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Wang Z, Deng Q, Gu Y, Li M, Chen Y, Wang J, Zhang Y, Zhang J, Hu Q, Zhang S, Chen W, Chen Z, Li J, Wang X, Liang H. Integrated single-nucleus sequencing and spatial architecture analysis identified distinct injured-proximal tubular types in calculi rats. Cell Biosci 2023; 13:92. [PMID: 37208718 DOI: 10.1186/s13578-023-01041-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 05/01/2023] [Indexed: 05/21/2023] Open
Abstract
BACKGROUND Urolithiasis with high prevalence and recurrence rate, has impacts on kidney injury in patients, becomes a socioeconomic and healthcare problem in worldwide. However, the biology of kidney with crystal formation and proximal tubular injury remains essentially unclear. The present study aims to evaluate the cell biology and immune-communications in urolithiasis mediated kidney injury, to provide new insights in the kidney stone treatment and prevention. RESULTS We identified 3 distinct injured-proximal tubular cell types based on the differentially expression injury markers (Havcr1 and lcn2) and functional solute carriers (slc34a3, slc22a8, slc38a3 and slc7a13), and characterized 4 main immune cell types in kidney and one undefined cell population, where F13a1+/high/CD163+/high monocyte & macrophage and Sirpa/Fcgr1a/Fcgr2a+/high granulocyte were the most enriched. We performed intercellular crosstalk analysis based on the snRNA-seq data and explored the potential immunomodulation of calculi stone formation, and founded that the interaction between ligand Gas6 and its receptors (Gas6-Axl, Gas6-Mertk) was specifically observed in the injured-PT1 cells, but not injured-PT2 and -PT3 cells. The interaction of Ptn-Plxnb2 was only observed between the injured-PT3 cells and its receptor enriched cells. CONCLUSIONS Present study comprehensively characterized the gene expression profile in the calculi rat kidney at single nucleus level, identified novel marker genes for all cell types of rat kidney, and determined 3 distinct sub-population of injured-PT clusters, as well as intercellular communication between injured-PTs and immune cells. Our collection of data provides a reliable resource and reference for studies on renal cell biology and kidney disease.
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Affiliation(s)
- Zhu Wang
- Department of Urology, People's Hospital of Longhua Shenzhen, Southern Medical University, Shenzhen, Guangdong, 518109, P.R. China
| | - Qiong Deng
- Department of Urology, People's Hospital of Longhua Shenzhen, Southern Medical University, Shenzhen, Guangdong, 518109, P.R. China
| | - Yanli Gu
- Central Laboratory, People's Hospital of Longhua Shenzhen, Southern Medical University, Shenzhen, Guangdong, 518109, P.R. China
| | - Min Li
- Department of Pathology, People's Hospital of Longhua Shenzhen, Southern Medical University, Shenzhen, Guangdong, 518109, P.R. China
| | - Yeda Chen
- Department of Urology, People's Hospital of Longhua Shenzhen, Southern Medical University, Shenzhen, Guangdong, 518109, P.R. China
| | - Jieyan Wang
- Department of Urology, People's Hospital of Longhua Shenzhen, Southern Medical University, Shenzhen, Guangdong, 518109, P.R. China
| | - Ying Zhang
- Department of Urology, People's Hospital of Longhua Shenzhen, Southern Medical University, Shenzhen, Guangdong, 518109, P.R. China
| | - Jianwen Zhang
- Department of Urology, People's Hospital of Longhua Shenzhen, Southern Medical University, Shenzhen, Guangdong, 518109, P.R. China
| | - Qiyi Hu
- Department of Urology, People's Hospital of Longhua Shenzhen, Southern Medical University, Shenzhen, Guangdong, 518109, P.R. China
| | - Shenping Zhang
- Department of Urology, People's Hospital of Longhua Shenzhen, Southern Medical University, Shenzhen, Guangdong, 518109, P.R. China
| | - Wei Chen
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 518109, P.R. China
| | - Zhenhua Chen
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 518109, P.R. China
| | - Jiaying Li
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 518109, P.R. China
| | - Xisheng Wang
- Department of Urology, People's Hospital of Longhua Shenzhen, Southern Medical University, Shenzhen, Guangdong, 518109, P.R. China.
- Department of Urology, People's Hospital of Longhua, Southern Medical University, 38 Jinglong Jianshe Road, Shenzhen, Guangdong, 518109, P.R. China.
| | - Hui Liang
- Department of Urology, People's Hospital of Longhua Shenzhen, Southern Medical University, Shenzhen, Guangdong, 518109, P.R. China.
- Department of Urology, People's Hospital of Longhua, Southern Medical University, 38 Jinglong Jianshe Road, Shenzhen, Guangdong, 518109, P.R. China.
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2
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Lan C, Wu Y, Wang N, Luo Y, Zhao J, Zheng Y, Zhang Y, Huang L, Zhu Y, Lu L, Zhong W, Zeng J, Xia H. Association between ABHD1 and DOK6 polymorphisms and susceptibility to Hirschsprung disease in Southern Chinese children. J Cell Mol Med 2021; 25:9609-9616. [PMID: 34545688 PMCID: PMC8505836 DOI: 10.1111/jcmm.16905] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 07/26/2021] [Accepted: 08/04/2021] [Indexed: 12/31/2022] Open
Abstract
Hirschsprung disease (HSCR) is an infrequent congenital intestinal dysplasia. The known genetic variations are unable to fully explain the pathogenesis of HSCR. The α/β‐hydratase domain 1 (ABHD1) interferes with the proliferation and migration of intestinal stem cells. Docking protein 6 (DOK6) is involved in neurodevelopment through RET signalling pathway. We examined the association of ABHD1 and DOK6 genetic variants with HSCR using 1470 controls and 1473 HSCR patients from Southern Chinese children. The results clarified that DOK6 rs12968648 G allele significantly increased HSCR susceptibility, in the allelic model (p = 0.034; OR = 1.12, 95%CI = 1.01~1.24) and the dominant model (p = 0.038; OR = 1.12, 95%CI = 1.01~1.25). Clinical stratification analysis showed that rs12968648 G allele was associated with increased risk of short‐segment HSCR (S‐HSCR), in the allelic model (p = 0.028; OR = 1.14, 95%CI = 1.01~1.28) and the additive model (p = 0.030; OR = 1.14, 95%CI = 1.01~1.28). ABHD1 rs2304678 C allele had higher risk to develop total colonic aganglionosis (TCA) in the allelic model (p = 7.04E‐03; OR = 1.67, 95%CI = 1.15~2.43) and the dominant model (p = 4.12E‐03; OR = 1.93, 95%CI = 1.23~3.04). DOK6 rs12968648 and ABHD1 rs2304678 had significant intergenic synergistic effect according to logical regression (p = 0.0081; OR = 0.76, 95%CI = 0.63~0.93) and multifactor dimensionality reduction (MDR, p = 0.0045; OR = 1.25, 95%CI = 1.07~1.46). This study verified two susceptible variations of HSCR on ABHD1 and DOK6. Their roles in HSCR should be conducted in further studies.
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Affiliation(s)
- Chaoting Lan
- The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Yuxin Wu
- The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Ning Wang
- Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Yun Luo
- Department of Neonatology, Guangzhou Baiyunshan Hospital, Guangzhou, Guangdong, China
| | - Jinglu Zhao
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Yi Zheng
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Yan Zhang
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Lihua Huang
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Yun Zhu
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Lifeng Lu
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Wei Zhong
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jixiao Zeng
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Huimin Xia
- The First Affiliated Hospital of Jinan University, Guangzhou, China.,Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
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3
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Kawai K, Takahashi M. Intracellular RET signaling pathways activated by GDNF. Cell Tissue Res 2020; 382:113-123. [PMID: 32816064 DOI: 10.1007/s00441-020-03262-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 07/20/2020] [Indexed: 01/16/2023]
Abstract
Activation of REarranged during Transfection (RET) proto-oncogene is responsible for various human cancers such as papillary and medullary thyroid carcinomas and non-small cell lung carcinomas. RET activation in these tumors is caused by point mutations or gene rearrangements, resulting in constitutive activation of RET tyrosine kinase. Physiologically, RET is activated by glial cell line-derived neurotrophic factor (GDNF) ligands that bind to coreceptor GDNF family receptor alphas (GFRαs), leading to RET dimerization. GDNF-GFRα1-RET signaling plays crucial roles in the development of the enteric nervous system, kidney and lower urinary tract as well as in spermatogenesis. Intracellular tyrosine phosphorylation in RET and recruitment of adaptor proteins to phosphotyrosines are essential for various biological functions. Significance of intracellular RET signaling pathways activated by GDNF is discussed and summarized in this review.
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Affiliation(s)
- Kumi Kawai
- Department of Pathology, Fujita Health University, 1-98 Kutsukake-cho, Dengakugakubo, Toyoake, 470-1192, Japan
| | - Masahide Takahashi
- International Center for Cell and Gene Therapy, Fujita Health University, 1-98 Kutsukake-cho, Dengakugakubo, Toyoake, 470-1192, Japan. .,Department of Pathology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan.
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Abstract
Breast cancer, which is the most common type of cancer among women, is a heterogenous disease. It results from progressive accumulation of genetic and epigenetic alterations in different genes. The Dok1 protein has been identified as the major substrate of protein tyrosine kinases in hematopoietic cells. It is considered as a tumor suppressor due to the reports which describe its inhibitory effect on major oncogenic signaling pathways such as Mek/Erk/PI3k/Akt and Wnt/β-catenin. In this study, we investigated the mutation frequency of the DOK1 gene in 118 breast tumors using Sanger sequencing and DOK1 mRNA expression level in 63 breast cancer samples using qRT-PCR methods. Although the mutation frequency was low DOK1 mRNA expression levels were significantly reduced (63.5%) in the tumors compared to adjacent non-cancerous tissue. We also correlated expression changes with clinicopathological characteristics. Low mRNA levels correlated with age (p = 0.01) and c-erbB-2 (p = 0.05). In most of the previous reports, down-regulation of DOK1 mRNA expression has been associated with promoter methylation. We identified four different coding sequence alterations in 5.1% (6/118) of the tumor samples. However, all of these alterations were located in the functional domains of the protein. Therefore, these mutations may affect the function and/or cellular localization of the protein and contribute to cancer progression by this way. In conclusion our data indicate that DOK1 acts as a tumor suppressor in breast cancer and association of Dok1 with the c-erbB-2 mediated mechanism of action in breast cancer needs to be investigated.
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Sun GK, Tang LJ, Zhou JD, Xu ZJ, Yang L, Yuan Q, Ma JC, Liu XH, Lin J, Qian J, Yao DM. DOK6 promoter methylation serves as a potential biomarker affecting prognosis in de novo acute myeloid leukemia. Cancer Med 2019; 8:6393-6402. [PMID: 31486300 PMCID: PMC6797566 DOI: 10.1002/cam4.2540] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 08/14/2019] [Accepted: 08/22/2019] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Downstream of tyrosine kinase 6 (DOK6), which is specifically expressed in the nervous system, was previously recognized as an adapter only in neurite outgrowth. Recent studies also demonstrated the potential role of DOK6 in solid tumors such as gastric cancer and breast cancer. However, previous studies of DOK6 have not dealt with its roles in myeloid malignancies. Herein, we verified the promoter methylation status of DOK6 and further explored its clinical implication in de novo acute myeloid leukemia (AML). METHODS A total of 100 newly diagnosed adult AML patients were involved in the current study. DOK6 expression and methylation were detected by real-time qPCR and methylation-specific PCR (MSP), respectively. Bisulfite sequencing PCR (BSP) was performed to assess the methylation density of the DOK6 promoter. RESULTS Downstream of tyrosine kinase 6 promoter methylation was significantly increased in AML patients compared to controls (P = .037), whereas DOK6 expression significantly decreased in AML patients (P < .001). The expression of DOK6 was markedly up-regulated after treated by 5-aza-2'-deoxycytidine (5-aza-dC) in THP-1 cell lines. The methylation status of the DOK6 promoter was associated with French-American-British classifications (P = .037). There was no significant correlation existed between DOK6 expression and its promoter methylation (R = .077, P = .635). Interestingly, of whole-AML and non-APL AML patients, both have a tendency pertaining to the DOK6 methylation group and a significantly longer overall survival (OS) than the DOK6 unmethylation group (P = .042 and .036, respectively). CONCLUSION Our study suggested that DOK6 promoter hypermethylation was a common molecular event in de novo AML patients. Remarkably, DOK6 promoter methylation could serve as an independent and integrated prognostic biomarker not only in non-APL AML patients but also in AML patients who are less than 60 years old.
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Affiliation(s)
- Guo-Kang Sun
- Laboratory Center, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City, Zhenjiang, Jiangsu, People's Republic of China
| | - Li-Juan Tang
- Laboratory Center, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City, Zhenjiang, Jiangsu, People's Republic of China
| | - Jing-Dong Zhou
- Laboratory Center, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City, Zhenjiang, Jiangsu, People's Republic of China
| | - Zi-Jun Xu
- Laboratory Center, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City, Zhenjiang, Jiangsu, People's Republic of China
| | - Lan Yang
- Laboratory Center, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City, Zhenjiang, Jiangsu, People's Republic of China
| | - Qian Yuan
- The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City, Zhenjiang, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, Jiangsu, People's Republic of China
| | - Ji-Chun Ma
- The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City, Zhenjiang, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, Jiangsu, People's Republic of China
| | - Xing-Hui Liu
- Department of Clinical Laboratory, Shanghai Gongli Hospital, The Second Military Medical University, Shanghai, China
| | - Jiang Lin
- The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City, Zhenjiang, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, Jiangsu, People's Republic of China
| | - Jun Qian
- The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City, Zhenjiang, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, Jiangsu, People's Republic of China.,Department of Hematology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China
| | - Dong-Ming Yao
- Laboratory Center, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City, Zhenjiang, Jiangsu, People's Republic of China
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6
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Fielder GC, Yang TWS, Razdan M, Li Y, Lu J, Perry JK, Lobie PE, Liu DX. The GDNF Family: A Role in Cancer? Neoplasia 2018; 20:99-117. [PMID: 29245123 PMCID: PMC5730419 DOI: 10.1016/j.neo.2017.10.010] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 10/31/2017] [Accepted: 10/31/2017] [Indexed: 02/07/2023]
Abstract
The glial cell line-derived neurotrophic factor (GDNF) family of ligands (GFLs) comprising of GDNF, neurturin, artemin, and persephin plays an important role in the development and maintenance of the central and peripheral nervous system, renal morphogenesis, and spermatogenesis. Here we review our current understanding of GFL biology, and supported by recent progress in the area, we examine their emerging role in endocrine-related and other non-hormone-dependent solid neoplasms. The ability of GFLs to elicit actions that resemble those perturbed in an oncogenic phenotype, alongside mounting evidence of GFL involvement in tumor progression, presents novel opportunities for therapeutic intervention.
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Affiliation(s)
| | | | - Mahalakshmi Razdan
- The Centre for Biomedical and Chemical Sciences, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Auckland, New Zealand
| | - Yan Li
- The Centre for Biomedical and Chemical Sciences, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Auckland, New Zealand
| | - Jun Lu
- The Centre for Biomedical and Chemical Sciences, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Auckland, New Zealand
| | - Jo K Perry
- Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Peter E Lobie
- Cancer Science Institute of Singapore and Department of Pharmacology, National University of Singapore, Singapore; Tsinghua Berkeley Shenzhen Institute, Tsinghua University, Shenzhen, Guangdong, P. R. China
| | - Dong-Xu Liu
- The Centre for Biomedical and Chemical Sciences, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Auckland, New Zealand.
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7
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Leong SH, Lwin KM, Lee SS, Ng WH, Ng KM, Tan SY, Ng BL, Carter NP, Tang C, Lian Kon O. Chromosomal breaks at FRA18C: association with reduced DOK6 expression, altered oncogenic signaling and increased gastric cancer survival. NPJ Precis Oncol 2017; 1:9. [PMID: 29872697 PMCID: PMC5859466 DOI: 10.1038/s41698-017-0012-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 02/16/2017] [Accepted: 02/21/2017] [Indexed: 12/13/2022] Open
Abstract
Chromosomal rearrangements are common in cancer. More than 50% occur in common fragile sites and disrupt tumor suppressors. However, such rearrangements are not known in gastric cancer. Here we report recurrent 18q2 breakpoints in 6 of 17 gastric cancer cell lines. The rearranged chromosome 18, t(9;18), in MKN7 cells was flow sorted and identified by reverse chromosome painting. High-resolution tiling array hybridization mapped breakpoints to DOK6 (docking protein 6) intron 4 in FRA18C (18q22.2) and an intergenic region in 9q22.2. The same rearrangement was detected by FISH in 22% of 99 primary gastric cancers. Intron 4 truncation was associated with reduced DOK6 transcription. Analysis of The Cancer Genome Atlas stomach adenocarcinoma cohort showed significant correlation of DOK6 expression with histological and molecular phenotypes. Multiple oncogenic signaling pathways (gastrin-CREB, NGF-neurotrophin, PDGF, EGFR, ERK, ERBB4, FGFR1, RAS, VEGFR2 and RAF/MAP kinase) known to be active in aggressive gastric cancers were strikingly diminished in gastric cancers with low DOK6 expression. Median survival of patients with low DOK6-expressing tumors was 2100 days compared with 533 days in patients with high DOK6-expressing tumors (log-rank P = 0.0027). The level of DOK6 expression in tumors predicted patient survival independent of TNM stage. These findings point to new functions of human DOK6 as an adaptor that interacts with diverse molecular components of signaling pathways. Our data suggest that DOK6 expression is an integrated biomarker of multiple oncogenic signals in gastric cancer and identify FRA18C as a new cancer-associated fragile site.
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Affiliation(s)
- Siew Hong Leong
- 1Division of Medical Sciences, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, 169610 Singapore.,2Department of Biochemistry, National University of Singapore, 8 Medical Drive, Singapore, 117596 Singapore
| | - Kyaw Myo Lwin
- 1Division of Medical Sciences, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, 169610 Singapore
| | - Sze Sing Lee
- 1Division of Medical Sciences, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, 169610 Singapore
| | - Wai Har Ng
- 1Division of Medical Sciences, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, 169610 Singapore
| | - Kia Min Ng
- 1Division of Medical Sciences, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, 169610 Singapore
| | - Soo Yong Tan
- 3Department of Pathology, Singapore General Hospital, Outram Road, Singapore, 169608 Singapore
| | - Bee Ling Ng
- 4Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Nigel P Carter
- 4Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Carol Tang
- 5National Neuroscience Institute, 11 Jalan Tan Tock Seng, Singapore, 308433 Singapore
| | - Oi Lian Kon
- 1Division of Medical Sciences, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, 169610 Singapore.,2Department of Biochemistry, National University of Singapore, 8 Medical Drive, Singapore, 117596 Singapore
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8
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Jiao S, Maltecca C, Gray KA, Cassady JP. Feed intake, average daily gain, feed efficiency, and real-time ultrasound traits in Duroc pigs: II. Genomewide association. J Anim Sci 2015; 92:2846-60. [PMID: 24962532 DOI: 10.2527/jas.2014-7337] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Efficient use of feed resources has become a clear challenge for the U.S. pork industry as feed costs continue to be the largest variable expense. The availability of the Illumina Porcine60K BeadChip has greatly facilitated whole-genome association studies to identify chromosomal regions harboring genes influencing those traits. The current study aimed at identifying genomic regions associated with variation in feed efficiency and several production traits in a Duroc terminal sire population, including ADFI, ADG, feed conversion ratio, residual feed intake (RFI), real-time ultrasound back fat thickness (BF), ultrasound muscle depth, intramuscular fat content (IMF), birth weight (BW at birth), and weaning weight (BW at weaning). Single trait association analyses were performed using Bayes B models with 35,140 SNP on 18 autosomes after quality control. Significance of nonoverlapping 1-Mb length windows (n = 2,380) were tested across 3 QTL inference methods: posterior distribution of windows variances from Monte Carlo Markov Chain, naive Bayes factor, and nonparametric bootstrapping. Genes within the informative QTL regions for the traits were annotated. A region ranging from166 to 140 Mb (4-Mb length) on SSC 1, approximately 8 Mb upstream of the MC4R gene, was significantly associated with ADFI, ADG, and BF, where SOCS6 and DOK6 are proposed as the most likely candidate genes. Another region affecting BW at weaning was identified on SSC 4 (84-85 Mb), harboring genes previously found to influence both human and cattle height: PLAG1, CHCHD7, RDHE2 (or SDR16C5), MOS, RPS20, LYN, and PENK. No QTL were identified for RFI, IMF, and BW at birth. In conclusion, we have identified several genomic regions associated with traits affecting nutrient utilization that could be considered for future genomic prediction to improve feed utilization.
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Affiliation(s)
- S Jiao
- Department of Animal Science, North Carolina State University, Raleigh 27695
| | - C Maltecca
- Department of Animal Science, North Carolina State University, Raleigh 27695
| | - K A Gray
- Smithfield Premium Genetics, Rose Hill, NC 28458
| | - J P Cassady
- Department of Animal Science, North Carolina State University, Raleigh 27695
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9
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Li G, Pan W, Yang X, Miao J. Gene co-expression network and function modules in three types of glioma. Mol Med Rep 2014; 11:3055-63. [PMID: 25435164 DOI: 10.3892/mmr.2014.3014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 04/25/2014] [Indexed: 11/06/2022] Open
Abstract
The aim of the present study was to identify the disease‑associated genes and their functions involved in the development of three types of glioma (astrocytoma, glioblastoma and oligodendroglioma) with DNA microarray technology, and to analyze their differences and correlations. First, the gene expression profile GSE4290 was downloaded from the Gene Expression Omnibus database, then the probe‑level data were pre‑processed and the differentially expressed genes (DEGs) were identified with limma package in R language. Gene functions of the selected DEGs were further analyzed with the Database for Annotation, Visualization and Integrated Discovery. After the co‑expression network of DEGs was constructed by Cytoscape, the functional modules were mined and enrichment analysis was performed, and then the similarities and differences between any two types of glioma were compared. A total of 1151 genes between normal and astrocytoma tissues, 684 genes between normal and malignant glioma tissues, and 551 genes between normal and oligodendroglioma tissues were filtered as DEGs, respectively. By constructing co‑expression networks of DEGs, a total of 77232, 455 and 987 interactions were involved in the differentially co‑expressed networks of astrocytoma, oligodendroglioma and glioblastoma, respectively. The functions of DEGs were consistent with the modules in astrocytoma, glioblastoma and oligodendroglioma, which were mainly enriched in neuron signal transmission, immune responses and synthesis of organic acids, respectively. Model functions of astrocytoma and glioblastoma were similar (mainly related with immune response), while the model functions of oligodendroglioma differed markedly from that of the other two types. The identification of the associations among these three types of glioma has potential clinical utility for improving the diagnosis of different types of glioma in the future. In addition, these results have marked significance in studying the underlying mechanisms, distinguishing between normal and cancer tissues, and examining novel therapeutic strategies for patients with glioma.
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Affiliation(s)
- Gang Li
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Weiran Pan
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Xiaoxiao Yang
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Jinming Miao
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
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10
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Ghanem T, Bracken J, Kasem A, Jiang WG, Mokbel K. mRNA expression of DOK1-6 in human breast cancer. World J Clin Oncol 2014; 5:156-163. [PMID: 24829863 PMCID: PMC4014788 DOI: 10.5306/wjco.v5.i2.156] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2013] [Revised: 01/08/2014] [Accepted: 01/20/2014] [Indexed: 02/06/2023] Open
Abstract
AIM: To examine the expression of downstream of tyrosine kinase (DOK)1-6 genes in normal and breast cancer tissue and correlated this with several clinico-pathological and prognostic factors.
METHODS: DOK1-6 mRNA extraction and reverse transcription were performed on fresh frozen breast cancer tissue samples (n = 112) and normal background breast tissue (n = 31). Tissues were collected between 1991 and 1996 at two centres and all patients underwent mastectomy and ipsilateral axillary node dissection. All tissues were randomly numbered and the details were only made known after all analyses were completed. Transcript levels of expression were determined using real-time polymerase chain reaction and analyzed against TNM stage, tumour grade and clinical outcome over a 10-year follow-up period.
RESULTS: DOK-2 and DOK-6 expression decreased with increasing TNM stage. DOK-6 expression decreased with increasing Nottingham Prognostic Index (NPI) [NPI-1 vs NPI-3 (mean copy number 15.4 vs 0.22, 95%CI: 2.7-27.6, P = 0.018) and NPI-2 vs NPI-3 (mean copy number 7.6 vs 0.22, 95%CI: 0.1-14.6, P = 0.048)]. After a median follow up period of 10 years, higher levels of DOK-2 expression were found among patients who remained disease-free compared to those who developed local or distant recurrence (mean copy number 3.94 vs 0.0000096, 95%CI: 1.0-6.85, P = 0.0091), and distant recurrence (mean copy number 3.94 vs 0.0025, 95%CI: 1.0-6.84, P = 0.0092). Patients who remained disease-free had higher levels of DOK-6 expression compared to those who died from breast cancer.
CONCLUSION: Decreasing expression levels of DOK-2 and DOK-6 with increased breast tumour progression supports the notion that DOK-2 and DOK-6 behave as tumour suppressors in human breast cancer.
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Ibáñez CF. Structure and physiology of the RET receptor tyrosine kinase. Cold Spring Harb Perspect Biol 2013; 5:5/2/a009134. [PMID: 23378586 DOI: 10.1101/cshperspect.a009134] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The identification of the ret oncogene by Masahide Takahashi and Geoffrey Cooper in 1985 was both serendipitous and paradigmatic ( Takahashi et al. 1985). By transfecting total DNA from a human lymphoma into mouse NIH3T3 cells, they obtained one clone, which in secondary transformants yielded more than 100-fold improvement in transformation efficiency. Subsequent investigations revealed that the ret oncogene was not present as such in the primary lymphoma, but was derived by DNA rearrangement during transfection from normal human sequences of the ret locus. At the time, activation by DNA rearrangement had not been previously described for a transforming gene with the NIH3T3 transfection assay. The discovery of ret opened a field of study that has had a profound impact in cancer research, developmental biology, and neuroscience, and that continues to yield surprises and important insights to this day.
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Affiliation(s)
- Carlos F Ibáñez
- Department of Neuroscience, Karolinska Institute, S-17177 Stockholm, Sweden.
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Martucciello G, Lerone M, Bricco L, Tonini GP, Lombardi L, Del Rossi CG, Bernasconi S. Multiple endocrine neoplasias type 2B and RET proto-oncogene. Ital J Pediatr 2012; 38:9. [PMID: 22429913 PMCID: PMC3368781 DOI: 10.1186/1824-7288-38-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Accepted: 03/19/2012] [Indexed: 02/06/2023] Open
Abstract
Multiple Endocrine Neoplasia type 2B (MEN 2B) is an autosomal dominant complex oncologic neurocristopathy including medullary thyroid carcinoma, pheochromocytoma, gastrointestinal disorders, marphanoid face, and mucosal multiple ganglioneuromas. Medullary thyroid carcinoma is the major cause of mortality in MEN 2B syndrome, and it often appears during the first years of life. RET proto-oncogene germline activating mutations are causative for MEN 2B. The 95% of MEN 2B patients are associated with a point mutation in exon 16 (M918/T). A second point mutation at codon 883 has been found in 2%-3% of MEN 2B cases. RET proto-oncogene is also involved in different neoplastic and not neoplastic neurocristopathies. Other RET mutations cause MEN 2A syndrome, familial medullary thyroid carcinoma, or Hirschsprung's disease. RET gene expression is also involved in Neuroblastoma. The main diagnosis standards are the acetylcholinesterase study of rectal mucosa and the molecular analysis of RET. In our protocol the rectal biopsy is, therefore, the first approach. RET mutation detection offers the possibility to diagnose MEN 2B predisposition at a pre-clinical stage in familial cases, and to perform an early total prophylactic thyroidectomy. The surgical treatment of MEN 2B is total thyroidectomy with cervical limphadenectomy of the central compartment of the neck. When possible, this intervention should be performed with prophylactic aim before 1 year of age in patients with molecular genetic diagnosis. Recent advances into the mechanisms of RET proto-oncogene signaling and pathways of RET signal transduction in the development of MEN 2 and MTC will allow new treatment possibilities.
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Affiliation(s)
- Giuseppe Martucciello
- University of Genova, Associate Professor of Pediatric Surgery - DIPE, Via Gaslini, 5 Genova (16147), Italy
| | - Margherita Lerone
- Laboratory of Molecular Genetic, Istituto G. Gaslini, Genova (16147), Italy
| | - Lara Bricco
- Laboratory of Molecular Genetic, Istituto G. Gaslini, Genova (16147), Italy
| | - Gian Paolo Tonini
- Traslational Oncopathology National Cancer Research Institute, Genova (16100), Italy
| | - Laura Lombardi
- Department of Pediatric Surgery, Ospedale Maggiore, Via Antonio Gramsci 14, Parma (43010), Italy
| | - Carmine G Del Rossi
- Department of Pediatric Surgery, Ospedale Maggiore, Via Antonio Gramsci 14, Parma (43010), Italy
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Abstract
Docking proteins comprise a distinct category of intracellular, noncatalytic signalling protein, that function downstream of a variety of receptor and receptor-associated tyrosine kinases and regulate diverse physiological and pathological processes. The growth factor receptor bound 2-associated binder/Daughter of Sevenless, insulin receptor substrate, fibroblast growth factor receptor substrate 2 and downstream of tyrosine kinases protein families fall into this category. This minireview focuses on the structure, function and regulation of these proteins.
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Affiliation(s)
- Tilman Brummer
- Centre for Biological Systems Analysis (ZBSA), Albert-Ludwigs-University of Freiburg, Freiburg, Germany
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