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Article: Paternal genetic structure analysis of the modern Han populations based on Y-SNP and Y-STR.

Xin, Zhu / Xin, Jin / Jun, Liu / Lan, Yang / Li-Xin, Zou / Cai-Xia, Li / Jiang, Huang / Li, Jiang

Yi chuan = Hereditas

2024 Volume 46, Issue 2, Page(s) 149–167

Abstract: The Han populations represent the largest ethnic group in China. Previous studies have primarily focused on investigating their genetic origins, migration and integration, as well as paternal genetic relationships within specific regional Han populations. ...

Abstract	The Han populations represent the largest ethnic group in China. Previous studies have primarily focused on investigating their genetic origins, migration and integration, as well as paternal genetic relationships within specific regional Han populations. However, a comprehensive analysis of the global paternal genetic structure of Han populations is lacking. In this study, we performed Y-chromosome sequencing on 362 unrelated male samples from Chinese Han individuals collected from Qinghai, Sichuan and Liaoning provinces. We then integrated relevant data from reported studies. Our final dataset comprised 1830 samples from 16 Han populations across 15 provinces in China, encompassing information on 89 Y-SNPs and 16 Y-STRs. Statistical analyses were conducted to assess Y-STR haplotype diversity (HD) and Y-SNP haplogroup frequencies. Additionally, we employed principal component analysis (PCA), phylogenetic tree and haplotype network to explore genetic differentiation within Han populations and the genetic relationships between Han populations and ethnic minorities surrounding them. Our results demonstrated that the O-M175 haplogroup represents the predominant paternal lineage in Han populations, with frequencies ranging from 60.53% (Qinghai Han) to 92.7% (Guangdong Han). Moreover, the subclades downstream of O-M175 showed distinct regional variations in their distribution patterns. The O2-M122 haplogroup was prevalent in all Han populations and demonstrated a gradual decline in frequency from north to south. Conversely, the distribution frequency of the O1b-M268 haplogroup decreased from south to north, particularly showed significant presence among Han populations in the Lingnan region. Haplogroup O1a-M119 distributed more frequently in the central Han populations. Our findings revealed that Chinese Han populations can be categorized into three subgroups: northern, central, and southern. Notably, there were significant differences among Han in Qinghai and other regions. Regarding the genetic relationships between Han populations and surrounding ethnic minorities, we observed a closer genetic affinity between different Han populations, but northern Han demonstrated a stronger relationship with the Hui ethnic group, while southern Han exhibited a closer connection with the Gelao and Li ethnic groups. In summary, this study presented a systematic analysis of haplogroup distribution, genetic substructure of Han populations and genetic relationships between Han populations and surrounding ethnic minorities based on 89 Y-SNPs and 16 Y-STRs systematically. Our research supplemented valuable insights into population genetics and forensic genetics, and provided data support for the forensic application of Y chromosome. The integration of Y-SNP haplogroups with Y-STR haplotypes offers enhanced understanding of the genetic substructure within Han populations, which holds significance for both population genetics research and forensic science applications.
MeSH term(s)	Humans ; Polymorphism, Single Nucleotide ; Phylogeny ; Microsatellite Repeats ; Genetics, Population ; Ethnicity/genetics ; Haplotypes ; Chromosomes, Human, Y/genetics ; China
Language	English
Publishing date	2024-02-10
Publishing country	China
Document type	Journal Article
ISSN	0253-9772
ISSN	0253-9772
DOI	10.16288/j.yczz.23-260
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Repressing IRS1/2 by NT157 inhibits the malignant behaviors of ovarian cancer through inactivating PI3K/AKT/mTOR pathway and inducing autophagy

Cai‐Xia Li / Chuan‐Di Men / Wei‐Hong Yang / Rong Chen / Ji‐Hui Zhu / Zhong‐Ping Cheng

Kaohsiung Journal of Medical Sciences, Vol 39, Iss 4, Pp 377-

2023 Volume 389

Abstract: Abstract Insulin receptor substrate 1 and 2 (IRS1/2) have been found involved in many cancers development and their inhibitors exert significant tumor‐suppressive effects. Here, we tried to explore the function of NT157, an IGF1R‐IRS1/2 inhibitor, in ... ...

Abstract	Abstract Insulin receptor substrate 1 and 2 (IRS1/2) have been found involved in many cancers development and their inhibitors exert significant tumor‐suppressive effects. Here, we tried to explore the function of NT157, an IGF1R‐IRS1/2 inhibitor, in ovarian cancer. We treated ovarian cancer cells with varying doses of NT157. The MTT assay was employed to evaluate cell proliferation and colony formation assay was used for detecting colony‐forming ability. TUNEL assay was adopted to test cell apoptosis. Cell invasion was checked by the Transwell assay. The expression of apoptosis‐related proteins, autophagy markers, IRS1/2, and PI3K/AKT/mTOR pathway was compared by Western blot, immunofluorescence, or qRT‐PCR. As indicated by the data, NT157 abated the viability, proliferation, and induced autophagy of ovarian cancer cells. Overexpressing IRS1/2 attenuated the tumor‐suppressive effect of NT157 and heightened the PI3K/AKT/mTOR pathway activation. Inhibition of the PI3K/AKT/mTOR pathway enhanced the tumor‐suppressive effect of NT157 and facilitated NT157‐mediated autophagy. However, the autophagy inhibitor 3‐MA partly reversed NT‐157‐mediated antitumor effects. In conclusion, this study disclosed that NT157 suppressed the malignant phenotypes of ovarian cancer cells by inducing autophagy and hampering the expression of IRS1/2 and PI3K/AKT/mTOR pathway.
Keywords	autophagy ; IRS1/2 ; NT157 ; ovarian cancer ; Medicine (General) ; R5-920
Subject code	616
Language	English
Publishing date	2023-04-01T00:00:00Z
Publisher	Wiley
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Systematic screening and validation of reliable reference genes for qRT-PCR analysis in Okra (Abelmoschus esculentus L.)

Jing-Rong Zhang / Yuan-Yuan Feng / Ma-Jin Yang / Yu Xiao / Yu-Shan Liu / Yuan Yuan / Zhen Li / Yan Zhang / Ming Zhuo / Jun Zhang / Cai-Xia Li

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

2022 Volume 10

Abstract: Abstract Quantitative real-time polymerase chain reaction (qRT-PCR) is a sensitive and widely used technique for quantifying gene expression levels, and its accuracy depends on the reference genes used for data normalization. To date, no reference gene ... ...

Abstract	Abstract Quantitative real-time polymerase chain reaction (qRT-PCR) is a sensitive and widely used technique for quantifying gene expression levels, and its accuracy depends on the reference genes used for data normalization. To date, no reference gene has been reported in the nutritious and functional vegetable okra (Abelmoschus esculentus L.). Herein, 11 candidates of reference genes were selected and evaluated for their expression stability in okra in different tissues at different developmental stages by using three software algorithms (geNorm, NormFinder, BestKeeper) and a web-based tool (RefFinder). Among them, eukaryotic initiation factor 4 alpha (eIF4A) and protein phosphatase 2A (PP2A) showed the highest stability, while TUA5 had the lowest stability. The combined usage of these two most stable reference genes was sufficient to normalize gene expression in okra. Then, the above results were further validated by normalizing the expression of the cellulose synthase gene CesA4. This work provides appropriate reference genes for transcript normalization in okra, which will facilitate subsequent functional gene research on this vegetable crop.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2022-07-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Exogenous 1′,4′- trans -Diol-ABA Induces Stress Tolerance by Affecting the Level of Gene Expression in Tobacco ( Nicotiana tabacum L.)

Teng Liu / Cai-Xia Li / Juan Zhong / Dan Shu / Di Luo / Zhe-Min Li / Jin-Yan Zhou / Jie Yang / Hong Tan / Xin-Rong Ma

International Journal of Molecular Sciences, Vol 22, Iss 5, p

2021 Volume 2555

Abstract: 1′,4′- trans -diol-ABA is a key precursor of the biosynthesis of abscisic acid (ABA) biosynthesis in fungi. We successfully obtained the pure compound from a mutant of Botrytis cinerea and explored its function and possible mechanism on plants by ... ...

Abstract	1′,4′- trans -diol-ABA is a key precursor of the biosynthesis of abscisic acid (ABA) biosynthesis in fungi. We successfully obtained the pure compound from a mutant of Botrytis cinerea and explored its function and possible mechanism on plants by spraying 2 mg/L 1′,4′- trans -diol-ABA on tobacco leaves. Our results showed that this compound enhanced the drought tolerance of tobacco seedlings. A comparative transcriptome analysis showed that a large number of genes responded to the compound, exhibiting 1523 genes that were differentially expressed at 12 h, which increased to 1993 at 24 h and 3074 at 48 h, respectively. The enrichment analysis demonstrated that the differentially expressed genes (DEGs) were primarily enriched in pathways related to hormones and resistance. The DEGs of transcription factors were generally up-regulated and included the bHLH, bZIP, ERF, MYB, NAC, WRKY and HSF families. Moreover, the levels of expression of PYL/PYR, PP2C, SnRK2, and ABF at the ABA signaling pathway responded positively to exogenous 1′,4′- trans -diol-ABA. Among them, seven ABF transcripts that were detected were significantly up-regulated. In addition, the genes involved in salicylic acid, ethylene and jasmonic acid pathways, reactive oxygen species scavenging system, and other resistance related genes were primarily induced by 1′,4′- trans -diol-ABA. These findings indicated that treatment with 1′,4′- trans -diol-ABA could improve tolerance to plant abiotic stress and potential biotic resistance by regulating gene expression, similar to the effects of exogenous ABA.
Keywords	1′,4′- trans -diol-ABA ; foliar spraying ; drought stress ; transcriptome ; ABA signaling pathway ; tobacco ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Subject code	580 ; 572
Language	English
Publishing date	2021-03-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: iTRAQ-based proteomics screen for potential regulators of wheat (Triticum aestivum L.) root cell wall component response to Al stress

Yang, Ye / Cai-Xia Li / Chun-Yan Dai / Hong Zeng / Hui-Lin Guan / Li Ma / Lu-Yao Chen / Nan Wu / Xi Mu / Xiu-Ming Cui / Ying Liu / Yun Zheng / Ze-Ping Yang

Gene. 2018,

2018

Abstract: The inhibition of Aluminum (Al)-induced root tip cell elongation is a major cause of plant root elongation suppression. The inhibition of root tip cell elongation is caused by a disruption of cell wall component metabolism, growth signaling, or cellular ... ...

Abstract	The inhibition of Aluminum (Al)-induced root tip cell elongation is a major cause of plant root elongation suppression. The inhibition of root tip cell elongation is caused by a disruption of cell wall component metabolism, growth signaling, or cellular damage. The aim of this study was to identify the proteins involved in the metabolism of the root cell wall components under Al stress in the Al-tolerant wheat (Triticum aestivum L.) cultivar ET8.Differentially expressed proteins of Al-tolerant wheat roots were screened via isobaric tags for relative and absolute quantification (iTRAQ). Furthermore, their expression changes were detected via RT-PCR analysis. The contents of major components of the cell wall and their changes in metabolic enzyme activities were also investigated.A total of 97 differentially expressed proteins from Al-tolerant wheat roots were screened and nine of these 97 proteins were root cell wall component related. The known nucleic acid sequences of proteins were 14-3-3 protein, the plasm membrane (PM) H+-ATPase, phospholipase D, peroxidase, and glycosyltransferase. For 14-3-3 protein, phospholipase D and peroxidase, the protein expression and mRNA expression were consistent with Al-treatment; however, for PM H+-ATPase and glycosyltransferase, the protein expression and mRNA expression were inconsistent under Al-stress. Furthermore, both cellulase activity and callase activity were down-regulated by Al stress, while the phenylalanineammonialyase (PAL), cinnamyl alcohol dehydrogenase (CAD), and peroxidase (POD) activities were up-regulated. Furthermore, the PM H+-ATPase activity was decreased in response to Al stress. In addition, the contents of callose, cellulose, lignin, and H2O2 varied significantly.The cell wall components, relative metabolism enzymes activity, and gene expression also changed followed by protein expression changed in response to Al stress. The results suggest that Al stress leads to marked variations in metabolic enzyme activity, carbohydrate content, followed by changes of root cell components in wheat roots.
Keywords	aluminum ; callose ; carbohydrate content ; cell growth ; cell wall components ; cellulose ; cinnamyl alcohol dehydrogenase ; cultivars ; endo-1,4-beta-glucanase ; enzyme activity ; gene expression ; glycosyltransferases ; H-transporting ATP synthase ; hydrogen peroxide ; lignin ; messenger RNA ; nucleotide sequences ; peroxidase ; phospholipase D ; protein synthesis ; proteins ; proteomics ; reverse transcriptase polymerase chain reaction ; root growth ; root tips ; Triticum aestivum ; wheat
Language	English
Size	p. .
Publishing place	Elsevier B.V.
Document type	Article
Note	Pre-press version
ZDB-ID	391792-7
ISSN	1879-0038 ; 0378-1119
ISSN (online)	1879-0038
ISSN	0378-1119
DOI	10.1016/j.gene.2018.07.008
Database	NAL-Catalogue (AGRICOLA)

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Article: Efficacy of Zhuling polyporus polysaccharide with BCG to inhibit bladder carcinoma

Zhang, Guo-wei / Bo Han / Cai-xia Li / Gui-fang Qin / Hong-Gai Yang / Pi-hu Nie / Xing Zeng

Carbohydrate polymers. 2015 Mar. 15, v. 118

2015

Abstract: There is growing interest in reducing Bacille Calmette-Guerin (BCG) side effects while keeping intact its therapeutic efficacy. In the present study, we evaluated the efficacy of Sclerotia of Polyporus umbellatus FRIES (Zhuling) and its main ingredient ... ...

Abstract	There is growing interest in reducing Bacille Calmette-Guerin (BCG) side effects while keeping intact its therapeutic efficacy. In the present study, we evaluated the efficacy of Sclerotia of Polyporus umbellatus FRIES (Zhuling) and its main ingredient Polyporus Polysaccharide (PPS) to attenuate side effects of BCG therapy in vivo. The results show that bladder cancer development in model rats exhibited significantly reduced cancer invasiveness with Zhuling PPS combined with BCG. Flow cytometric (FCM) analysis showed expression of costimulatory molecules CD86, CD40, and TLR4/CD14 significantly increased with Zhuling PPS in combination with BCG. Similarly, immunohistochemical analysis revealed stronger CD86 and CD40 staining. Our findings show Zhuling PPS strongly reduced side effects and displayed synergistic effects during BCG instillation in rat bladder cancer models. The findings also suggest that the attenuation effect may result from direct activation of dendritic cell (DC) TLR4.
Keywords	adverse effects ; bladder ; carcinogenesis ; carcinoma ; flow cytometry ; immunohistochemistry ; ingredients ; models ; Polyporus ; polysaccharides ; rats ; sclerotia ; staining ; synergism ; therapeutics ; Toll-like receptor 4 ; urinary bladder neoplasms
Language	English
Dates of publication	2015-0315
Size	p. 30-35.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	1501516-6
ISSN	1879-1344 ; 0144-8617
ISSN (online)	1879-1344
ISSN	0144-8617
DOI	10.1016/j.carbpol.2014.11.012
Database	NAL-Catalogue (AGRICOLA)

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Article: Cytotoxicity of anti-tumor herbal Marsdeniae tenacissimae extract on erythrocytes

Hao, Ke / Bing-yu Chen / Kai-qiang Li / Yu Zhang / Cai-xia Li / Ying Wang / Lu-xi Jiang / Jiang Shen / Xiang-chai Guo / Wei Zhang / Meng-hua Zhu / Zhen Wang

Journal of Zhejiang University. 2017 July, v. 18, no. 7

2017

Abstract: Marsdeniae tenacissimae extract (MTE) has been used as an adjuvant medicine for cancer therapy for a long time. Although massive studies demonstrated its considerable anti-cancer effect, there is no research on its influence on erythrocytes, which are ... ...

Abstract	Marsdeniae tenacissimae extract (MTE) has been used as an adjuvant medicine for cancer therapy for a long time. Although massive studies demonstrated its considerable anti-cancer effect, there is no research on its influence on erythrocytes, which are firstly interacted with MTE in the circulation. To investigate the influence of MTE on erythrocytes, we used a flow cytometer to detect the MTE-treated alternations of morphology, calcium concentration, and reactive oxygen species (ROS) level in erythrocytes. We used hemolysis under different osmotic solutions to evaluate the fragility of erythrocytes. Data showed that MTE treatment dose-dependently increased the ratio of erythrocyte fragmentation (P<0.001) and shrinking, and elevated the forward scatter (FSC) value (P<0.001) and calcium accumulation (P<0.001). MTE induced ROS production of erythrocytes under the high glucose condition (P<0.01) and consequently caused a rise in fragility (P<0.05). These results suggest that MTE induces cytotoxicity and aging in erythrocytes in a dose-dependent manner, and presents the possibility of impairment on cancer patientsâ circulating erythrocytes when MTE is used as an anti-cancer adjuvant medicine.
Keywords	adjuvants ; antineoplastic activity ; calcium ; cytotoxicity ; dose response ; erythrocytes ; flow cytometry ; glucose ; hemolysis ; medicine ; neoplasms ; patients ; reactive oxygen species ; therapeutics
Language	English
Dates of publication	2017-07
Size	p. 597-604.
Publishing place	Zhejiang University Press
Document type	Article
ZDB-ID	2247290-3
ISSN	1862-1783 ; 1673-1581
ISSN (online)	1862-1783
ISSN	1673-1581
DOI	10.1631/jzus.B1600228
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Acid sphingomyelinase gene knockout ameliorates hyperhomocysteinemic glomerular injury in mice lacking cystathionine-β-synthase.

Krishna M Boini / Min Xia / Justine M Abais / Ming Xu / Cai-xia Li / Pin-Lan Li

PLoS ONE, Vol 7, Iss 9, p e

2012 Volume 45020

Abstract: Acid sphingomyelinase (ASM) has been implicated in the development of hyperhomocysteinemia (hHcys)-induced glomerular oxidative stress and injury. However, it remains unknown whether genetically engineering of ASM gene produces beneficial or detrimental ... ...

Abstract	Acid sphingomyelinase (ASM) has been implicated in the development of hyperhomocysteinemia (hHcys)-induced glomerular oxidative stress and injury. However, it remains unknown whether genetically engineering of ASM gene produces beneficial or detrimental action on hHcys-induced glomerular injury. The present study generated and characterized the mice lacking cystathionine β-synthase (Cbs) and Asm mouse gene by cross breeding Cbs(+/-) and Asm(+/-) mice. Given that the homozygotes of Cbs(-/-/)Asm(-/-) mice could not survive for 3 weeks. Cbs(+/-/)Asm(+/+), Cbs(+/-/)Asm(+/-) and Cbs(+/-/)Asm(-/-) as well as their Cbs wild type littermates were used to study the role of Asm(-/-) under a background of Cbs(+/-) with hHcys. HPLC analysis revealed that plasma Hcys level was significantly elevated in Cbs heterozygous (Cbs(+/-)) mice with different copies of Asm gene compared to Cbs(+/+) mice with different Asm gene copies. Cbs(+/-/)Asm(+/+) mice had significantly increased renal Asm activity, ceramide production and O(2.)(-) level compared to Cbs(+/+)/Asm(+/+), while Cbs(+/-/)Asm(-/-) mice showed significantly reduced renal Asm activity, ceramide production and O(2.)(-) level due to increased plasma Hcys levels. Confocal microscopy demonstrated that colocalization of podocin with ceramide was much lower in Cbs(+/-/)Asm(-/-) mice compared to Cbs(+/-/)Asm(+/+) mice, which was accompanied by a reduced glomerular damage index, albuminuria and proteinuria in Cbs(+/-/)Asm(-/-) mice. Immunofluorescent analyses of the podocin, nephrin and desmin expression also illustrated less podocyte damages in the glomeruli from Cbs(+/-/)Asm(-/-) mice compared to Cbs(+/-/)Asm(+/+) mice. In in vitro studies of podocytes, hHcys-enhanced O(2.)(-) production, desmin expression, and ceramide production as well as decreases in VEGF level and podocin expression in podocytes were substantially attenuated by prior treatment with amitriptyline, an Asm inhibitor. In conclusion, Asm gene knockout or corresponding enzyme inhibition protects the podocytes ...
Keywords	Medicine ; R ; Science ; Q
Subject code	572
Language	English
Publishing date	2012-01-01T00:00:00Z
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: DNA profiling of spermatozoa by laser capture microdissection and low volume-PCR.

Cai-xia Li / Jun-ping Han / Wen-yan Ren / An-quan Ji / Xiu-lan Xu / Lan Hu

PLoS ONE, Vol 6, Iss 8, p e

2011 Volume 22316

Abstract: Genetic profiling of sperm from complex biological mixtures such as sexual assault casework samples requires isolation of a pure sperm population and the ability to analyze low abundant samples. Current standard procedure for sperm isolation includes ... ...

Abstract	Genetic profiling of sperm from complex biological mixtures such as sexual assault casework samples requires isolation of a pure sperm population and the ability to analyze low abundant samples. Current standard procedure for sperm isolation includes preferential lysis of epithelial contaminants followed by collection of intact sperm by centrifugation. While effective for samples where sperm are abundant, this method is less effective when samples contain few spermatozoa. Laser capture microdissection (LCM) is a proven method for the isolation of cells biological mixtures, even when found in low abundance. Here, we demonstrate the efficacy of LCM coupled with on-chip low volume PCR (LV-PCR) for the isolation and genotyping of low abundance sperm samples. Our results indicate that this method can obtain complete profiles (13-16 loci) from as few as 15 sperm cells with 80% reproducibility, whereas at least 40 sperm cells are required to profile 13-16 loci by standard 'in-tube' PCR. Further, LCM and LV-PCR of a sexual assault casework sample generated a DNA genotype that was consistent with that of the suspect. This method was unable, however, to analyze a casework sample from a gang rape case in which two or more sperm contributors were in a mixed population. The results indicate that LCM and LV-PCR is sensitive and effective for genotyping sperm from sperm/epithelial cell mixtures when epithelial lysis may be insufficient due to low abundance of sperm; LCM and LV-PCR, however, failed in a casework sample when spermatozoa from multiple donors was present, indicating that further study is necessitated.
Keywords	Medicine ; R ; Science ; Q
Subject code	630
Language	English
Publishing date	2011-01-01T00:00:00Z
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: VHL deficiency augments anthracycline sensitivity of clear cell renal cell carcinomas by down-regulating ALDH2

Yao-Hui Gao / Zhao-Xia Wu / Li-Qi Xie / Cai-Xia Li / Yu-Qin Mao / Yan-Tao Duan / Bing Han / San-Feng Han / Yun Yu / Hao-Jie Lu / Peng-Yuan Yang / Tian-Rui Xu / Jing-Lin Xia / Guo-Qiang Chen / Li-Shun Wang

Nature Communications, Vol 8, Iss 1, Pp 1-

2017 Volume 14

Abstract: The VHL tumour suppressor gene is lost in approximately 70% of clear cell renal cell carcinoma (ccRCC). In this study, the authors demonstrate that VHL loss in these tumours augments anthracyclines chemotherapy by down-regulation of ALDH2. ...

Abstract	The VHL tumour suppressor gene is lost in approximately 70% of clear cell renal cell carcinoma (ccRCC). In this study, the authors demonstrate that VHL loss in these tumours augments anthracyclines chemotherapy by down-regulation of ALDH2.
Keywords	Science ; Q
Language	English
Publishing date	2017-06-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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