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Article ; Online: Regulon analysis identifies protective FXR and CREB5 in proximal tubules in early diabetic kidney disease.

Shi, Wanting / Le, Weibo / Tang, Qiaoli / Shi, Shaolin / Shi, Jingsong

2023 Volume 24, Issue 1, Page(s) 180

Abstract: Diabetic kidney disease (DKD) is the most common complication of diabetes mellitus and a leading cause of kidney failure worldwide. Despite its prevalence, the mechanisms underlying early kidney damage in DKD remain poorly understood. In this study, we ... ...

Abstract	Diabetic kidney disease (DKD) is the most common complication of diabetes mellitus and a leading cause of kidney failure worldwide. Despite its prevalence, the mechanisms underlying early kidney damage in DKD remain poorly understood. In this study, we used single nucleus RNA-seq to construct gene regulatory networks (GRNs) in the kidney cortex of patients with early DKD. By comparing these networks with those of healthy controls, we identify cell type-specific changes in genetic regulation associated with diabetic status. The regulon activities of FXR (NR1H4) and CREB5 were found to be upregulated in kidney proximal convoluted tubule epithelial cells (PCTs), which were validated using immunofluorescence staining in kidney biopsies from DKD patients. In vitro experiments using cultured HK2 cells showed that FXR and CREB5 protected cells from apoptosis and epithelial-mesenchymal transition. Our findings suggest that FXR and CREB5 may be promising targets for early intervention in patients with DKD.
MeSH term(s)	Humans ; Cyclic AMP Response Element-Binding Protein A/genetics ; Diabetes Mellitus/genetics ; Diabetic Nephropathies/pathology ; Gene Expression Regulation ; Kidney/pathology ; Kidney Tubules, Proximal/pathology ; Regulon ; Receptors, Cytoplasmic and Nuclear/genetics
Chemical Substances	CREB5 protein, human ; Cyclic AMP Response Element-Binding Protein A ; farnesoid X-activated receptor (0C5V0MRU6P) ; Receptors, Cytoplasmic and Nuclear
Language	English
Publishing date	2023-06-19
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2041348-8
ISSN	1471-2369 ; 1471-2369
ISSN (online)	1471-2369
ISSN	1471-2369
DOI	10.1186/s12882-023-03239-6
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Article: A new species of

Min, Rui / Zhao, Yahui / Shi, Jingsong / Yang, Junxing

ZooKeys

2022 Volume 1089, Page(s) 109–124

Abstract: Based on morphological and molecular analysis ... ...

Abstract	Based on morphological and molecular analysis of
Language	English
Publishing date	2022-03-17
Publishing country	Bulgaria
Document type	Journal Article
ZDB-ID	2445640-8
ISSN	1313-2970 ; 1313-2989
ISSN (online)	1313-2970
ISSN	1313-2989
DOI	10.3897/zookeys.1089.77203
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Article: A new species of Homatula (Teleostei, Cobitoidea, Nemacheilidae) from the Pearl River drainage, Yunnan, China

Min, Rui / Zhao, Yahui / Shi, Jingsong / Yang, Junxing

ZooKeys. 2022 Mar. 17, v. 1089

2022

Abstract: AbstractBased on morphological and molecular analysis of Homatula species distributed in the Nanpanjiang River in Yunnan, China, we described a new species, Homatula robusta sp. nov. It differs from its congeners by a combination of the following ... ...

Abstract	AbstractBased on morphological and molecular analysis of Homatula species distributed in the Nanpanjiang River in Yunnan, China, we described a new species, Homatula robusta sp. nov. It differs from its congeners by a combination of the following characters: naked and robust body with well-developed crests (caudal peduncle depth as a percentage of its length: 70.5–78.5%); lateral line complete; median notch on lower jaw; median gap on lower lip; three pairs of short barbels, with maxillary barbels extending posteriorly to anterior edge of eyes; branched dorsal-fin rays 8½; and vertebrae 37–39. It can further be distinguished from H. nanpanjiangensis by several differences of the caudal skeleton such as the number of hypural elements, the presence of epurale and the shape of neural and haemal spines. Phylogenetic analysis of the mitochondrial cytochrome c oxidase subunit I (COI) gene indicated that the new species represents an independent lineage. It is separated from other Homatula species by a minimum of 5.3% Kimura-2-parameter distance in the COI gene. Furthermore, we confirmed that Homatula wenshanensis should be a member of Homatula based on both skeleton and molecular evidence.
Keywords	Homatula ; drainage ; fins ; genes ; mitochondria ; new species ; phylogeny ; rivers ; skeleton ; China
Language	English
Dates of publication	2022-0317
Size	p. 109-124.
Publishing place	Pensoft Publishers
Document type	Article
ZDB-ID	2445640-8
ISSN	1313-2970 ; 1313-2989
ISSN (online)	1313-2970
ISSN	1313-2989
DOI	10.3897/zookeys.1089.77203
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Article ; Online: Re-analysis of single-cell RNA-seq data reveals the origin and roles of cycling myeloid cells.

Zhang, Jiawei / Shi, Jingsong / Wang, Liangge / Liu, Xinjie / Cao, Zemin / Ruan, Cihan / Ning, Guangzhi / Feng, Shiqing / Yao, Xue / Gao, Shan

Stem cells (Dayton, Ohio)

2024

Abstract: Cycling myeloid cells (CMCs) are often detected from various tissues using single-cell RNA sequencing (scRNA-seq) datasets, however, their research value was not noticed before. For the first time, our study preliminarily revealed the origin, ... ...

Abstract	Cycling myeloid cells (CMCs) are often detected from various tissues using single-cell RNA sequencing (scRNA-seq) datasets, however, their research value was not noticed before. For the first time, our study preliminarily revealed the origin, differentiation, and roles of CMCs in physiological processes. Particularly, subgroup a of cycling myeloid cells (aCMCs) were conclusively identified as belonging to a specific cell type. In an active state, aCMCs rapidly proliferate during the early stages of an embryonic development. With an individual maturing, most aCMCs differentiate into specialized cells, while a small portion of them enter an inactive or dormant state. Under pathological conditions, aCMCs restore their proliferative and differentiation capacities via activation or revival. The present study has set the stage for future research on CMCs by linking them with progenitors of immune cells, and provided a crucial starting point to understand the origin, differentiation, and roles of CMCs in various physiological and pathological processes, particularly those related to traumatic injury, cancer, and pathogen infection, leading to develop targeted therapies or interventions.
Language	English
Publishing date	2024-04-24
Publishing country	England
Document type	Journal Article
ZDB-ID	1143556-2
ISSN	1549-4918 ; 1066-5099
ISSN (online)	1549-4918
ISSN	1066-5099
DOI	10.1093/stmcls/sxae030
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Article ; Online: HLA Alleles and Prognosis of PLA2R-Related Membranous Nephropathy.

Le, Wei-Bo / Shi, Jing-Song / Fan, Yang / Gong, Si-Wen

Clinical journal of the American Society of Nephrology : CJASN

2021 Volume 16, Issue 8, Page(s) 1221–1227

Abstract: Background and objectives: Associations between HLA alleles and susceptibility to M-type phospholipase A2 receptor (PLA2R)-related membranous nephropathy have been well defined previously in Chinese patients. However, the relationships between HLA ... ...

Abstract	Background and objectives: Associations between HLA alleles and susceptibility to M-type phospholipase A2 receptor (PLA2R)-related membranous nephropathy have been well defined previously in Chinese patients. However, the relationships between HLA alleles and kidney outcome remain unclear. Design, setting, participants, & measurements: Five HLA genes (DRB1, DQA1, DQB1, DRB3, and DRB5) were genotyped in a prospective cohort of 392 patients with PLA2R-related membranous nephropathy. The associations between HLA alleles and kidney outcomes were studied. Results: A total of 79 HLA alleles were identified in this study. Four HLA alleles, DRB113:01 ( Conclusions:* Carrying any of the HLA alleles, DRB113:01/DQB106:03, DRB104:05, and DQB103:02, was independently associated with poor prognosis in Chinese patients with PLA2R-related membranous nephropathy.
MeSH term(s)	Adult ; Alleles ; Asian People/genetics ; China ; Disease Progression ; Female ; Genotype ; Glomerular Filtration Rate ; Glomerulonephritis, Membranous/genetics ; Glomerulonephritis, Membranous/physiopathology ; HLA-DQ alpha-Chains/genetics ; HLA-DQ beta-Chains/genetics ; HLA-DR beta-Chains/genetics ; HLA-DRB1 Chains/genetics ; HLA-DRB3 Chains/genetics ; HLA-DRB5 Chains/genetics ; Humans ; Male ; Middle Aged ; Prognosis ; Prospective Studies ; Receptors, Phospholipase A2/genetics ; Risk Factors
Chemical Substances	HLA-DQ alpha-Chains ; HLA-DQ beta-Chains ; HLA-DQA1 antigen ; HLA-DQB1 antigen ; HLA-DR beta-Chains ; HLA-DRB1 Chains ; HLA-DRB3 Chains ; HLA-DRB5 Chains ; PLA2R1 protein, human ; Receptors, Phospholipase A2
Language	English
Publishing date	2021-06-03
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2226665-3
ISSN	1555-905X ; 1555-9041
ISSN (online)	1555-905X
ISSN	1555-9041
DOI	10.2215/CJN.18021120
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Article ; Online: An equation to estimate 24-hour total urine protein excretion rate in patients who underwent urine protein testing.

Yang, Fan / Shi, Jing-Song / Gong, Si-Wen / Xu, Xiao-Dong / Le, Wei-Bo

BMC nephrology

2022 Volume 23, Issue 1, Page(s) 49

Abstract: Background: The urine protein-creatinine ratio (UPCR) in a spot first-morning urine sample is used to estimate 24-h urine proteinuria (24hUP) in patients who underwent urine protein testing. UPCR cannot be directly compared with 24-h proteinuria. Thus, ... ...

Abstract	Background: The urine protein-creatinine ratio (UPCR) in a spot first-morning urine sample is used to estimate 24-h urine proteinuria (24hUP) in patients who underwent urine protein testing. UPCR cannot be directly compared with 24-h proteinuria. Thus, an equation to estimate 24-h total protein excretion rate, using age, gender, and the UPCR may improve its bias and accuracy in patients who underwent urine protein testing. Methods: We simultaneously measured 24-h urine protein and the same day's first-morning spot urine from patients with kidney disease. Generalized linear and no-linear models, using age, gender, and UPCR, were constructed to estimate for 24-h urine protein and the best model (NJ equation) was selected to estimated 24 hUP (e24hUP). Results: A total of 5435 paired samples (including a training cohort of 3803 patients and a validation cohort of 1632 patients) were simultaneously measured for UPCR and 24-h urine protein. In the training cohort, the unadjusted UPCR obviously underestimated 24-h urine protein when UPCR ≤1.2 g/g (median bias - 0.17 g/24 h) and overestimated 24-h urine protein when UPCR > 1.2 g/g (median bias 0.53 g/24 h). In the validation cohort, the NJ equation performed better than the unadjusted UPCR, with lower root mean square error (0.81 vs. 1.02, P < 0.001), less bias (median difference between measured and estimated urine protein, - 0.008 vs. 0.12), improved precision (interquartile range of the differences, 0.34 vs. 0.50), and greater accuracy (percentage of estimated urine protein within 30% of measured urine protein, 53.4% vs. 32.2%). Bland-Altman plot indicated that the agreement of spot and daily estimates was less pronounced with 24 hUP > 2 g than lower values. Conclusions: The NJ e24hUP equation is more accurate than unadjusted UPCR to estimate 24 hUP in patients with kidney disease and could be used for laboratory application.
MeSH term(s)	Adult ; Creatinine/urine ; Female ; Humans ; Male ; Mathematical Concepts ; Middle Aged ; Monitoring, Physiologic ; Proteinuria/urine ; Urinalysis/methods
Chemical Substances	Creatinine (AYI8EX34EU)
Language	English
Publishing date	2022-01-29
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2041348-8
ISSN	1471-2369 ; 1471-2369
ISSN (online)	1471-2369
ISSN	1471-2369
DOI	10.1186/s12882-022-02673-2
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Article: Multiple lines of evidence reveal a new species of Krait (Squamata, Elapidae, Bungarus) from Southwestern China and Northern Myanmar

Chen, Ze-Ning / Shi, Sheng-Chao / Vogel, Gernot / Ding, Li / Shi, Jing-Song

ZooKeys. 2021 Mar. 18, v. 1025

2021

Abstract: Kraits of the genus Bungarus Daudin 1803 are widely known venomous snakes distributed from Iran to China and Indonesia. Here, we use a combination of mitochondrial DNA sequence data and morphological data to describe a new species from Yingjiang County, ... ...

Abstract	Kraits of the genus Bungarus Daudin 1803 are widely known venomous snakes distributed from Iran to China and Indonesia. Here, we use a combination of mitochondrial DNA sequence data and morphological data to describe a new species from Yingjiang County, Yunnan Province, China: Bungarus suzhenae sp. nov. Phylogenetically, this species forms a monophyletic lineage sister to the Bungarus candidus /multicinctus /wanghaotingi complex based on cyt b and ND4 genes but forms a sister species pair with the species B. magnimaculatus Wall & Evans, 1901 based on COI gene fragments. Morphologically, B. suzhenae sp. nov. is similar to the B. candidus/multicinctus/wanghaotingi complex but differs from these taxa by a combination of dental morphology, squamation, coloration pattern, as well as hemipenial morphology. A detailed description of the cranial osteology of the new species is given based on micro-CT tomography images. We revised the morphological characters of B. candidus/multicinctus/wanghaotingi complex and verified the validity of three species in this complex. The distribution of these species was revised; the records of B. candidus in China should be attributed to B. wanghaotingi. We also provide an updated key to species of Bungarus.
Keywords	Bungarus ; color ; genes ; micro-computed tomography ; monophyly ; new species ; nucleotide sequences ; taxonomic keys ; China ; Indonesia ; Iran ; Myanmar
Language	English
Dates of publication	2021-0318
Size	p. 35-71.
Publishing place	Pensoft Publishers
Document type	Article
Note	NAL-light
ZDB-ID	2445640-8
ISSN	1313-2970 ; 1313-2989
ISSN (online)	1313-2970
ISSN	1313-2989
DOI	10.3897/zookeys.1025.62305
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Article ; Online: The validity of Pelophylax chosenicus (Okada, 1931) and P. hubeiensis (Fei & Ye, 1982) (Amphibia, Ranidae)

Zhou, Sheng-Bo / Zhang, Qiu-Yi / Hu, Zi-Qiang / Xia, Zu-Yao / Miao, Qing / Guan, Ping / Shi, Jing-Song

Herpetozoa. 2023 June 21, v. 36 p.143-152

2023

Abstract: AbstractPelophylax plancyi (Lataste, 1880), Pelophylax chosenicus (Okada, 1931) and Pelophylax hubeiensis (Fei & Ye, 1982) were described chronologically from East Asia. The three species have similar morphological and molecular characteristics, but the ...

Abstract	AbstractPelophylax plancyi (Lataste, 1880), Pelophylax chosenicus (Okada, 1931) and Pelophylax hubeiensis (Fei & Ye, 1982) were described chronologically from East Asia. The three species have similar morphological and molecular characteristics, but the taxonomic relationships amongst them have long been ambiguous. To deal with this taxonomic issue, we examined newly-obtained topotypic specimens of P. plancyi, P. chosenicus and P. hubeiensis for morphological comparison. Furthermore, we investigated the phylogeny of pond frogs in Eurasia by Bayesian Inference and Maximum Likelihood analyses of a fragment consisting of mitochondrial DNA gene 16s and provided a molecular phylogeny of the genus Pelophylax. There were no morphological and molecular differences between P. plancyi and P. chosenicus, but both morphological and molecular differences between P. hubeiensis and P. plancyi. Hence, we conclude that P. chosenicus is a junior synonym of P. plancyi and P. hubeiensis is a separate species from P. plancyi.
Keywords	Bayesian theory ; Pelophylax ; genes ; mitochondrial DNA ; phylogeny ; statistical analysis ; East Asia ; Eurasia ; amphibians ; morphology ; synonym ; taxonomy
Language	English
Dates of publication	2023-0621
Size	p. 143-152.
Publishing place	Pensoft Publishers
Document type	Article ; Online
ZDB-ID	2474932-1
ISSN	2682-955X
ISSN	2682-955X
DOI	10.3897/herpetozoa.36.e100072
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Article: Distinct effects of ANGPT2 on gene expression of glomerular podocytes and mesangial cells.

Ren, Lu / Zhang, Sipan / Shi, Jingsong / Wang, Xia / Qin, Weisong / Liu, Zhihong / Shi, Shaolin

American journal of translational research

2021 Volume 13, Issue 11, Page(s) 12249–12263

Abstract: Glomerular diseases are the leading cause of chronic kidney diseases with the pathomechanisms largely unclear. ANGPT2 is known to regulate endothelial cell homeostasis through TEK/Tie2 and its dysregulation causes endothelial damage. Here, we found that ... ...

Abstract	Glomerular diseases are the leading cause of chronic kidney diseases with the pathomechanisms largely unclear. ANGPT2 is known to regulate endothelial cell homeostasis through TEK/Tie2 and its dysregulation causes endothelial damage. Here, we found that ANGPT2 is upregulated in glomerular diseases and wondered whether it also acts on the other two glomerular cell types, podocytes and mesangial cells. We treated podocytes and mesangial cells in culture with ANGPT2 but didn't find changes in morphology and survival. RNA-seq analysis revealed that gene expression was altered in both podocytes and mesangial cells and that the differentially expressed genes in the two cell types were fundamentally different and enriched in distinct cellular processes and pathways according to GO and KEGG analyses. Mechanistically, the Ingenuity Pathway Analysis (IPA) analysis revealed that ERK and AKT were the most connected nodes in the networks of the regulated genes of both podocytes and mesangial cells, suggesting that ANGPT2 affected ERK and AKT in both cell types. Interestingly, immunoblotting showed that phosphorylated ERK and AKT were both increased in podocytes while decreased in mesangial cells by ANGPT2. We found that mesangial cells, but not podocytes, expressed TEK and ANGPT1, suggesting that ANGPT2 could antagonize ANGPT1-TEK-ERK axis in mesangial cells similarly to endothelial cells. We searched databases and found that integrin alpha(v) (ITGAV) is an ANGPT2 interacting protein and expressed in podocytes, suggesting that ITGAV mediates ANGPT2 effect on podocytes. In conclusion, increased ANGPT2 may be involved in glomerular injury by affecting podocytes and mesangial cells in addition to endothelial cells. The complexity of the effect of ANGPT2 in glomeruli may apply to other factors.
Language	English
Publishing date	2021-11-15
Publishing country	United States
Document type	Journal Article
ZDB-ID	2471058-1
ISSN	1943-8141
ISSN	1943-8141
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Article: MCC Regulator of WNT Signaling Pathway (MCC) Is a Podocyte Essential Gene.

Song, Hui / Zhuang, Lulu / Xu, Xiaodong / Shi, Jingsong / Hu, Weixin / Liu, Zhihong / Shi, Shaolin

Frontiers in medicine

2021 Volume 8, Page(s) 777563

Abstract: Podocytes are an integral part of the glomerular filtration barrier. Many genes are already known to be essential for podocyte survival, structure and function, but there are more podocyte essential genes to be identified. By single-cell RNA-seq of mouse ...

Abstract	Podocytes are an integral part of the glomerular filtration barrier. Many genes are already known to be essential for podocyte survival, structure and function, but there are more podocyte essential genes to be identified. By single-cell RNA-seq of mouse podocytes, we detected the expression of gene encoding MCC regulator of WNT signaling pathway (MCC) in majority of the podocytes and speculated that MCC is essential for podocytes. We confirmed MCC expression in mouse podocytes and further showed its expression in human podocytes. To experimentally prove the essentiality of MCC for podocytes, we knocked down MCC in cultured podocytes and found marked morphological change of cell shape, cytoskeletal F-actin stress fiber disruption, increased apoptosis, and downregulation of podocyte essential genes, CD2AP and WT1, demonstrating that MCC is essential for podocytes. Since MCC has been implicated in cell cycle and β-catenin signaling, we examined the expression of cell cycle related genes and activity of β-catenin in the MCC knockdown podocytes, but did not find significant changes. To further explore the mechanism underlying the role of MCC in podocytes, we performed RNA-sequencing and bioinformatics analysis of MCC knockdown podocytes and found a significant enrichment of the regulated genes in lamellipodia formation. Consistently, we found that MCC is present in lamellipodia and MCC knockdown resulted in loss of lamellipodia in the cells. Lastly, we found that MCC was downregulated in podocytes treated with puromycin aminonucleosides and in glomeruli of diabetic mice and FSGS patients, implicating MCC is involved in the development of podocytopathy and proteinuria. In conclusion, MCC is potentially essential for podocytes and its downregulation may be involved in podocytopathy.
Language	English
Publishing date	2021-12-02
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2775999-4
ISSN	2296-858X
ISSN	2296-858X
DOI	10.3389/fmed.2021.777563
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