1
|
Jiang K, Ning N, Huang J, Chang Y, Wang R, Ma J. Psilostachyin C reduces malignant properties of hepatocellular carcinoma cells by blocking CREBBP-mediated transcription of GATAD2B. Funct Integr Genomics 2024; 24:75. [PMID: 38600341 DOI: 10.1007/s10142-024-01353-8] [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: 02/05/2024] [Revised: 03/16/2024] [Accepted: 03/30/2024] [Indexed: 04/12/2024]
Abstract
Hepatocellular carcinoma (HCC) is a leading cause of cancer-related mortality globally. Many herbal medicines and their bioactive compounds have shown anti-tumor properties. This study was conducted to examine the effect of psilostachyin C (PSC), a sesquiterpenoid lactone isolated from Artemisia vulgaris L., in the malignant properties of HCC cells. CCK-8, flow cytometry, wound healing, and Transwell assays revealed that 25 μM PSC treatment significantly suppressed proliferation, cell cycle progression, migration, and invasion of two HCC cell lines (Hep 3B and Huh7) while promoting cell apoptosis. Bioinformatics prediction suggests CREB binding protein (CREBBP) as a promising target of PSC. CREBBP activated transcription of GATA zinc finger domain containing 2B (GATAD2B) by binding to its promoter. CREBBP and GATAD2B were highly expressed in clinical HCC tissues and the acquired HCC cell lines, but their expression was reduced by PSC. Either upregulation of CREBBP or GATAD2B restored the malignant properties of HCC cells blocked by PSC. Collectively, this evidence demonstrates that PSC pocessess anti-tumor functions in HCC cells by blocking CREBBP-mediated transcription of GATAD2B.
Collapse
Affiliation(s)
- Kai Jiang
- Department of Clinical Pharmacy, Honghui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, 710054, P.R. China
| | - Ning Ning
- Department of Orthopedics, Honghui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, 710054, P.R. China
| | - Jing Huang
- Department of Clinical Pharmacy, Honghui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, 710054, P.R. China
| | - Yu Chang
- Department of Clinical Pharmacy, Honghui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, 710054, P.R. China
| | - Rao Wang
- Department of TCM Orthopedic Center, Honghui Hospital, Xi'an Jiaotong University, No. 555, Youyi East Road, Beilin District, Xi'an, Shaanxi, 710054, P.R. China.
| | - Jie Ma
- Department of Neurology, Honghui Hospital, Xi'an Jiaotong University, No. 555, Youyi East Road, Beilin District, Xi'an, Shaanxi, 710054, P.R. China.
| |
Collapse
|
2
|
Proteomics and Metabolomics Profiling of Platelets and Plasma Mediators of Thrombo-Inflammation in Gestational Hypertension and Preeclampsia. Cells 2022; 11:cells11081256. [PMID: 35455936 PMCID: PMC9027992 DOI: 10.3390/cells11081256] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/02/2022] [Accepted: 04/05/2022] [Indexed: 02/04/2023] Open
Abstract
Platelets may be pivotal mediators of the thrombotic and coagulopathic complications of preeclampsia (PE), linking inflammation and thrombosis with endothelial and vascular dysfunction. Both PE and gestational hypertension (GH) fall within the spectrum of hypertensive complications of pregnancy, with GH being a risk factor for preeclampsia. However, it is unclear what biomarkers distinguish PE from GH. Using a discovery size cohort, we aimed to characterize specific plasma and platelet thrombo-inflammatory drivers indicative of PE and differentiate PE from GH. We performed multiplex immunoassays, platelet and plasma quantitative proteomics and metabolomics of PE patients, comparing with non-pregnant (NP), healthy pregnant controls (PC) and GH participants. The expression pattern of plasma proteins and metabolites in PE/GH platelets was distinct from that of NP and PC. Whilst procoagulation in PC may be fibrinogen driven, inter-alpha-trypsin inhibitors ITIH2 and ITIH3 are likely mediators of thrombo-inflammation in GH and PE, and fibronectin and S100A8/9 may be major procoagulant agonists in PE only. Also enriched in PE were CCL1 and CCL27 plasma cytokines, and the platelet leucine-rich repeat-containing protein 27 and 42 (LRRC27/42), whose effects on platelets were explored using STRING analysis. Through protein-protein interactions analysis, we generated a new hypothesis for platelets’ contribution to the thrombo-inflammatory states of preeclampsia.
Collapse
|
3
|
Moody L, Chen H, Pan YX. Considerations for feature selection using gene pairs and applications in large-scale dataset integration, novel oncogene discovery, and interpretable cancer screening. BMC Med Genomics 2020; 13:148. [PMID: 33087122 PMCID: PMC7579924 DOI: 10.1186/s12920-020-00778-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Background Advancements in transcriptomic profiling have led to the emergence of new challenges regarding data integration and interpretability. Variability between measurement platforms makes it difficult to compare between cohorts, and large numbers of gene features have encouraged the use black box methods that are not easily translated into biologically and clinically meaningful findings. We propose that gene rankings and algorithms that rely on relative expression within gene pairs can address such obstacles. Methods We implemented an innovative process to evaluate the performance of five feature selection methods on simulated gene-pair data. Along with TSP, we consider other methods that retain more information in their score calculations, including the magnitude of gene expression change as well as within-class variation. Tree-based rule extraction was also applied to serum microRNA (miRNA) pairs in order to devise a noninvasive screening tool for pancreatic and ovarian cancer. Results Gene pair data were simulated using different types of signal and noise. Pairs were filtered using feature selection approaches, including top-scoring pairs (TSP), absolute differences between gene ranks, and Fisher scores. Methods that retain more information, such as the magnitude of expression change and within-class variance, yielded higher classification accuracy using a random forest model. We then demonstrate two powerful applications of gene pairs by first performing large-scale integration of 52 breast cancer datasets consisting of 10,350 patients. Not only did we confirm known oncogenes, but we also propose novel tumorigenic genes, such as BSDC1 and U2AF1, that could distinguish between tumor subtypes. Finally, circulating miRNA pairs were filtered and salient rules were extracted to build simplified tree ensemble learners (STELs) for four types of cancer. These accessible clinical frameworks detected pancreatic and ovarian cancer with 84.8 and 93.6% accuracy, respectively. Conclusion Rank-based gene pair classification benefits from careful feature selection methods that preserve maximal information. Gene pairs enable dataset integration for greater statistical power and discovery of robust biomarkers as well as facilitate construction of user-friendly clinical screening tools.
Collapse
Affiliation(s)
- Laura Moody
- Division of Nutritional Sciences, University of Illinois Urbana-Champaign, 461 Bevier Hall, 905 South Goodwin Avenue, Urbana, IL, 61801, USA
| | - Hong Chen
- Division of Nutritional Sciences, University of Illinois Urbana-Champaign, 461 Bevier Hall, 905 South Goodwin Avenue, Urbana, IL, 61801, USA.,Department of Food Science and Human Nutrition, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Yuan-Xiang Pan
- Division of Nutritional Sciences, University of Illinois Urbana-Champaign, 461 Bevier Hall, 905 South Goodwin Avenue, Urbana, IL, 61801, USA. .,Department of Food Science and Human Nutrition, University of Illinois Urbana-Champaign, Urbana, IL, USA. .,Illinois Informatics Institute, University of Illinois Urbana-Champaign, Urbana, IL, USA.
| |
Collapse
|
4
|
Nakamura M, Takano A, Thang PM, Tsevegjav B, Zhu M, Yokose T, Yamashita T, Miyagi Y, Daigo Y. Characterization of KIF20A as a prognostic biomarker and therapeutic target for different subtypes of breast cancer. Int J Oncol 2020; 57:277-288. [PMID: 32467984 DOI: 10.3892/ijo.2020.5060] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 03/06/2020] [Indexed: 11/05/2022] Open
Abstract
The aim of the present study was to identify novel prognostic biomarkers and therapeutic targets for breast cancer; thus, genes that are frequently overexpressed in several types of breast cancer were screened. Kinesin family member 20A (KIF20A) was identified as a candidate molecule during this process. Immunohistochemical staining performed using tissue microarrays from 257 samples of different breast cancer subtypes revealed that KIF20A was expressed in 195 (75.9%) of these samples, whereas it was seldom expressed in normal breast tissue. KIF20A protein was expressed in all types of breast cancer observed. However, it was more frequently expressed in human epidermal growth factor receptor 2 (HER2)‑positive and triple‑negative breast cancer than in the luminal type. Moreover, KIF20A expression was significantly associated with the poor prognosis of patients with breast cancer. A multivariate analysis indicated that KIF20A expression was an independent prognostic factor for patients with breast cancer. The suppression of endogenous KIF20A expression using small interfering ribonucleic acids or via treatment with paprotrain, a selective inhibitor of KIF20A, significantly inhibited breast cancer cell growth through cell cycle arrest at the G2/M phase and subsequent mitotic cell death. These results suggest that KIF20A is a candidate prognostic biomarker and therapeutic target for different types of breast cancer.
Collapse
Affiliation(s)
- Masako Nakamura
- Department of Medical Oncology and Cancer Center, Shiga University of Medical Science, Otsu, Shiga 520‑2192, Japan
| | - Atsushi Takano
- Department of Medical Oncology and Cancer Center, Shiga University of Medical Science, Otsu, Shiga 520‑2192, Japan
| | - Phung Manh Thang
- Department of Medical Oncology and Cancer Center, Shiga University of Medical Science, Otsu, Shiga 520‑2192, Japan
| | - Bayarbat Tsevegjav
- Department of Medical Oncology and Cancer Center, Shiga University of Medical Science, Otsu, Shiga 520‑2192, Japan
| | - Ming Zhu
- Department of Medical Oncology and Cancer Center, Shiga University of Medical Science, Otsu, Shiga 520‑2192, Japan
| | - Tomoyuki Yokose
- Department of Pathology, Kanagawa Cancer Center, Yokohama, Kanagawa 241‑8515, Japan
| | - Toshinari Yamashita
- Department of Breast and Endocrine Surgery, Kanagawa Cancer Center, Yokohama, Kanagawa 241‑8515, Japan
| | - Yohei Miyagi
- Molecular Pathology and Genetics Division, Kanagawa Cancer Center Research Institute, Yokohama, Kanagawa 241‑8515, Japan
| | - Yataro Daigo
- Department of Medical Oncology and Cancer Center, Shiga University of Medical Science, Otsu, Shiga 520‑2192, Japan
| |
Collapse
|
5
|
Yasuoka Y, Matsumoto M, Yagi K, Okazaki Y. Evolutionary History of GLIS Genes Illuminates Their Roles in Cell Reprograming and Ciliogenesis. Mol Biol Evol 2020; 37:100-109. [PMID: 31504761 PMCID: PMC6984359 DOI: 10.1093/molbev/msz205] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The GLIS family transcription factors, GLIS1 and GLIS3, potentiate generation of induced pluripotent stem cells (iPSCs). In contrast, another GLIS family member, GLIS2, suppresses cell reprograming. To understand how these disparate roles arose, we examined evolutionary origins and genomic organization of GLIS genes. Comprehensive phylogenetic analysis shows that GLIS1 and GLIS3 originated during vertebrate whole genome duplication, whereas GLIS2 is a sister group to the GLIS1/3 and GLI families. This result is consistent with their opposing functions in cell reprograming. Glis1 evolved faster than Glis3, losing many protein-interacting motifs. This suggests that Glis1 acquired new functions under weakened evolutionary constraints. In fact, GLIS1 induces induced pluripotent stem cells more strongly. Transcriptomic data from various animal embryos demonstrate that glis1 is maternally expressed in some tetrapods, whereas vertebrate glis3 and invertebrate glis1/3 genes are rarely expressed in oocytes, suggesting that vertebrate (or tetrapod) Glis1 acquired a new expression domain and function as a maternal factor. Furthermore, comparative genomic analysis reveals that glis1/3 is part of a bilaterian-specific gene cluster, together with rfx3, ndc1, hspb11, and lrrc42. Because known functions of these genes are related to cilia formation and function, the last common ancestor of bilaterians may have acquired this cluster by shuffling gene order to establish more sophisticated epithelial tissues involving cilia. This evolutionary study highlights the significance of GLIS1/3 for cell reprograming, development, and diseases in ciliated organs such as lung, kidney, and pancreas.
Collapse
Affiliation(s)
- Yuuri Yasuoka
- Laboratory for Comprehensive Genomic Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Masahito Matsumoto
- Laboratory for Comprehensive Genomic Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Tokyo, Japan.,Advanced Diabetic Therapeutics, Department of Metabolic Endocrinology, Graduate School of Medicine, Juntendo University, Tokyo, Japan.,Department of Biofunction Research, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, Tokyo, Japan
| | - Ken Yagi
- Laboratory for Comprehensive Genomic Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yasushi Okazaki
- Laboratory for Comprehensive Genomic Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| |
Collapse
|
6
|
Xie XP, Xie YF, Liu YT, Wang HQ. Adaptively capturing the heterogeneity of expression for cancer biomarker identification. BMC Bioinformatics 2018; 19:401. [PMID: 30390627 PMCID: PMC6215657 DOI: 10.1186/s12859-018-2437-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 10/15/2018] [Indexed: 11/25/2022] Open
Abstract
Background Identifying cancer biomarkers from transcriptomics data is of importance to cancer research. However, transcriptomics data are often complex and heterogeneous, which complicates the identification of cancer biomarkers in practice. Currently, the heterogeneity still remains a challenge for detecting subtle but consistent changes of gene expression in cancer cells. Results In this paper, we propose to adaptively capture the heterogeneity of expression across samples in a gene regulation space instead of in a gene expression space. Specifically, we transform gene expression profiles into gene regulation profiles and mathematically formulate gene regulation probabilities (GRPs)-based statistics for characterizing differential expression of genes between tumor and normal tissues. Finally, an unbiased estimator (aGRP) of GRPs is devised that can interrogate and adaptively capture the heterogeneity of gene expression. We also derived an asymptotical significance analysis procedure for the new statistic. Since no parameter needs to be preset, aGRP is easy and friendly to use for researchers without computer programming background. We evaluated the proposed method on both simulated data and real-world data and compared with previous methods. Experimental results demonstrated the superior performance of the proposed method in exploring the heterogeneity of expression for capturing subtle but consistent alterations of gene expression in cancer. Conclusions Expression heterogeneity largely influences the performance of cancer biomarker identification from transcriptomics data. Models are needed that efficiently deal with the expression heterogeneity. The proposed method can be a standalone tool due to its capacity of adaptively capturing the sample heterogeneity and the simplicity in use. Software availability The source code of aGRP can be downloaded from https://github.com/hqwang126/aGRP. Electronic supplementary material The online version of this article (10.1186/s12859-018-2437-2) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Xin-Ping Xie
- School of Mathematics and Physics, Anhui Jianzhu University, Hefei, 230022, Anhui, China
| | - Yu-Feng Xie
- School of Mathematics and Physics, Anhui Jianzhu University, Hefei, 230022, Anhui, China.,Institute of Intelligent Machines, Hefei Institutes of Physical Science, CAS, 350 Shushanhu Road, P.O.Box 1130, Hefei, 230031, Anhui, China.,Present Address: School of Electronics and Information, Northwestern Polytechnical University, Xi'an, 710100, China
| | - Yi-Tong Liu
- School of Mathematics and Physics, Anhui Jianzhu University, Hefei, 230022, Anhui, China.,Institute of Intelligent Machines, Hefei Institutes of Physical Science, CAS, 350 Shushanhu Road, P.O.Box 1130, Hefei, 230031, Anhui, China
| | - Hong-Qiang Wang
- Institute of Intelligent Machines, Hefei Institutes of Physical Science, CAS, 350 Shushanhu Road, P.O.Box 1130, Hefei, 230031, Anhui, China.
| |
Collapse
|
7
|
Daigo K, Takano A, Thang PM, Yoshitake Y, Shinohara M, Tohnai I, Murakami Y, Maegawa J, Daigo Y. Characterization of KIF11 as a novel prognostic biomarker and therapeutic target for oral cancer. Int J Oncol 2017; 52:155-165. [PMID: 29115586 PMCID: PMC5743338 DOI: 10.3892/ijo.2017.4181] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 10/21/2017] [Indexed: 11/16/2022] Open
Abstract
Oral cancer has a high mortality rate, and its incidence is increasing gradually worldwide. As the effectiveness of standard treatments is still limited, the development of new therapeutic strategies is eagerly awaited. Kinesin family member 11 (KIF11) is a motor protein required for establishing a bipolar spindle in cell division. The role of KIF11 in oral cancer is unclear. Therefore, the present study aimed to assess the role of KIF11 in oral cancer and evaluate its role as a prognostic biomarker and therapeutic target for treating oral cancer. Immunohistochemical analysis demonstrated that KIF11 was expressed in 64 of 99 (64.6%) oral cancer tissues but not in healthy oral epithelia. Strong KIF11 expression was significantly associated with poor prognosis among oral cancer patients (P=0.034), and multivariate analysis confirmed its independent prognostic value. In addition, inhibition of KIF11 expression by transfection of siRNAs into oral cancer cells or treatment of cells with a KIF11 inhibitor significantly suppressed cell proliferation, probably through G2/M arrest and subsequent induction of apoptosis. These results suggest that KIF11 could be a potential prognostic biomarker and therapeutic target for oral cancer.
Collapse
Affiliation(s)
- Kayo Daigo
- Center for Antibody and Vaccine Therapy, Research Hospital, Institute of Medical Science Hospital, The University of Tokyo, Tokyo, Japan
| | - Atsushi Takano
- Center for Antibody and Vaccine Therapy, Research Hospital, Institute of Medical Science Hospital, The University of Tokyo, Tokyo, Japan
| | - Phung Manh Thang
- Center for Antibody and Vaccine Therapy, Research Hospital, Institute of Medical Science Hospital, The University of Tokyo, Tokyo, Japan
| | - Yoshihiro Yoshitake
- Department of Oral and Maxillofacial Surgery, Kumamoto University, Kumamoto, Japan
| | - Masanori Shinohara
- Department of Oral and Maxillofacial Surgery, Kumamoto University, Kumamoto, Japan
| | - Iwau Tohnai
- Department of Oral and Maxillofacial Surgery, Yokohama City University, Yokohama, Japan
| | - Yoshinori Murakami
- Division of Molecular Pathology, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Jiro Maegawa
- Department of Plastic and Reconstructive Surgery, Yokohama City University, Yokohama, Japan
| | - Yataro Daigo
- Center for Antibody and Vaccine Therapy, Research Hospital, Institute of Medical Science Hospital, The University of Tokyo, Tokyo, Japan
| |
Collapse
|
8
|
Thang PM, Takano A, Yoshitake Y, Shinohara M, Murakami Y, Daigo Y. Cell division cycle associated 1 as a novel prognostic biomarker and therapeutic target for oral cancer. Int J Oncol 2016; 49:1385-93. [PMID: 27499128 DOI: 10.3892/ijo.2016.3649] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Accepted: 07/25/2016] [Indexed: 11/06/2022] Open
Abstract
Oral cavity carcinoma (OCC) is one of the most common causes of cancer-related death worldwide and has poor clinical outcome after standard therapies. Therefore, new prognostic biomarkers and therapeutic targets for OCC are urgently needed. We selected cell division cycle associated 1 (CDCA1) as a candidate OCC biomarker. Immunohistochemical analysis confirmed that CDCA1 protein was expressed in 67 of 99 OCC tissues (67.7%), but not in healthy oral epithelia. CDCA1 expression was significantly associated with poor prognosis in OCC patients (P=0.0244). Knockdown of CDCA1 by siRNAs significantly increased apoptosis of tumor cells. These data suggest that CDCA1 represents a novel prognostic biomarker and therapeutic target for OCC.
Collapse
Affiliation(s)
- Phung Manh Thang
- Center for Antibody and Vaccine Therapy, Research Hospital, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Atsushi Takano
- Center for Antibody and Vaccine Therapy, Research Hospital, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yoshihiro Yoshitake
- Department of Oral and Maxillofacial Surgery, Kumamoto University, Kumamoto, Japan
| | - Masanori Shinohara
- Department of Oral and Maxillofacial Surgery, Kumamoto University, Kumamoto, Japan
| | - Yoshinori Murakami
- Division of Molecular Pathology, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yataro Daigo
- Center for Antibody and Vaccine Therapy, Research Hospital, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| |
Collapse
|