9 were overexpressed in B cells vs. other cell types from SLE patients, and this pattern was validated by RT‒qPCR. Because CD70 is the cellular ligand of CD27, previous studies on CD70 have focused mainly on T cells from SLE patients. LY9 appears to have different functions in mice and humans: its expression is decreased in lupus-prone mice but is increased in T cells and some B-cell subpopulations in SLE patients. Here, we describe the overexpression of two costimulatory molecules, CD70 and LY9, which may be a novel feature of B cells in SLE patients.
Keywords	Systemic lupus erythematosus ; Transcriptomic analysis ; B cells ; CD70 ; LY9 ; Science (General) ; Q1-390 ; Social sciences (General) ; H1-99
Subject code	610
Language	English
Publishing date	2023-05-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Construction of liver hepatocellular carcinoma-specific lncRNA-miRNA-mRNA network based on bioinformatics analysis.

Ruifang Wang / Xiaobo Hu / Xiaorui Liu / Lu Bai / Junsheng Gu / Qinggang Li

PLoS ONE, Vol 16, Iss 4, p e

2021 Volume 0249881

Abstract: Liver hepatocellular carcinoma (LIHC) is one of the major causes of cancer-related death worldwide with increasing incidences, however there are very few studies about the underlying mechanisms and pathways in the development of LIHC. We obtained LIHC ... ...

Abstract	Liver hepatocellular carcinoma (LIHC) is one of the major causes of cancer-related death worldwide with increasing incidences, however there are very few studies about the underlying mechanisms and pathways in the development of LIHC. We obtained LIHC samples from The Cancer Genome Atlas (TCGA) to screen differentially expressed mRNAs, lncRNAs, miRNAs and driver mutations. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, Gene ontology enrichment analyses and protein-protein interaction (PPI) network were performed. Moreover, we constructed a competing endogenous lncRNAs-miRNAs-mRNAs network. Finally, cox proportional hazards regression analysis was used to identify important prognostic differentially expressed genes. Total of 1284 mRNAs, 123 lncRNAs, 47 miRNAs were identified within different tissues of LIHC patients. GO analysis indicated that upregulated and downregulated differentially expressed mRNAs (DEmRNAs) were mainly associated with cell division, DNA replication, mitotic sister chromatid segregation and complement activation respectively. Meanwhile, KEGG terms revealed that upregulated and downregulated DEmRNAs were primarily involved in DNA replication, Metabolic pathways, cell cycle and Metabolic pathways, chemical carcinogenesis, retinol metabolism pathway respectively. Among the DERNAs, 542 lncRNAs-miRNAs-mRNAs pairs were predicted to construct a ceRNA regulatory network including 35 DElncRNAs, 26 DEmiRNAs and 112 DEmRNAs. In the Kaplan-Meier analysis, total of 43 mRNAs, 14 lncRNAs and 3 miRNAs were screened out to be significantly correlated with overall survival of LIHC. The mutation signatures were analyzed and its correlation with immune infiltrates were evaluated using the TIMER in LIHC. Among the mutation genes, TTN mutation is often associated with poor immune infiltration and a worse prognosis in LIHC. This work conducted a novel lncRNAs-miRNAs-mRNAs network and mutation signatures for finding potential molecular mechanisms underlying the development of LIHC. The biomarkers also ...
Keywords	Medicine ; R ; Science ; Q
Subject code	570
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Establishment of PLAFMCi004-A induced pluripotent stem cells derived from PBMCs from a healthy individual

Shunlai Shang / Keng Chen / Guangyan Cai / Xueyuan Bai / Xiangmei Chen / Qinggang Li

Stem Cell Research, Vol 53, Iss , Pp 102316- (2021)

2021

Abstract: Peripheral blood mononuclear cells (PBMCs) were isolated from a healthy male individual. PBMCs were reprogrammed into human induced pluripotent stem cells (iPSCs) using plasmids carrying the following reprogramming factors: NANOG, LIN28, OCT4, SOX2, c- ... ...

Abstract	Peripheral blood mononuclear cells (PBMCs) were isolated from a healthy male individual. PBMCs were reprogrammed into human induced pluripotent stem cells (iPSCs) using plasmids carrying the following reprogramming factors: NANOG, LIN28, OCT4, SOX2, c-MYC, and KLF4. This cell line expressed pluripotency markers, exhibited the normal male karyotype (46, XY), and had the potential to differentiate into 3 germ layers, as confirmed by techniques such as flow cytometry. The iPSC obtained from a healthy individual can be used for organoids to reveal developmental mechanism of tissue and organ regeneration, stem cell therapy and drug screening.
Keywords	Biology (General) ; QH301-705.5
Language	English
Publishing date	2021-05-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Generation of iPSC from peripheral blood mononuclear cells obtained from a patient with TSC2-PKD1 contiguous gene deletion syndrome

Jian Li / Shunlai Shang / Tao Wang / Bo Fu / Peng Wang / Guangyan Cai / Xiangmei Chen / Qinggang Li

Stem Cell Research, Vol 51, Iss , Pp 102181- (2021)

2021

Abstract: TSC2-PKD1 contiguous gene deletion syndrome is characterized by tuberous sclerosis complex and polycystic kidney disease. We obtained peripheral blood mononuclear cells from a patient with TSC2-PKD1 contiguous gene deletion syndrome. We performed ... ...

Abstract	TSC2-PKD1 contiguous gene deletion syndrome is characterized by tuberous sclerosis complex and polycystic kidney disease. We obtained peripheral blood mononuclear cells from a patient with TSC2-PKD1 contiguous gene deletion syndrome. We performed reprogramming using non-integrative episomal vectors to obtain human induced pluripotent stem cells (iPSCs). The obtained iPSCs had a normal karyotype and expressed human ES cell-specific cell surface markers and genes; in teratomas, iPSCs differentiated into derivatives of all three germ layers. The iPSCs can be used to study pathogenesis of TSC2-PKD1 contiguous gene deletion syndrome and serve as a potential therapeutic target.
Keywords	Biology (General) ; QH301-705.5
Language	English
Publishing date	2021-03-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Analysis of Multi-Layer RNA Modification Patterns for the Characterization of Tumor Immune Microenvironment in Hepatocellular Carcinoma

Jiyuan Xing / Shen Shen / Zihui Dong / Xiaobo Hu / Lixia Xu / Xiaorui Liu / Qinggang Li / Yize Zhang / Gangying Cui / Zujiang Yu

Frontiers in Cell and Developmental Biology, Vol

2021 Volume 9

Abstract: Background: RNA modifications have emerged as important posttranscriptional changes in multiple tumor cellular processes and tumorigenesis, including hepatocellular carcinoma (HCC). However, the potential roles and the interaction between regulators of ... ...

Abstract	Background: RNA modifications have emerged as important posttranscriptional changes in multiple tumor cellular processes and tumorigenesis, including hepatocellular carcinoma (HCC). However, the potential roles and the interaction between regulators of RNA modifications and the tumor microenvironment (TME) are unclear in HCC.Methods: The gene expression profiles of 26 RNA modification “writers” were investigated in the TCGA cohort. The unsupervised clustering approach was used to class these RNA modification regulators. The characteristics of immune cell infiltration from TME for each cluster was tested by the CIBERSORT method. Additionally, we established a scoring model to evaluate the RNA modification characteristics of individual tumors. The associations between the scoring model and genetic as well as clinical characteristics, drug sensitivity, and response to immunotherapy were also analyzed.Results: We mapped the somatic mutations and somatic copy number variation of the RNA modification regulators. The expression of all selected regulators was detected, and two modification patterns were identified that featured distinct immune cell infiltration characteristics. Subsequently, we developed a score model (termed as WM-Score model). Furthermore, the survival analysis showed that the WM-Score value was associated with HCC patient prognosis. The results of the ROC curves analysis and multivariate analysis all confirmed that the WM-Score value was strongly associated with anti-cancer drug resistance and therapeutic efficacy of immunotherapy, thus could be used as an independent risk factor in HCC.Conclusion: Our research identified two RNA modification patterns characterized by distinct TME, and the WM-Score model was developed that might serve as reliable prognostic and immunotherapeutic effect predictor of HCC.
Keywords	hepatocellular carcinoma ; RNA methylation modification ; TME ; immunotherapy ; prognosis ; Biology (General) ; QH301-705.5
Subject code	616
Language	English
Publishing date	2021-11-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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