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Pekdemir B, Karav S. Exploring the diverse biological significance and roles of fucosylated oligosaccharides. Front Mol Biosci 2024; 11:1403727. [PMID: 38863964 PMCID: PMC11165149 DOI: 10.3389/fmolb.2024.1403727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 05/08/2024] [Indexed: 06/13/2024] Open
Abstract
Long since, carbohydrates were thought to be used just as an energy source and structural material. However, in recent years, with the emergence of the field of glycobiology and advances in glycomics, much has been learned about the biological role of oligosaccharides, a carbohydrate polymer containing a small number of monosaccharides, in cell-cell interaction, signal transduction, immune response, pathogen adhesion processes, early embryogenesis, and apoptosis. The function of oligosaccharides in these processes is diversified by fucosylation, also known as modification of oligosaccharides. Fucosylation has allowed the identification of more than 100 different oligosaccharide structures that provide functional diversity. ABO blood group and Lewis antigens are among the best known fucosyl-linked oligosaccharides. In addition, the antigens in the ABO system are composed of various sugar molecules, including fucosylated oligosaccharides, and Lewis antigens are structurally similar to ABO antigens but differ in the linkage of sugars. Variation in blood group antigen expression affects the host's susceptibility to many infections. However, altered expression of ABO and Lewis antigens is related with prognosis in carcinoma types. In addition, many pathogens recognize and bind to human tissues using a protein receptor with high affinity for the fucose molecule in glycoconjugates, such as lectin. Fucosylated oligosaccharides also play vital roles during fertilization and early embryogenesis. Learning and memory-related processes such as neurite growth, neurite migration, and synapse formation seen during the development of the brain, which is among the first organs to develop in embryogenesis, are regulated by fucosylated oligosaccharides. In conclusion, this review mentions the vital roles of fucosylated oligosaccharides in biology, drawing attention to their importance in the development of chemical tools to be used in function analysis and the investigation of various therapeutic targets.
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Affiliation(s)
| | - Sercan Karav
- Department of Molecular Biology and Genetics, Çanakkale Onsekiz Mart University, Çanakkale, Türkiye
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2
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Xu X, Zhang X, Kou R, Liu Y, Chen S, Li Z, Jian Z, Wang Z. Prognosis and immunotherapy response prediction based on M2 macrophage-related genes in colon cancer. J Cancer Res Clin Oncol 2024; 150:31. [PMID: 38270646 PMCID: PMC10811099 DOI: 10.1007/s00432-023-05573-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 12/12/2023] [Indexed: 01/26/2024]
Abstract
BACKGROUND M2 macrophage were revealed to play a crucial role in immune evasion and immunotherapies. This study aims to explore the potential significance of M2 macrophage-related genes in colon adenocarcinoma (COAD) by analysizing the transcriptome data in a comprehensive way. METHODS We collected RNA-sequencing (RNA-seq) data of COAD from The Cancer Genome Atlas (TCGA) and Gene Expression Ominibus (GEO) databases. We calculated the immune infiltration scores of every sample using CIBERSORT algorithm. Through weighted gene co-expression network analysis (WGCNA), we picked out M2 macrophage-related genes. With these genes we screened out prognosis related genes which were utilized to construct a signature to assess the prognosis of patients. To extend the potential application of the signature, we also calculated the correlations with immune infiltration. Finally, we applied techniques such as quantitative reverse transcription polymerase chain reaction (qRT-PCR) and immunoblotting (Western Blotting) to validate the RNF32 gene in cellular in vitro assays. RESULTS Seven M2 macrophage-related genes signature was constructed, which was an excellent prognostic predictor in two independent groups. The high-risk group showed lower immune infiltration and poorer response to immunotherapies than those of the low-risk group. The cell vitro experiments showed that the expression level of RNF32 was upregulated in colon cancer cell lines compared with normal cell lines. Moreover, we found that RNF32 may promote the proliferation, migration and invasion of cancer cells in vitro by inhibiting apoptosis. CONCLUSION A novel M2 macrophage-related gene signature affects the prognosis and immune characteristics of colon cancer.
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Affiliation(s)
- Xiaochen Xu
- Department of Gastrointestinal Surgery, Affiliated Hospital of Guilin Medical University, Guangxi Zhuang Autonomous Region, Guilin, 541001, China
| | - Xinwen Zhang
- Department of Gastrointestinal Surgery, Affiliated Hospital of Guilin Medical University, Guangxi Zhuang Autonomous Region, Guilin, 541001, China
| | - Ruilong Kou
- Department of Gastrointestinal Surgery, Affiliated Hospital of Guilin Medical University, Guangxi Zhuang Autonomous Region, Guilin, 541001, China
| | - Yihao Liu
- Department of Gastrointestinal Surgery, Affiliated Hospital of Guilin Medical University, Guangxi Zhuang Autonomous Region, Guilin, 541001, China
| | - Siqi Chen
- Department of Gastrointestinal Surgery, Affiliated Hospital of Guilin Medical University, Guangxi Zhuang Autonomous Region, Guilin, 541001, China
| | - Zuguo Li
- Department of Gastrointestinal Surgery, Affiliated Hospital of Guilin Medical University, Guangxi Zhuang Autonomous Region, Guilin, 541001, China
| | - Zhiyuan Jian
- Department of Gastrointestinal Surgery, Affiliated Hospital of Guilin Medical University, Guangxi Zhuang Autonomous Region, Guilin, 541001, China.
| | - Zhenran Wang
- Department of Gastrointestinal Surgery, Affiliated Hospital of Guilin Medical University, Guangxi Zhuang Autonomous Region, Guilin, 541001, China.
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3
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Apanovich N, Matveev A, Ivanova N, Burdennyy A, Apanovich P, Pronina I, Filippova E, Kazubskaya T, Loginov V, Braga E, Alimov A. Prediction of Distant Metastases in Patients with Kidney Cancer Based on Gene Expression and Methylation Analysis. Diagnostics (Basel) 2023; 13:2289. [PMID: 37443682 DOI: 10.3390/diagnostics13132289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 06/28/2023] [Accepted: 07/04/2023] [Indexed: 07/15/2023] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is the most common and aggressive histological type of cancer in this location. Distant metastases are present in approximately 30% of patients at the time of first examination. Therefore, the ability to predict the occurrence of metastases in patients at early stages of the disease is an urgent task aimed at personalized treatment. Samples of tumor and paired histologically normal kidney tissue from patients with metastatic and non-metastatic ccRCC were studied. Gene expression was analyzed using real-time PCR. The level of gene methylation was evaluated using bisulfite conversion followed by quantitative methylation-specific PCR. Two groups of genes were analyzed in this study. The first group includes genes whose expression is significantly reduced during metastasis: CA9, NDUFA4L2, EGLN3, and BHLHE41 (p < 0.001, ROC analysis). The second group includes microRNA genes: MIR125B-1, MIR137, MIR375, MIR193A, and MIR34B/C, whose increased methylation levels are associated with the development of distant metastases (p = 0.002 to <0.001, ROC analysis). Based on the data obtained, a combined panel of genes was formed to identify patients whose tumors have a high metastatic potential. The panel can estimate the probability of metastasis with an accuracy of up to 92%.
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Affiliation(s)
- Natalya Apanovich
- Research Centre for Medical Genetics, 1 Moskvorechye St., Moscow 115522, Russia
| | - Alexey Matveev
- Federal State Budgetary Institution (N.N. Blokhin National Medical Research Center of Oncology) of the Ministry of Health of the Russian Federation, 24 Kashirskoe Shosse, Moscow 115478, Russia
| | - Natalia Ivanova
- Institute of General Pathology and Pathophysiology, Baltijskaya St. 8, Moscow 125315, Russia
| | - Alexey Burdennyy
- Institute of General Pathology and Pathophysiology, Baltijskaya St. 8, Moscow 125315, Russia
| | - Pavel Apanovich
- Research Centre for Medical Genetics, 1 Moskvorechye St., Moscow 115522, Russia
| | - Irina Pronina
- Institute of General Pathology and Pathophysiology, Baltijskaya St. 8, Moscow 125315, Russia
| | - Elena Filippova
- Institute of General Pathology and Pathophysiology, Baltijskaya St. 8, Moscow 125315, Russia
| | - Tatiana Kazubskaya
- Federal State Budgetary Institution (N.N. Blokhin National Medical Research Center of Oncology) of the Ministry of Health of the Russian Federation, 24 Kashirskoe Shosse, Moscow 115478, Russia
| | - Vitaly Loginov
- Institute of General Pathology and Pathophysiology, Baltijskaya St. 8, Moscow 125315, Russia
| | - Eleonora Braga
- Research Centre for Medical Genetics, 1 Moskvorechye St., Moscow 115522, Russia
- Institute of General Pathology and Pathophysiology, Baltijskaya St. 8, Moscow 125315, Russia
| | - Andrei Alimov
- Research Centre for Medical Genetics, 1 Moskvorechye St., Moscow 115522, Russia
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4
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Cao W, Zeng Z, Lan J, Yang Y, Lu M, Lei S. Knockdown of FUT11 inhibits the progression of gastric cancer via the PI3K/AKT pathway. Heliyon 2023; 9:e17600. [PMID: 37483811 PMCID: PMC10362185 DOI: 10.1016/j.heliyon.2023.e17600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 06/17/2023] [Accepted: 06/22/2023] [Indexed: 07/25/2023] Open
Abstract
Gastric cancer (GC) is a common and highly malignant tumor of the digestive tract. Members of the focused fucosyltransferase (FUT) family participate in the advancement of various types of cancer. However, research of FUT family members in the progression of GC known to be limited. The purpose of the research was to determine the function of important affiliates of the FUT family in GC and to explore its impacts on the proliferation and migration of GC cells and molecular mechanisms. For the study, fucosyltransferase11 (FUT11) was confirmed to be the only affiliate of the FUT family that was upmodulated in GC tissues and linked to poor survival according to GEPIA data. Furthermore, compared with adjacent noncancerous tissues, the expression of FUT11 was increased in GC tissues. The elevated FUT11 expression suggested that the overall survival (OS) rate of GC is low. Inhibition of FUT11 significantly reduced the proliferation and migration and suppressed the PI3K/AKT pathway by down-regulated collagen type VI alpha 3 chain (COL6A3) in GC cells. The present study has demonstrated that reinstating the expression of COL6A3 in gastric cancer (GC) cells can counteract the inhibitory impact of FUT11 knockdown on the proliferation and migration of GC cells. In conclusion, FUT11 may serve as a novel biomarker for GC, as it modulates GC cell proliferation and migration through the PI3K/AKT signaling pathway.
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Affiliation(s)
- Wenpeng Cao
- Department of Anatomy, School of Basic Medicine, Guizhou Medical University, Guiyang 550009, Guizhou, China
| | - Zhirui Zeng
- Department of Physiology, School of Basic Medicine, Guizhou Medical University, Guiyang 550009, Guizhou, China
| | - Jinzhi Lan
- Department of Physiology, School of Basic Medicine, Guizhou Medical University, Guiyang 550009, Guizhou, China
| | - Yushi Yang
- Department of Pathology, Affiliated Hospital of Guizhou Medical University, Guiyang 550009, Guizhou, China
| | - Min Lu
- Department of Gastroenterology, Zhujiang Hospital, Southern Medical University, Guangzhou, 510000, Guangdong, China
| | - Shan Lei
- Department of Physiology, School of Basic Medicine, Guizhou Medical University, Guiyang 550009, Guizhou, China
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5
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Zhang P, Tang W, Jiang Y, Lyu F, Liu Z, Xiao Y, Wang D. Dry and wet experiments reveal the significant role of FUT11 in clear cell renal cell carcinoma. Int Immunopharmacol 2022; 113:109447. [PMID: 36403525 DOI: 10.1016/j.intimp.2022.109447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 11/18/2022]
Abstract
BACKGROUND Renal cancer is one of the most common urogenital tumors worldwide. Although numerous traditional and relatively new therapeutic strategies have been adopted for clear cell renal cell carcinoma (ccRCC) patients, their effects are not satisfactory enough for the improvement of patients. The pathogenesis and progression of ccRCC requires further investigations. METHODS Using a series of bioinformatic analyses, the expression levels, clinical relevance, and prognostic potential of FUT11 as well as its correlations with immune cells in ccRCC were investigated. The mRNA and protein expression levels of FUT11 in renal cancer cell lines and human tissues were determined using quantitative real-time-polymerase chain reaction (RT-PCR) and Western blot analyses. MTT, colony formation, Edu, and wound healing assays were performed to explore the function of FUT11 in renal cancer cell lines. The immunohistochemical staining of human and mouse tissues was performed to reveal the correlations between the expression levels of FUT11 and the infiltration level of immune cell subtypes. Using mouse xenograft models, the role of FUT11 was further investigated in-vivo. RESULTS The data mining and corresponding analyses indicated that the expression levels of FUT11 were elevated in renal cancer and independently correlated with the prognosis of ccRCC patients. The cibersort and ssGSEA algorithms revealed differential infiltration levels of immune cells between the patients with distinct expression levels of FUT11; these results were verified by the consequent human renal cancer tissues and animal models. The MTT, colony formation, EdU, and wound healing assays showed that the decreased expression level of FUT11 could promote the proliferation and migration of renal cancer cell lines. The animal models-based analysis showed similar results. CONCLUSIONS In conclusion, this study identified a novel important molecule correlated with the prognosis of ccRCC patients and revealed its immune-related role and its function in the proliferation and migration of renal cancer cells. This study might provide a novel basis for the treatment of renal cancer.
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Affiliation(s)
- Pu Zhang
- Department of Urology Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, China
| | - Wensen Tang
- Department of Urology Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, China
| | - Yidi Jiang
- Sichuan Regenerative Medicine Engineering and Technology Center, Chengdu Qingke Biotechnology Co., Ltd., China
| | - Fang Lyu
- Department of Urology Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, China
| | - Zijian Liu
- Department of Head and Neck Oncology and Department of Radiation oncology, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yajun Xiao
- Department of Urology Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, China.
| | - Decai Wang
- Department of Urology Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, China.
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6
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Glycosylation in Renal Cell Carcinoma: Mechanisms and Clinical Implications. Cells 2022; 11:cells11162598. [PMID: 36010674 PMCID: PMC9406705 DOI: 10.3390/cells11162598] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/11/2022] [Accepted: 08/17/2022] [Indexed: 11/16/2022] Open
Abstract
Renal cell carcinoma (RCC) is one of the most prevalent malignant tumors of the urinary system, accounting for around 2% of all cancer diagnoses and deaths worldwide. Clear cell RCC (ccRCC) is the most prevalent and aggressive histology with an unfavorable prognosis and inadequate treatment. Patients' progression-free survival is considerably improved by surgery; however, 30% of patients develop metastases following surgery. Identifying novel targets and molecular markers for RCC prognostic detection is crucial for more accurate clinical diagnosis and therapy. Glycosylation is a critical post-translational modification (PMT) for cancer cell growth, migration, and invasion, involving the transfer of glycosyl moieties to specific amino acid residues in proteins to form glycosidic bonds through the activity of glycosyltransferases. Most cancers, including RCC, undergo glycosylation changes such as branching, sialylation, and fucosylation. In this review, we discuss the latest findings on the significance of aberrant glycans in the initiation, development, and progression of RCC. The potential biomarkers of altered glycans for the diagnosis and their implications in RCC have been further highlighted.
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7
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Tanio M, Fukiage Y, Muramoto A, Yokoyama O, Kobayashi M. Proposal of sialyl Lewis x/a as prognostic biomarkers in clear cell renal cell carcinoma: A study on a cohort of 117 patients submitted to curative surgery. JOURNAL OF CLINICAL UROLOGY 2022. [DOI: 10.1177/20514158221082884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Objective: Metastatic recurrence has been reported to occur in 20–30% of patients with clear cell renal cell carcinoma (ccRCC). Although the prognosis of these patients is poor, no marker has been established to predict metastatic potential and/or prognosis. Therefore, we investigated membrane expression of sialyl Lewis x (sLex) and sialyl Lewis a (sLea), which is generally considered to be associated with cancer metastasis. Materials and methods: We enrolled 117 patients who underwent curative surgery for RCC and were pathologically diagnosed as ccRCC. Immunohistochemistry for sLex and sLea was performed to evaluate the signal intensity on the cell membrane. We statistically analysed whether membrane expression of sLex/sLea is correlated with clinicopathological parameters and prognosis. Results: Of the 117 patients, 72 were classified as sLex-positive and 44 as sLea-positive. The sLex-positive group had significantly shorter progression-free survival (PFS) and overall survival (OS) than the negative group. Similarly, the sLea-positive group had significantly shorter PFS than the negative group, and it showed a trend towards a reduction of OS, although it did not reach statistical significance, a fact that could be due to the small sample size. Conclusion: Both sLex and sLea could be possible future prognostic indicators in ccRCC. Level of evidence: Level 3
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Affiliation(s)
- Makoto Tanio
- Department of Tumor Pathology, Faculty of Medical Sciences, University of Fukui, Japan
- Department of Urology, Faculty of Medical Sciences, University of Fukui, Japan
| | - Yusuke Fukiage
- Department of Tumor Pathology, Faculty of Medical Sciences, University of Fukui, Japan
- Department of Urology, Faculty of Medical Sciences, University of Fukui, Japan
| | - Akifumi Muramoto
- Department of Tumor Pathology, Faculty of Medical Sciences, University of Fukui, Japan
- Division of Surgical Pathology, University of Fukui Hospital, Japan
| | - Osamu Yokoyama
- Department of Urology, Faculty of Medical Sciences, University of Fukui, Japan
| | - Motohiro Kobayashi
- Department of Tumor Pathology, Faculty of Medical Sciences, University of Fukui, Japan
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8
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Rosa-Fernandes L, Oba-Shinjo SM, Macedo-da-Silva J, Marie SKN, Palmisano G. Aberrant Protein Glycosylation in Brain Cancers, with Emphasis on Glioblastoma. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1382:39-70. [DOI: 10.1007/978-3-031-05460-0_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
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9
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Fucosylation in Urological Cancers. Int J Mol Sci 2021; 22:ijms222413333. [PMID: 34948129 PMCID: PMC8708646 DOI: 10.3390/ijms222413333] [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: 11/10/2021] [Revised: 12/03/2021] [Accepted: 12/05/2021] [Indexed: 02/08/2023] Open
Abstract
Fucosylation is an oligosaccharide modification that plays an important role in immune response and malignancy, and specific fucosyltransferases (FUTs) catalyze the three types of fucosylations: core-type, Lewis type, and H type. FUTs regulate cancer proliferation, invasiveness, and resistance to chemotherapy by modifying the glycosylation of signaling receptors. Oligosaccharides on PD-1/PD-L1 proteins are specifically fucosylated, leading to functional modifications. Expression of FUTs is upregulated in renal cell carcinoma, bladder cancer, and prostate cancer. Aberrant fucosylation in prostate-specific antigen (PSA) could be used as a novel biomarker for prostate cancer. Furthermore, elucidation of the biological function of fucosylation could result in the development of novel therapeutic targets. Further studies are needed in the field of fucosylation glycobiology in urological malignancies.
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10
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Haan JC, Bhaskaran R, Ellappalayam A, Bijl Y, Griffioen CJ, Lujinovic E, Audeh WM, Penault-Llorca F, Mittempergher L, Glas AM. MammaPrint and BluePrint comprehensively capture the cancer hallmarks in early-stage breast cancer patients. Genes Chromosomes Cancer 2021; 61:148-160. [PMID: 34841595 PMCID: PMC9299843 DOI: 10.1002/gcc.23014] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 11/16/2021] [Accepted: 11/16/2021] [Indexed: 12/19/2022] Open
Abstract
MammaPrint® (MP) is a 70‐gene signature that stratifies early‐stage breast cancer patients into low‐ and high risk of distant relapse. Further stratification of MP risk results identifies four risk subgroups, ultra‐low (UL), low, high 1, and high 2, with specific prognostic and predictive outcomes. BluePrint® (BP) is an 80‐gene signature that classifies breast tumors as basal, luminal, or HER2 molecular subtype. To gain insight into their biological significance, we annotated the MP 70‐ and BP 80‐genes with respect to the 10 hallmarks of cancer (HoC). Furthermore, we related gene expression profiles of the extreme ends of the MP low‐ and high‐risk patients (here called, ultra‐low (UL) and ultra‐high (UH) or High2, respectively), to the 10 HoC per BP subtype by differential gene expression and pathway analysis. MP and BP gene functions reflected all 10 HoCs. Most MP and BP genes were associated with sustaining proliferative signaling, followed by genome instability and mutation categories. Based on the gene expression profiles, UL and UH subgroup pathways were down ‐or upregulated, respectively, reflecting proliferative and metastatic features, such as G2M checkpoint, DNA repair, oxidative phosphorylation, immune invasion, PI3K/AKT/mTOR signaling, and hypoxia pathways. Notably, the UH HER2‐type was enriched in several immune signaling pathways, such as IL2/STAT5 signaling and TNFα signaling via NFκB. Our results show that MP and BP gene signatures represent and capture all 10 HoCs and highlight underlying biological processes of MP extreme samples, which might guide treatment decisions as the signature captures the full spectrum of early breast cancers.
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Affiliation(s)
- Josien C Haan
- Department of Research and Development, Agendia NV, Amsterdam, The Netherlands
| | - Rajith Bhaskaran
- Department of Research and Development, Agendia NV, Amsterdam, The Netherlands
| | | | - Yannick Bijl
- Department of Research and Development, Agendia NV, Amsterdam, The Netherlands
| | | | | | | | - Frédérique Penault-Llorca
- Department of Pathology and Molecular Pathology, Centre Jean Perrin, Clermont-Ferrand, France.,UMR INSERM 1240, Universite Clermont Auvergne, Clermont-Ferrand, France
| | | | - Annuska M Glas
- Department of Research and Development, Agendia NV, Amsterdam, The Netherlands
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11
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Ruan W, Yang Y, Yu Q, Huang T, Wang Y, Hua L, Zeng Z, Pan R. FUT11 is a target gene of HIF1α that promotes the progression of hepatocellular carcinoma. Cell Biol Int 2021; 45:2275-2286. [PMID: 34288238 DOI: 10.1002/cbin.11675] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 06/29/2021] [Accepted: 07/19/2021] [Indexed: 01/16/2023]
Abstract
Hypoxia promotes the progression of hepatocellular carcinoma. However, the hypoxia regulatory network in hepatocellular carcinoma is known to be limited. Thus, this study aimed to identify the crucial hypoxia-associated genes and to explore their effects and molecular mechanisms in hepatocellular carcinoma cells. FUT11 was first identified as a crucial hypoxia-associated gene through bioinformatics analysis. High FUT11 mRNA levels were positively correlated with poor clinical parameters. FUT11 knockdown under normoxia and hypoxia both decreased hepatocellular carcinoma cell proliferation, colony formation, migration, and invasion. HIF1α binds to the promoter of FUT11 and increases its transcription and co-expression with FUT11 in hepatocellular carcinoma tissues. Overexpression of FUT11 in HIF1α knockdown cells reversed the inhibitory effects of HIF1α suppression on hepatocellular carcinoma cell proliferation and mobility under hypoxia. Therefore, our findings indicate that FUT11 is a key target gene of HIF1α, which can promote the proliferation and mobility of hepatocellular carcinoma cells. FUT11 may be a novel and effective target for blocking the hypoxia response of hepatocellular carcinoma cells.
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Affiliation(s)
- Wanyuan Ruan
- School of Clinical Medicine, Hubei University of Science and Technology, Xianning, China.,Department of Infection, The Second Affiliated Hospital of Hubei University of Science and Technology, Xianning, China
| | - Yushi Yang
- School of Basic Medical Sciences, Guizhou Medical University, Guiyang, Guizhou, China.,Department of Pathology, Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, China
| | - Qionghua Yu
- School of Clinical Medicine, Hubei University of Science and Technology, Xianning, China.,Department of Infection, The Second Affiliated Hospital of Hubei University of Science and Technology, Xianning, China
| | - Tiejun Huang
- School of Clinical Medicine, Hubei University of Science and Technology, Xianning, China.,Department of Infection, The Second Affiliated Hospital of Hubei University of Science and Technology, Xianning, China
| | - Yaofen Wang
- School of Clinical Medicine, Hubei University of Science and Technology, Xianning, China.,Department of Infection, The Second Affiliated Hospital of Hubei University of Science and Technology, Xianning, China
| | - Li Hua
- School of Clinical Medicine, Hubei University of Science and Technology, Xianning, China
| | - Zhirui Zeng
- School of Basic Medical Sciences, Guizhou Medical University, Guiyang, Guizhou, China
| | - Runsang Pan
- Department of Orthopedics, Guiyang Maternal and Child Health-care Hospital, Guiyang, Guizhou, China
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12
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Drake RR, McDowell C, West C, David F, Powers TW, Nowling T, Bruner E, Mehta AS, Angel PM, Marlow LA, Tun HW, Copland JA. Defining the human kidney N-glycome in normal and cancer tissues using MALDI imaging mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2020; 55:e4490. [PMID: 31860772 PMCID: PMC7187388 DOI: 10.1002/jms.4490] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 11/27/2019] [Accepted: 12/16/2019] [Indexed: 05/03/2023]
Abstract
Clear-cell renal cell carcinoma (ccRCC) presents challenges to clinical management because of late-stage detection, treatment resistance, and frequent disease recurrence. Metabolically, ccRCC has a well-described Warburg effect utilization of glucose, but how this affects complex carbohydrate synthesis and alterations to protein and cell surface glycosylation is poorly defined. Using an imaging mass spectrometry approach, N-glycosylation patterns and compositional differences were assessed between tumor and nontumor regions of formalin-fixed clinical ccRCC specimens and tissue microarrays. Regions of normal kidney tissue samples were also evaluated for N-linked glycan-based distinctions between cortex, medullar, glomeruli, and proximal tubule features. Most notable was the proximal tubule localized detection of abundant multiantennary N-glycans with bisecting N-acetylglucosamine and multziple fucose residues. These glycans are absent in ccRCC tissues, while multiple tumor-specific N-glycans were detected with tri- and tetra-antennary structures and varying levels of fucosylation and sialylation. A polycystic kidney disease tissue was also characterized for N-glycan composition, with specific nonfucosylated glycans detected in the cyst fluid regions. Complementary to the imaging mass spectrometry analyses was an assessment of transcriptomic gene array data focused on the fucosyltransferase gene family and other glycosyltransferase genes. The transcript levels of the FUT3 and FUT6 genes responsible for the enzymes that add fucose to N-glycan antennae were significantly decreased in all ccRCC tissues relative to matching nontumor tissues. These striking differences in glycosylation associated with ccRCC could lead to new mechanistic insight into the glycobiology underpinning kidney malignancies and suggest the potential for new therapeutic interventions and diagnostic markers.
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Affiliation(s)
- Richard R. Drake
- Department of Cell and Molecular Pharmacology and Experimental TherapeuticsMedical University of South CarolinaCharlestonSC29425USA
| | - Colin McDowell
- Department of Cell and Molecular Pharmacology and Experimental TherapeuticsMedical University of South CarolinaCharlestonSC29425USA
| | - Connor West
- Department of Cell and Molecular Pharmacology and Experimental TherapeuticsMedical University of South CarolinaCharlestonSC29425USA
| | - Fred David
- Department of Cell and Molecular Pharmacology and Experimental TherapeuticsMedical University of South CarolinaCharlestonSC29425USA
| | - Thomas W. Powers
- Department of Cell and Molecular Pharmacology and Experimental TherapeuticsMedical University of South CarolinaCharlestonSC29425USA
| | - Tamara Nowling
- Department of Medicine, Division of Rheumatology and ImmunologyMedical University of South CarolinaCharlestonSC29425USA
| | - Evelyn Bruner
- Department of Pathology and Laboratory MedicineMedical University of South CarolinaCharlestonSC29425USA
| | - Anand S. Mehta
- Department of Cell and Molecular Pharmacology and Experimental TherapeuticsMedical University of South CarolinaCharlestonSC29425USA
| | - Peggi M. Angel
- Department of Cell and Molecular Pharmacology and Experimental TherapeuticsMedical University of South CarolinaCharlestonSC29425USA
| | - Laura A. Marlow
- Department of Cancer BiologyMayo ClinicJacksonvilleFL32224USA
| | - Han W. Tun
- Department of Cancer BiologyMayo ClinicJacksonvilleFL32224USA
- Division of Hematology/Oncology, Internal Medicine DepartmentMayo ClinicJacksonvilleFL32224USA
| | - John A. Copland
- Department of Cancer BiologyMayo ClinicJacksonvilleFL32224USA
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13
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Apanovich N, Peters M, Apanovich P, Mansorunov D, Markova A, Matveev V, Karpukhin A. The Genes-Candidates for Prognostic Markers of Metastasis by Expression Level in Clear Cell Renal Cell Cancer. Diagnostics (Basel) 2020; 10:diagnostics10010030. [PMID: 31936274 PMCID: PMC7168144 DOI: 10.3390/diagnostics10010030] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 12/29/2019] [Accepted: 01/07/2020] [Indexed: 02/07/2023] Open
Abstract
The molecular prognostic markers of metastasis are important for personalized approaches to clear cell renal cell carcinoma (ccRCC) treatment but markers for practical use are still missing. To address this gap we studied the expression of ten genes—CA9, NDUFA4L2, VWF, IGFBP3, BHLHE41, EGLN3, SAA1, CSF1R, C1QA, and FN1—through RT-PCR, in 56 ccRCC patients without metastases and with metastases. All of these, excluding CSF1R, showed differential and increased (besides SAA1) expression in non-metastasis tumors. The gene expression levels in metastasis tumors were decreased, besides CSF1R, FN1 (not changed), and SAA1 (increased). There were significant associations of the differentially expressed genes with ccRCC metastasis by ROC analysis and the Fisher exact test. The association of the NDUFA4L2, VWF, EGLN3, SAA1, and C1QA expression with ccRCC metastasis is shown for the first time. The CA9, NDUFA4L2, BHLHE4, and EGLN3 were distinguished as the strongest candidates for ccRCC metastasis biomarkers. We used an approach that presupposed that the metastasis marker was the expression levels of any three genes from the selected panel and received sensitivity (88%) and specificity (73%) levels with a relative risk of RR > 3. In conclusion, a panel of selected genes—the candidates in biomarkers of ccRCC metastasis—was created for the first time. The results might shed some light on the ccRCC metastasis processes.
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Affiliation(s)
- Natalya Apanovich
- Bochkov Research Centre for Medical Genetics, 1 Moskvorechye St., Moscow 115522, Russia; (N.A.); (P.A.); (D.M.)
| | - Maria Peters
- N.N. Blokhin National Medical Research Center of Oncology of the Ministry of Health of Russia, 24 Kashirskoe Shosse, Moscow 115478, Russia; (M.P.); (A.M.); (V.M.)
| | - Pavel Apanovich
- Bochkov Research Centre for Medical Genetics, 1 Moskvorechye St., Moscow 115522, Russia; (N.A.); (P.A.); (D.M.)
| | - Danzan Mansorunov
- Bochkov Research Centre for Medical Genetics, 1 Moskvorechye St., Moscow 115522, Russia; (N.A.); (P.A.); (D.M.)
| | - Anna Markova
- N.N. Blokhin National Medical Research Center of Oncology of the Ministry of Health of Russia, 24 Kashirskoe Shosse, Moscow 115478, Russia; (M.P.); (A.M.); (V.M.)
| | - Vsevolod Matveev
- N.N. Blokhin National Medical Research Center of Oncology of the Ministry of Health of Russia, 24 Kashirskoe Shosse, Moscow 115478, Russia; (M.P.); (A.M.); (V.M.)
| | - Alexander Karpukhin
- Bochkov Research Centre for Medical Genetics, 1 Moskvorechye St., Moscow 115522, Russia; (N.A.); (P.A.); (D.M.)
- Correspondence: ; Tel.: +7-499-324-12-39
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14
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Identification of Prognostic Biomarkers in the Urinary Peptidome of the Small Renal Mass. THE AMERICAN JOURNAL OF PATHOLOGY 2019; 189:2366-2376. [DOI: 10.1016/j.ajpath.2019.08.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 08/12/2019] [Accepted: 08/20/2019] [Indexed: 01/10/2023]
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15
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Chen G, Chen J, Liu H, Chen S, Zhang Y, Li P, Thierry-Mieg D, Thierry-Mieg J, Mattes W, Ning B, Shi T. Comprehensive Identification and Characterization of Human Secretome Based on Integrative Proteomic and Transcriptomic Data. Front Cell Dev Biol 2019; 7:299. [PMID: 31824949 PMCID: PMC6881247 DOI: 10.3389/fcell.2019.00299] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 11/07/2019] [Indexed: 12/25/2022] Open
Abstract
Secreted proteins (SPs) play important roles in diverse important biological processes; however, a comprehensive and high-quality list of human SPs is still lacking. Here we identified 6,943 high-confidence human SPs (3,522 of them are novel) based on 330,427 human proteins derived from databases of UniProt, Ensembl, AceView, and RefSeq. Notably, 6,267 of 6,943 (90.3%) SPs have the supporting evidences from a large amount of mass spectrometry (MS) and RNA-seq data. We found that the SPs were broadly expressed in diverse tissues as well as human body fluid, and a significant portion of them exhibited tissue-specific expression. Moreover, 14 cancer-specific SPs that their expression levels were significantly associated with the patients’ survival of eight different tumors were identified, which could be potential prognostic biomarkers. Strikingly, 89.21% of 6,943 SPs (2,927 novel SPs) contain known protein domains. Those novel SPs we mainly enriched with the known domains regarding immunity, such as Immunoglobulin V-set and C1-set domain. Specifically, we constructed a user-friendly and freely accessible database, SPRomeDB (www.unimd.org/SPRomeDB), to catalog those SPs. Our comprehensive SP identification and characterization gain insights into human secretome and provide valuable resource for future researches.
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Affiliation(s)
- Geng Chen
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Jiwei Chen
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Huanlong Liu
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Shuangguan Chen
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Yang Zhang
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Peng Li
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Danielle Thierry-Mieg
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States
| | - Jean Thierry-Mieg
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States
| | - William Mattes
- National Center for Toxicological Research, Food and Drug Administration, Jefferson City, AR, United States
| | - Baitang Ning
- National Center for Toxicological Research, Food and Drug Administration, Jefferson City, AR, United States
| | - Tieliu Shi
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
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16
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Zhang X, Wang Y. Identification of hub genes and key pathways associated with the progression of gynecological cancer. Oncol Lett 2019; 18:6516-6524. [PMID: 31788113 PMCID: PMC6865827 DOI: 10.3892/ol.2019.11004] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 06/05/2019] [Indexed: 12/20/2022] Open
Abstract
Gynecological cancer is the leading cause of cancer mortality in women. However, the mechanisms underlying gynecological cancer progression have remained largely unclear. In the present study, 799 dysregulated genes were identified in ovarian serous cystadenocarcinoma (OV), 488 dysregulated genes in cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC), and 621 dysregulated genes in uterine corpus endometrial carcinoma (UCEC). Bioinformatics analysis revealed that mRNA splicing and cell proliferation-associated biological processes served important roles in OV progression. Metabolism-associated biological processes played important roles in CESC progression, and protein phosphorylation and small GTPase-mediated signal transduction served important roles in UCEC progression. The present study also constructed OV, CESC and UCEC progression-associated protein-protein interaction networks to reveal the associations among these genes. Furthermore, Kaplan-Meier curve analysis showed that progression-related genes were associated with the duration of overall survival. Finally, NARS2 and TPT1 in OV, SMYD2, EGLN1, TNFRSF10D, FUT11, SYTL3, MMP8 and EREG in CESC, and SLC5A1, TXN, KDM4B, TXNDC11, HSDL2, COX16, MGAT4A, DAGLA, ELOVL7, THRB and PCOLCE2 in UCEC were identified as hub genes in cancer progression. Therefore, this study may assist in the identification of novel mechanisms underlying cancer progression and new biomarkers for gynecological cancer prognosis and therapy.
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Affiliation(s)
- Xi Zhang
- Department of Gynecology, Changning Maternity and Infant Health Hospital, Shanghai 200051, P.R. China
| | - Yudong Wang
- Department of Gynecology, International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University, Shanghai 200030, P.R. China
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17
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Montgomery MR, Hull EE. Alterations in the glycome after HDAC inhibition impact oncogenic potential in epigenetically plastic SW13 cells. BMC Cancer 2019; 19:79. [PMID: 30651077 PMCID: PMC6335691 DOI: 10.1186/s12885-018-5129-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 11/23/2018] [Indexed: 02/07/2023] Open
Abstract
Background Defects in the type and degree of cellular glycosylation impact oncogenesis on multiple levels. Although the type of glycosylation is determined by protein sequence encoded by the genome, the extent and modifications of glycosylation depends on the activity of biosynthetic enzymes and recent data suggests that the glycome is also subject to epigenetic regulation. This study focuses on the ability of HDAC inhibition to alter glycosylation and to lead to pro-oncogenic alterations in the glycome as assessed by metastatic potential and chemoresistance. Methods Epigenetically plastic SW13 adrenocortical carcinoma cells were treated with FK228, an HDAC inhibitor with high affinity for HDAC1 and, to a lesser extent, HDAC2. In comparing HDAC inhibitor treated and control cells, differential expression of glycome-related genes were assessed by microarray. Differential glycosylation was then assessed by lectin binding arrays and the ability of cellular proteins to bind to glycans was assessed by glycan binding arrays. Differential sensitivity to paclitaxel, proliferation, and MMP activity were also assessed. Results Treatment with FK228 alters expression of enzymes in the biosynthetic pathways for a large number of glycome related genes including enzymes in all major glycosylation pathways and several glycan binding proteins. 84% of these differentially expressed glycome-related genes are linked to cancer, some as prognostic markers and others contributing basic oncogenic functions such as metastasis or chemoresistance. Glycan binding proteins also appear to be differentially expressed as protein extracts from treated and untreated cells show differential binding to glycan arrays. The impact of differential mRNA expression of glycosylation enzymes was documented by differential lectin binding. However, the assessment of changes in the glycome is complicated by the fact that detection of differential glycosylation through lectin binding is dependent on the methods used to prepare samples as protein-rich lysates show different binding than fixed cells in several cases. Paralleling the alterations in the glycome, treatment of SW13 cells with FK228 increases metastatic potential and reduces sensitivity to paclitaxel. Conclusions The glycome is substantially altered by HDAC inhibition and these changes may have far-reaching impacts on oncogenesis. Electronic supplementary material The online version of this article (10.1186/s12885-018-5129-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- McKale R Montgomery
- College of Human Sciences, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Elizabeth E Hull
- Biomedical Sciences Program, College of Graduate Studies, Midwestern University, Glendale, AZ, 85308, USA.
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18
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Ye IC, Fertig EJ, DiGiacomo JW, Considine M, Godet I, Gilkes DM. Molecular Portrait of Hypoxia in Breast Cancer: A Prognostic Signature and Novel HIF-Regulated Genes. Mol Cancer Res 2018; 16:1889-1901. [PMID: 30037853 PMCID: PMC6279594 DOI: 10.1158/1541-7786.mcr-18-0345] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 06/20/2018] [Accepted: 07/11/2018] [Indexed: 01/21/2023]
Abstract
Intratumoral hypoxia has been associated with invasion, metastasis, and treatment failure, prompting the need for a global characterization of the response to hypoxic conditions. The current study presents the results of a large-scale RNA sequencing (RNA-seq) effort, analyzing 31 breast cancer cell lines representative of breast cancer subtypes or normal mammary epithelial (NME) cells exposed to control tissue culture conditions (20% O2) or hypoxic conditions (1% O2). The results demonstrate that NME have a stronger response to hypoxia both in terms of number of genes induced by hypoxia as well as level of expression. A conserved 42-gene hypoxia signature shared across PAM50 subtypes and genes that are exclusively upregulated in Luminal A, Luminal B, and normal-like mammary epithelial cells is identified. The 42-gene expression signature is enriched in a subset of basal-like cell lines and tumors and differentiates survival among patients with basal-like tumors. Mechanistically, the hypoxia-inducible factors (HIF-1 and/or HIF-2) mediate the conserved hypoxic response. Also, four novel hypoxia-regulated and HIF-1-responsive genes were identified as part of the conserved signature. This dataset provides a novel resource to query transcriptional changes that occur in response to hypoxia and serves as a starting point for a clinical assay to aid in stratifying patients that would benefit from hypoxia-targeted therapies, some of which are currently in clinical trials. IMPLICATIONS: RNA-seq of 31 breast cancer cells exposed to control or hypoxic conditions reveals a conserved genomic signature that contains novel HIF-regulated genes and is prognostic for the survival of patients with triple-negative breast cancer.
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Affiliation(s)
- I Chae Ye
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Elana J Fertig
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Josh W DiGiacomo
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Michael Considine
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Inês Godet
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Daniele M Gilkes
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland
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19
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Exosomes impact survival to radiation exposure in cell line models of nervous system cancer. Oncotarget 2018; 9:36083-36101. [PMID: 30546829 PMCID: PMC6281426 DOI: 10.18632/oncotarget.26300] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 10/21/2018] [Indexed: 12/24/2022] Open
Abstract
Radiation is utilized in the therapy of more than 50% of cancer patients. Unfortunately, many malignancies become resistant to radiation over time. We investigated the hypothesis that one method of a cancer cell's ability to survive radiation occurs through cellular communication via exosomes. Exosomes are cell-derived vesicles containing DNA, RNA, and protein. Three properties were analyzed: 1) exosome function, 2) exosome profile and 3) exosome uptake/blockade. To analyze exosome function, we show radiation-derived exosomes increased proliferation and enabled recipient cancer cells to survive radiation in vitro. Furthermore, radiation-derived exosomes increased tumor burden and decreased survival in an in vivo model. To address the mechanism underlying the alterations by exosomes in recipient cells, we obtained a profile of radiation-derived exosomes that showed expression changes favoring a resistant/proliferative profile. Radiation-derived exosomes contain elevated oncogenic miR-889, oncogenic mRNAs, and proteins of the proteasome pathway, Notch, Jak-STAT, and cell cycle pathways. Radiation-derived exosomes contain decreased levels of tumor-suppressive miR-516, miR-365, and multiple tumor-suppressive mRNAs. Ingenuity pathway analysis revealed the most represented networks included cell cycle, growth/survival. Upregulation of DNM2 correlated with increased exosome uptake. To analyze the property of exosome blockade, heparin and simvastatin were used to inhibit uptake of exosomes in recipient cells resulting in inhibited induction of proliferation and cellular survival. Because these agents have shown some success as cancer therapies, our data suggest their mechanism of action could be limiting exosome communication between cells. The results of our study identify a novel exosome-based mechanism that may underlie a cancer cell's ability to survive radiation.
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20
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Duan X, Yang S, Zhang L, Yang T. V-ATPases and osteoclasts: ambiguous future of V-ATPases inhibitors in osteoporosis. Theranostics 2018; 8:5379-5399. [PMID: 30555553 PMCID: PMC6276090 DOI: 10.7150/thno.28391] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 10/10/2018] [Indexed: 12/11/2022] Open
Abstract
Vacuolar ATPases (V-ATPases) play a critical role in regulating extracellular acidification of osteoclasts and bone resorption. The deficiencies of subunit a3 and d2 of V-ATPases result in increased bone density in humans and mice. One of the traditional drug design strategies in treating osteoporosis is the use of subunit a3 inhibitor. Recent findings connect subunits H and G1 with decreased bone density. Given the controversial effects of ATPase subunits on bone density, there is a critical need to review the subunits of V-ATPase in osteoclasts and their functions in regulating osteoclasts and bone remodeling. In this review, we comprehensively address the following areas: information about all V-ATPase subunits and their isoforms; summary of V-ATPase subunits associated with human genetic diseases; V-ATPase subunits and osteopetrosis/osteoporosis; screening of all V-ATPase subunits variants in GEFOS data and in-house data; spectrum of V-ATPase subunits during osteoclastogenesis; direct and indirect roles of subunits of V-ATPases in osteoclasts; V-ATPase-associated signaling pathways in osteoclasts; interactions among V-ATPase subunits in osteoclasts; osteoclast-specific V-ATPase inhibitors; perspective of future inhibitors or activators targeting V-ATPase subunits in the treatment of osteoporosis.
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Affiliation(s)
- Xiaohong Duan
- State Key Laboratory of Military Stomatology, National Clinical Research Center for Oral Diseases, Department of Oral Biology, Clinic of Oral Rare and Genetic Diseases, School of Stomatology, the Fourth Military Medical University, 145 West Changle Road, Xi'an 710032, P. R. China
| | - Shaoqing Yang
- State Key Laboratory of Military Stomatology, National Clinical Research Center for Oral Diseases, Department of Oral Biology, Clinic of Oral Rare and Genetic Diseases, School of Stomatology, the Fourth Military Medical University, 145 West Changle Road, Xi'an 710032, P. R. China
| | - Lei Zhang
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, 199 Renai Road, Suzhou, Jiangsu, P. R. China
| | - Tielin Yang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, 28 West Xianning Road, Xi'an 710049, People's Republic of China
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21
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Nam HY, Chandrashekar DS, Kundu A, Shelar S, Kho EY, Sonpavde G, Naik G, Ghatalia P, Livi CB, Varambally S, Sudarshan S. Integrative Epigenetic and Gene Expression Analysis of Renal Tumor Progression to Metastasis. Mol Cancer Res 2018; 17:84-96. [PMID: 30131446 DOI: 10.1158/1541-7786.mcr-17-0636] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 04/20/2018] [Accepted: 08/03/2018] [Indexed: 12/21/2022]
Abstract
The Cancer Genome Atlas (TCGA) and other large-scale genomic data pipelines have been integral to the current understanding of the molecular events underlying renal cell carcinoma (RCC). These data networks have focused mostly on primary RCC, which often demonstrates indolent behavior. However, metastatic disease is the major cause of mortality associated with RCC and data sets examining metastatic tumors are sparse. Therefore, a more comprehensive analysis of gene expression and DNA methylome profiling of metastatic RCC in addition to primary RCC and normal kidney was performed. Integrative analysis of the methylome and transcriptome identified over 30 RCC-specific genes whose mRNA expression inversely correlated with promoter methylation, including several known targets of hypoxia inducible factors. Notably, genes encoding several metabolism-related proteins were identified as differentially regulated via methylation including hexokinase 2, aldolase C, stearoyl-CoA desaturase, and estrogen-related receptor-γ (ESRRG), which has a known role in the regulation of nuclear-encoded mitochondrial metabolism genes. Several gene expression changes could portend prognosis in the TCGA cohort. Mechanistically, ESRRG loss occurs via DNA methylation and histone repressive silencing mediated by the polycomb repressor complex 2. Restoration of ESRRG in RCC lines suppresses migratory and invasive phenotypes independently of its canonical role in mitochondrial metabolism. IMPLICATIONS: Collectively, these data provide significant insight into the biology of aggressive RCC and demonstrate a novel role for DNA methylation in the promotion of HIF signaling and invasive phenotypes in renal cancer.
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Affiliation(s)
- Hye-Young Nam
- Department of Urology, University of Alabama at Birmingham, Birmingham, Alabama
| | | | - Anirban Kundu
- Department of Urology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Sandeep Shelar
- Department of Urology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Eun-Young Kho
- Department of Urology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Guru Sonpavde
- Department of Medical Oncology, Dana Farber Cancer Institute, Massachusetts
| | - Gurudatta Naik
- Department of Medicine, Section of Hematology-Oncology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Pooja Ghatalia
- Department of Hematology/Oncology, Fox Chase Cancer Center, Philadelphia Pennsylvania
| | - Carolina B Livi
- Department of Molecular Medicine, University of Texas Health Sciences Center at San Antonio, Texas
| | - Sooryanarayana Varambally
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama. .,Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama.,Department of Pathology, Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan
| | - Sunil Sudarshan
- Department of Urology, University of Alabama at Birmingham, Birmingham, Alabama. .,Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama.,Birmingham Veterans Affairs Medical Center, Birmingham, Alabama
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22
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Polo A, Marchese S, De Petro G, Montella M, Ciliberto G, Budillon A, Costantini S. Identifying a panel of genes/proteins/miRNAs modulated by arsenicals in bladder, prostate, kidney cancers. Sci Rep 2018; 8:10395. [PMID: 29991691 PMCID: PMC6039466 DOI: 10.1038/s41598-018-28739-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 06/28/2018] [Indexed: 02/07/2023] Open
Abstract
Arsenic and arsenic-derivative compounds, named as arsenicals, represent a worldwide problem for their effect on the human health and, in particular, for their capability to increase the risk of developing cancer such as kidney, bladder and prostate cancer. The main source of arsenical exposure is drinking water. Nowadays, it is well known that the chronic exposure to arsenicals leads to a series of epigenetic alterations that have a role in arsenic-induced effects on human health including cancer. Based on these observations, the aim of our study was to select by network analysis the genes/proteins/miRNAs implicated in kidney, bladder and prostate cancer development upon arsenical exposure. From this analysis we identified: (i) the nodes linking the three molecular networks specific for kidney, bladder and prostate cancer; (ii) the relative HUB nodes (RXRA, MAP3K7, NR3C1, PABPC1, NDRG1, RELA and CTNNB1) that link the three cancer networks; (iii) the miRNAs able to target these HUB nodes. In conclusion, we highlighted a panel of potential molecules related to the molecular mechanisms of arsenical-induced cancerogenesis and suggest their utility as biomarkers or therapeutic targets.
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Affiliation(s)
- Andrea Polo
- Experimental Pharmacology Unit, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Silvia Marchese
- Experimental Pharmacology Unit, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Giuseppina De Petro
- Dipartimento di Medicina Molecolare e Traslazionale, Università di Brescia, Brescia, Italy
| | - Maurizio Montella
- Epidemiology Unit, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Gennaro Ciliberto
- Scientific Directorate, IRCCS Istituto Nazionale Tumori "Regina Elena", Roma, Italy
| | - Alfredo Budillon
- Experimental Pharmacology Unit, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy.
| | - Susan Costantini
- Experimental Pharmacology Unit, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy.
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23
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Lapek JD, Mills RH, Wozniak JM, Campeau A, Fang RH, Wei X, van de Groep K, Perez-Lopez A, van Sorge NM, Raffatellu M, Knight R, Zhang L, Gonzalez DJ. Defining Host Responses during Systemic Bacterial Infection through Construction of a Murine Organ Proteome Atlas. Cell Syst 2018; 6:579-592.e4. [PMID: 29778837 PMCID: PMC7868092 DOI: 10.1016/j.cels.2018.04.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 01/30/2018] [Accepted: 04/12/2018] [Indexed: 12/18/2022]
Abstract
Group A Streptococcus (GAS) remains one of the top 10 deadliest human pathogens worldwide despite its sensitivity to penicillin. Although the most common GAS infection is pharyngitis (strep throat), it also causes life-threatening systemic infections. A series of complex networks between host and pathogen drive invasive infections, which have not been comprehensively mapped. Attempting to map these interactions, we examined organ-level protein dynamics using a mouse model of systemic GAS infection. We quantified over 11,000 proteins, defining organ-specific markers for all analyzed tissues. From this analysis, an atlas of dynamically regulated proteins and pathways was constructed. Through statistical methods, we narrowed organ-specific markers of infection to 34 from the defined atlas. We show these markers are trackable in blood of infected mice, and a subset has been observed in plasma samples from GAS-infected clinical patients. This proteomics-based strategy provides insight into host defense responses, establishes potentially useful targets for therapeutic intervention, and presents biomarkers for determining affected organs during bacterial infection.
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Affiliation(s)
- John D Lapek
- Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Robert H Mills
- Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Department of Computer Science and Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Center for Microbiome Innovation, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Jacob M Wozniak
- Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Anaamika Campeau
- Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Ronnie H Fang
- Department of Nanoengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Xiaoli Wei
- Department of Nanoengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Kirsten van de Groep
- Department of Epidemiology, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Heidelberglaan 100, G04.614, 3584 CX Utrecht, the Netherlands; Department of Intensive Care Medicine, University Medical Center Utrecht, Heidelberglaan 100, G04.614, 3584 CX Utrecht, the Netherlands
| | - Araceli Perez-Lopez
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Nina M van Sorge
- Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, G04.614, 3584 CX Utrecht, the Netherlands
| | - Manuela Raffatellu
- Chiba University-UC San Diego Center for Mucosal Immunology, Allergy, and Vaccines, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Center for Microbiome Innovation, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Department of Computer Science and Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Center for Microbiome Innovation, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Liangfang Zhang
- Department of Nanoengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - David J Gonzalez
- Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Center for Microbiome Innovation, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
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Novianti PW, van der Tweel I, Jong VL, Roes KC, Eijkemans MJ. An Application of Sequential Meta-Analysis to Gene Expression Studies. Cancer Inform 2015; 14:1-10. [PMID: 26401096 PMCID: PMC4567049 DOI: 10.4137/cin.s27718] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 06/03/2015] [Accepted: 06/04/2015] [Indexed: 11/15/2022] Open
Abstract
Most of the discoveries from gene expression data are driven by a study claiming an optimal subset of genes that play a key role in a specific disease. Meta-analysis of the available datasets can help in getting concordant results so that a real-life application may be more successful. Sequential meta-analysis (SMA) is an approach for combining studies in chronological order while preserving the type I error and pre-specifying the statistical power to detect a given effect size. We focus on the application of SMA to find gene expression signatures across experiments in acute myeloid leukemia. SMA of seven raw datasets is used to evaluate whether the accumulated samples show enough evidence or more experiments should be initiated. We found 313 differentially expressed genes, based on the cumulative information of the experiments. SMA offers an alternative to existing methods in generating a gene list by evaluating the adequacy of the cumulative information.
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Affiliation(s)
- Putri W Novianti
- Biostatistics and Research Support, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Ingeborg van der Tweel
- Biostatistics and Research Support, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Victor L Jong
- Biostatistics and Research Support, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands ; Department of Viroscience, Erasmus Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Kit Cb Roes
- Biostatistics and Research Support, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Marinus Jc Eijkemans
- Biostatistics and Research Support, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
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25
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Wrzesiński T, Szelag M, Cieślikowski WA, Ida A, Giles R, Zodro E, Szumska J, Poźniak J, Kwias Z, Bluyssen HAR, Wesoly J. Expression of pre-selected TMEMs with predicted ER localization as potential classifiers of ccRCC tumors. BMC Cancer 2015; 15:518. [PMID: 26169495 PMCID: PMC5015219 DOI: 10.1186/s12885-015-1530-4] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 07/01/2015] [Indexed: 11/24/2022] Open
Abstract
Background VHL inactivation is the most established molecular characteristic of clear cell renal cell carcinoma (ccRCC), with only a few additional genes implicated in development of this kidney tumor. In recently published ccRCC gene expression meta-analysis study we identified a number of deregulated genes with limited information available concerning their biological role, represented by gene transcripts belonging to transmembrane proteins family (TMEMs). TMEMs are predicted to be components of cellular membranes, such as mitochondrial membranes, ER, lysosomes and Golgi apparatus. Interestingly, the function of majority of TMEMs remains unclear. Here, we analyzed expression of ten TMEM genes in the context of ccRCC progression and development, and characterized these proteins bioinformatically. Methods The expression of ten TMEMs (RTP3, SLC35G2, TMEM30B, TMEM45A, TMEM45B, TMEM61, TMEM72, TMEM116, TMEM207 and TMEM213) was measured by qPCR. T-test, Pearson correlation, univariate and multivariate logistic and Cox regression were used in statistical analysis. The topology of studied proteins was predicted with Metaserver, together with PSORTII, Pfam and Localizome tools. Results We observed significant deregulation of expression of 10 analyzed TMEMs in ccRCC tumors. Cluster analysis of expression data suggested the down-regulation of all tested TMEMs to be a descriptor of the most advanced tumors. Logistic and Cox regression potentially linked TMEM expression to clinical parameters such as: metastasis, Fuhrman grade and overall survival. Topology predictions classified majority of analyzed TMEMs as type 3 and type 1 transmembrane proteins, with predicted localization mainly in ER. Conclusions The massive down-regulation of expression of TMEM family members suggests their importance in the pathogenesis of ccRCC and the bioinformatic analysis of TMEM topology implies a significant involvement of ER proteins in ccRCC pathology. Electronic supplementary material The online version of this article (doi:10.1186/s12885-015-1530-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tomasz Wrzesiński
- Laboratory of High Throughput Technologies, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Malgorzata Szelag
- Department of Human Molecular Genetics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Wojciech A Cieślikowski
- Department of Urology and Urological Oncology, Poznan University of Medical Sciences, Szwajcarska 3, 61-285, Poznan, Poland.
| | - Agnieszka Ida
- Department of Urology and Urological Oncology, Poznan University of Medical Sciences, Szwajcarska 3, 61-285, Poznan, Poland.
| | - Rachel Giles
- Department of Nephrology and Hypertension, University Medical Center, Postbus 85500, 3508 GA, Utrecht, Netherlands.
| | - Elżbieta Zodro
- Laboratory of High Throughput Technologies, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Joanna Szumska
- Laboratory of High Throughput Technologies, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Joanna Poźniak
- Laboratory of High Throughput Technologies, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Zbigniew Kwias
- Department of Urology and Urological Oncology, Poznan University of Medical Sciences, Szwajcarska 3, 61-285, Poznan, Poland.
| | - Hans A R Bluyssen
- Department of Human Molecular Genetics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Joanna Wesoly
- Laboratory of High Throughput Technologies, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
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26
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Shinmura K, Igarashi H, Kato H, Koda K, Ogawa H, Takahashi S, Otsuki Y, Yoneda T, Kawanishi Y, Funai K, Takayama T, Ozono S, Sugimura H. BSND and ATP6V1G3: Novel Immunohistochemical Markers for Chromophobe Renal Cell Carcinoma. Medicine (Baltimore) 2015; 94:e989. [PMID: 26091477 PMCID: PMC4616546 DOI: 10.1097/md.0000000000000989] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Differentiating between chromophobe renal cell carcinoma (RCC) and other RCC subtypes can be problematic using routine light microscopy. This study aimed to identify novel immunohistochemical markers useful for a differential diagnosis between chromophobe RCC and other RCC subtypes. We selected 3 genes (including BSND and ATP6V1G3) that showed specific transcriptional expression in chromophobe RCC using expression data (n = 783) from The Cancer Genome Atlas (TCGA) database. A subsequent immunohistochemical examination of 186 RCCs obtained in our patient series resulted in a strong diffuse positivity of BSND and ATP6V1G3 proteins (both of which are involved in the regulation of membrane transport) in all the chromophobe RCC specimens (23/23 cases, 100%) but not in the clear cell RCC specimens (0/153 cases, 0%) or the papillary RCC specimens (0/10 cases, 0%). BSND and ATP6V1G3 protein expressions were also detected in renal oncocytoma (13/14 cases, 92.9%) and in the distal nephron, including the collecting duct, in the normal kidney. A computational analysis of TCGA data suggested that DNA methylation was involved in the differential expression pattern of both genes among RCC subtypes. Finally, an immunohistochemical analysis showed lung carcinomas were negative (0/85 cases, 0%) for the expression of both proteins. These results suggest that BSND and ATP6V1G3 are excellent novel immunohistochemical markers for differentiating between chromophobe RCC and other subtypes of RCC, including clear cell and papillary RCCs.
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Affiliation(s)
- Kazuya Shinmura
- From the Department of Tumor Pathology (KS, HI, HK, HS); ResearchEquipment Center (YK); Department of Surgery 1 (KF); Department ofUrology(TT, SO), Hamamatsu University School of Medicine, Hamamatsu; Department of Pathology, Fujieda Municipal General Hospital,Fujieda (KK); Division of Pathology, Seirei Mikatahara General Hospital, Hamamatsu (HO, ST); and Department of Pathology (YO); Department of Urology(TY),Seirei Hamamatsu General Hospital, Hamamatsu, Japan
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27
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Kucharzewska P, Christianson HC, Belting M. Global profiling of metabolic adaptation to hypoxic stress in human glioblastoma cells. PLoS One 2015; 10:e0116740. [PMID: 25633823 PMCID: PMC4310608 DOI: 10.1371/journal.pone.0116740] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Accepted: 12/12/2014] [Indexed: 01/09/2023] Open
Abstract
Oncogenetic events and unique phenomena of the tumor microenvironment together induce adaptive metabolic responses that may offer new diagnostic tools and therapeutic targets of cancer. Hypoxia, or low oxygen tension, represents a well-established and universal feature of the tumor microenvironment and has been linked to increased tumor aggressiveness as well as resistance to conventional oncological treatments. Previous studies have provided important insights into hypoxia induced changes of the transcriptome and proteome; however, how this translates into changes at the metabolite level remains to be defined. Here, we have investigated dynamic, time-dependent effects of hypoxia on the cancer cell metabolome across all families of macromolecules, i.e., carbohydrate, protein, lipid and nucleic acid, in human glioblastoma cells. Using GC/MS and LC/MS/MS, 345 and 126 metabolites were identified and quantified in cells and corresponding media, respectively, at short (6 h), intermediate (24 h), and prolonged (48 h) incubation at normoxic or hypoxic (1% O2) conditions. In conjunction, we performed gene array studies with hypoxic and normoxic cells following short and prolonged incubation. We found that levels of several key metabolites varied with the duration of hypoxic stress. In some cases, metabolic changes corresponded with hypoxic regulation of key pathways at the transcriptional level. Our results provide new insights into the metabolic response of glioblastoma cells to hypoxia, which should stimulate further work aimed at targeting cancer cell adaptive mechanisms to microenvironmental stress.
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Affiliation(s)
- Paulina Kucharzewska
- Department of Clinical Sciences, Section of Oncology and Pathology, Lund University, Lund, Sweden
| | - Helena C. Christianson
- Department of Clinical Sciences, Section of Oncology and Pathology, Lund University, Lund, Sweden
| | - Mattias Belting
- Department of Clinical Sciences, Section of Oncology and Pathology, Lund University, Lund, Sweden
- Skåne Oncology Clinic, Skåne University Hospital, Lund, Sweden
- * E-mail:
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