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Bell I, Khan H, Stutt N, Horn M, Hydzik T, Lum W, Rea V, Clapham E, Hoeg L, Van Raay TJ. Nkd1 functions downstream of Axin2 to attenuate Wnt signaling. Mol Biol Cell 2024; 35:ar93. [PMID: 38656801 PMCID: PMC11244159 DOI: 10.1091/mbc.e24-02-0059-t] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 04/10/2024] [Accepted: 04/19/2024] [Indexed: 04/26/2024] Open
Abstract
Wnt signaling is a crucial developmental pathway involved in early development as well as stem-cell maintenance in adults and its misregulation leads to numerous diseases. Thus, understanding the regulation of this pathway becomes vitally important. Axin2 and Nkd1 are widely utilized negative feedback regulators in Wnt signaling where Axin2 functions to destabilize cytoplasmic β-catenin, and Nkd1 functions to inhibit the nuclear localization of β-catenin. Here, we set out to further understand how Axin2 and Nkd1 regulate Wnt signaling by creating axin2gh1/gh1, nkd1gh2/gh2 single mutants and axin2gh1/gh1;nkd1gh2/gh2 double mutant zebrafish using sgRNA/Cas9. All three Wnt regulator mutants were viable and had impaired heart looping, neuromast migration defects, and behavior abnormalities in common, but there were no signs of synergy in the axin2gh1/gh1;nkd1gh2/gh2 double mutants. Further, Wnt target gene expression by qRT-PCR and RNA-seq, and protein expression by mass spectrometry demonstrated that the double axin2gh1/gh1;nkd1gh2/gh2 mutant resembled the nkd1gh2/gh2 phenotype demonstrating that Nkd1 functions downstream of Axin2. In support of this, the data further demonstrates that Axin2 uniquely alters the properties of β-catenin-dependent transcription having novel readouts of Wnt activity compared with nkd1gh2/gh2 or the axin2gh1/gh1;nkd1gh2/gh2 double mutant. We also investigated the sensitivity of the Wnt regulator mutants to exacerbated Wnt signaling, where the single mutants displayed characteristic heightened Wnt sensitivity, resulting in an eyeless phenotype. Surprisingly, this phenotype was rescued in the double mutant, where we speculate that cross-talk between Wnt/β-catenin and Wnt/Planar Cell Polarity pathways could lead to altered Wnt signaling in some scenarios. Collectively, the data emphasizes both the commonality and the complexity in the feedback regulation of Wnt signaling.
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Affiliation(s)
- Ian Bell
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, N1G 2W1 Ontario, Canada
| | - Haider Khan
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, N1G 2W1 Ontario, Canada
| | - Nathan Stutt
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Matthew Horn
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, N1G 2W1 Ontario, Canada
| | - Teesha Hydzik
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, N1G 2W1 Ontario, Canada
| | - Whitney Lum
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, N1G 2W1 Ontario, Canada
| | - Victoria Rea
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, N1G 2W1 Ontario, Canada
| | - Emma Clapham
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, N1G 2W1 Ontario, Canada
| | - Lisa Hoeg
- Department of Bioinformatics, University of Guelph, Guelph, Ontario, N1G 2W1 Canada
| | - Terence J. Van Raay
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, N1G 2W1 Ontario, Canada
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Roller A, Davydov II, Schwalie PC, Serrano-Serrano ML, Heller A, Staedler N, Ferreira CS, Dietmann G, Klaman I, Valdeolivas A, Korski K, Cannarile MA. Tumor-agnostic transcriptome-based classifier identifies spatial infiltration patterns of CD8+T cells in the tumor microenvironment and predicts clinical outcome in early-phase and late-phase clinical trials. J Immunother Cancer 2024; 12:e008185. [PMID: 38649280 PMCID: PMC11043740 DOI: 10.1136/jitc-2023-008185] [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] [Accepted: 03/18/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND The immune status of a patient's tumor microenvironment (TME) may guide therapeutic interventions with cancer immunotherapy and help identify potential resistance mechanisms. Currently, patients' immune status is mostly classified based on CD8+tumor-infiltrating lymphocytes. An unmet need exists for comparable and reliable precision immunophenotyping tools that would facilitate clinical treatment-relevant decision-making and the understanding of how to overcome resistance mechanisms. METHODS We systematically analyzed the CD8 immunophenotype of 2023 patients from 14 phase I-III clinical trials using immunohistochemistry (IHC) and additionally profiled gene expression by RNA-sequencing (RNA-seq). CD8 immunophenotypes were classified by pathologists into CD8-desert, CD8-excluded or CD8-inflamed tumors using CD8 IHC staining in epithelial and stromal areas of the tumor. Using regularized logistic regression, we developed an RNA-seq-based classifier as a surrogate to the IHC-based spatial classification of CD8+tumor-infiltrating lymphocytes in the TME. RESULTS The CD8 immunophenotype and associated gene expression patterns varied across indications as well as across primary and metastatic lesions. Melanoma and kidney cancers were among the strongest inflamed indications, while CD8-desert phenotypes were most abundant in liver metastases across all tumor types. A good correspondence between the transcriptome and the IHC-based evaluation enabled us to develop a 92-gene classifier that accurately predicted the IHC-based CD8 immunophenotype in primary and metastatic samples (area under the curve inflamed=0.846; excluded=0.712; desert=0.855). The newly developed classifier was prognostic in The Cancer Genome Atlas (TCGA) data and predictive in lung cancer: patients with predicted CD8-inflamed tumors showed prolonged overall survival (OS) versus patients with CD8-desert tumors (HR 0.88; 95% CI 0.80 to 0.97) across TCGA, and longer OS on immune checkpoint inhibitor administration (phase III OAK study) in non-small-cell lung cancer (HR 0.75; 95% CI 0.58 to 0.97). CONCLUSIONS We provide a new precision immunophenotyping tool based on gene expression that reflects the spatial infiltration patterns of CD8+ lymphocytes in tumors. The classifier enables multiplex analyses and is easy to apply for retrospective, reverse translation approaches as well as for prospective patient enrichment to optimize the response to cancer immunotherapy.
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Affiliation(s)
- Andreas Roller
- Roche Pharma Research and Early Development, Early Development Oncology, Roche Innovation Center, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Iakov I Davydov
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Petra C Schwalie
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Martha L Serrano-Serrano
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Astrid Heller
- Roche Pharma Research and Early Development, Early Development Oncology, Roche Innovation Center, Roche Diagnostics GmbH, Munich, Germany
| | - Nicolas Staedler
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Cláudia S Ferreira
- Roche Pharma Research and Early Development, Early Development Oncology, Roche Innovation Center, Roche Diagnostics GmbH, Munich, Germany
| | - Gabriele Dietmann
- Roche Pharma Research and Early Development, Early Development Oncology, Roche Innovation Center, Roche Diagnostics GmbH, Munich, Germany
| | - Irina Klaman
- Roche Pharma Research and Early Development, Early Development Oncology, Roche Innovation Center, Roche Diagnostics GmbH, Munich, Germany
| | - Alberto Valdeolivas
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Konstanty Korski
- Roche Product Development, PHC Data, Analytics and Imaging, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Michael A Cannarile
- Roche Pharma Research and Early Development, Early Development Oncology, Roche Innovation Center, Roche Diagnostics GmbH, Munich, Germany
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Tang C, Wang A, Zhao Y, Mou W, Jiang J, Kuang J, Sun B, Tang E. Leukotriene B4 receptor knockdown affects PI3K/AKT/mTOR signaling and apoptotic responses in colorectal cancer. BIOMOLECULES & BIOMEDICINE 2024; 24:968-981. [PMID: 38259082 PMCID: PMC11293244 DOI: 10.17305/bb.2024.10119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/12/2024] [Accepted: 01/20/2024] [Indexed: 01/24/2024]
Abstract
Colorectal cancer (CRC) presents a landscape of intricate molecular dynamics. In this study, we focused on the role of the leukotriene B4 receptor (LTB4R) in CRC, exploring its significance in the disease's progression and potential therapeutic approaches. Using bioinformatics analysis of the GSE164191 and the Cancer Genome Atlas-colorectal adenocarcinoma (TCGA-COAD) datasets, we identified LTB4R as a hub gene influencing CRC prognosis. Subsequently, we examined the relationship between LTB4R expression, apoptosis, and the phosphoinositide 3-kinase/protein kinase B/mammalian target of rapamycin (PI3K/AKT/mTOR) signaling pathway through cellular and mice experiments. Our findings revealed that LTB4R is highly expressed in CRC samples and is pivotal for determining prognosis. In vitro experiments demonstrated that silencing LTB4R significantly impeded CRC cell viability, migration, invasion, and colony formation. Correspondingly, in vivo tests indicated that LTB4R knockdown led to markedly slower tumor growth in mice models. Further in-depth investigation revealed that LTB4R knockdown significantly amplified the apoptosis in CRC cells and upregulated the expression of apoptosis-related proteins, such as caspase-3 and caspase-9, while diminishing p53 expression. Interestingly, silencing LTB4R also resulted in a significant downregulation of the PI3K/AKT/mTOR signaling pathway. Moreover, pretreatment with the PI3K activator 740Y-P only partially attenuated the effects of LTB4R knockdown on CRC cell behavior, emphasizing LTB4R's dominant influence in CRC cell dynamics and signaling pathways. LTB4R stands out as a critical factor in CRC progression, profoundly affecting cellular behavior, apoptotic responses, and the PI3K/AKT/mTOR signaling pathway. These findings not only shed light on LTB4R's role in CRC but also establish it as a potential diagnostic biomarker and a promising target for therapeutic intervention.
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Affiliation(s)
- Cui Tang
- Department of Radiology, Yangpu Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Aili Wang
- Center for Clinical Research and Translational Medicine, Yangpu Hospital, School of Medicine, Tongji University, Shanghai, China
| | - YanLin Zhao
- Department of Radiology, Yangpu Hospital, School of Medicine, Tongji University, Shanghai, China
| | - WenYing Mou
- Department of Radiology, Yangpu Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Jun Jiang
- Endoscopy Center, Minhang District Central Hospital of Fudan University, Shanghai, China
| | - Jie Kuang
- Department of Radiology, Yangpu Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Bin Sun
- Center for Clinical Research and Translational Medicine, Yangpu Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Erjiang Tang
- Center for Clinical Research and Translational Medicine, Yangpu Hospital, School of Medicine, Tongji University, Shanghai, China
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Zhang Y, Li L, Ke XP, Liu P. The identification of a PTEN-associated gene signature for the prediction of prognosis and planning of therapeutic strategy in endometrial cancer. Transl Cancer Res 2023; 12:3409-3424. [PMID: 38192993 PMCID: PMC10774041 DOI: 10.21037/tcr-23-1436] [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: 08/10/2023] [Accepted: 10/29/2023] [Indexed: 01/10/2024]
Abstract
Background Endometrial cancer (EC) is one of the most common malignancies among women. To improve the prognosis and treatment of EC, finding out a phosphatase and tensin homolog deleted on chromosome 10 (PTEN)-associated prognostic signature would be beneficial. Methods EC clinical data, genetic mutation data, and transcriptome data were downloaded from The Cancer Genome Atlas (TCGA) database. To clarify the specific PTEN-associated signature, cox regression analyses were performed. The clinical value of the selected signature on the overall survival (OS) and the secretoglobin family 2A member 1 (SCGB2A1)-independent analysis, immune and functional analysis were investigated respectively. Results Five hundred and fourteen EC samples were screened and PTEN mutation occupied 57%. Enrichment analysis indicated that mutant-type PTEN was enriched for pathways related to the upregulated human T-cell leukemia virus-1 (HTLV-1) infection and estrogen signaling pathway. SCGB2A1 was identified by cox regression analysis. Immune analysis exhibited significant immune infiltration with higher expression of T cells, B cells, and macrophage groups. Immune-checkpoint transcripts CD274 molecule (CD274), and cytotoxic T-lymphocyte associated protein 4 (CTLA4), hepatitis A virus cellular receptor 2 (HAVCR2), lymphocyte activation gene 3 (LAG3), programmed cell death 1 (PDCD1), PDCD1 ligand 2 (PDCD1LG2), T cell immunoreceptor with immunoglobulin and immunoreceptor tyrosine-based inhibition motif domains (TIGIT), and sialic acid binding immunoglobulin like lectin 15 (SIGLEC15) were discovered statistically different. In addition, the low-SCGB2A1 group had worse OS than the high-SCGB2A1 group. SCGB2A1 showed significant area under the curve (AUC) values in a time-dependent receiver operating characteristic (ROC) analysis. Prevalence of microsatellite instability (MSI) was detected and SCGB2A1 showed a negative correlation with EC. Immune checkpoint blockade (ICB) response indicated a worse immune response in the low-SCGB2A1 group. The distribution of one-class linear regression (OCLR) scores reflected the negative correlation between messenger RNA expression-based stemness index (mRNAsi) and prognostic gene expression. Furthermore, several SCGB2A1-related signaling pathways in EC were identified. Conclusions SCGB2A1 is a prognostic immunometabolic signature for patients with EC, which may help improve the prognosis and therapeutic effect.
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Affiliation(s)
- Yuan Zhang
- Department of General Surgery, Yangpu Hospital, School of Medicine, Tongji University, Shanghai, China
- Department of Obstetrics, International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Li Li
- Department of Obstetrics and Gynaecology, Yangpu Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Xiao-Ping Ke
- Department of Obstetrics and Gynaecology, Yangpu Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Ping Liu
- Department of Obstetrics and Gynaecology, Yangpu Hospital, School of Medicine, Tongji University, Shanghai, China
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Wei S, Lin L, Jiang W, Chen J, Gong G, Sui D. Naked cuticle homolog 1 prevents mouse pulmonary arterial hypertension via inhibition of Wnt/β-catenin and oxidative stress. Aging (Albany NY) 2023; 15:11114-11130. [PMID: 37857014 PMCID: PMC10637826 DOI: 10.18632/aging.205105] [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: 07/27/2023] [Accepted: 09/18/2023] [Indexed: 10/21/2023]
Abstract
Pulmonary arterial hypertension (PAH) is a poorly prognostic cardiopulmonary disease characterized by abnormal contraction and remodeling of pulmonary artery (PA). Excessive proliferation and migration of pulmonary arterial smooth muscle cells (PASMCs) are considered as the major etiology of PA remodeling. As a negative regulator of Wnt/β-catenin pathway, naked cuticle homolog 1 (NKD1) is originally involved in the tumor growth and metastasis via affecting the proliferation and migration of different types of cancer cells. However, the effect of NKD1 on PAH development has not been investigated. In the current study, downregulated NKD1 was identified in hypoxia-challenged PASMCs. NKD1 overexpression by adenovirus carrying vector encoding Nkd1 (Ad-Nkd1) repressed hypoxia-induced proliferation and migration of PASMCs. Mechanistically, upregulating NKD1 inhibited excessive reactive oxygen species (ROS) generation and β-catenin expression in PASMCs after hypoxia stimulus. Both inducing ROS and recovering β-catenin expression abolished NKD1-mediated suppression of proliferation and migration in PASMCs. In vivo, we also observed decreased expression of NKD1 in dissected PAs of monocrotaline (MCT)-induced PAH model. Upregulating NKD1 by Ad-Nkd1 transfection attenuated the increase in right ventricular systolic pressure (RVSP), right ventricular hypertrophy index (RVHI), pulmonary vascular wall thickening, and vascular β-catenin expression after MCT treatment. After recovering β-catenin expression by SKL2001, the vascular protection of external expression of NKD1 was also abolished. Taken together, our data suggest that NKD1 inhibits the proliferation, migration of PASMC, and PAH via inhibition of β-catenin and oxidative stress. Thus, targeting NKD1 may provide novel insights into the prevention and treatment of PAH.
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Affiliation(s)
- Shanwu Wei
- Department of Anesthesiology, The General Hospital of Western Theater Command, Chengdu 610083, China
| | - Lu Lin
- Department of Anesthesiology, The General Hospital of Western Theater Command, Chengdu 610083, China
| | - Wen Jiang
- Department of Outpatient, The General Hospital of Western Theater Command, Chengdu 610083, China
| | - Jie Chen
- Department of Cardiac Surgery, The General Hospital of Western Theater Command, Chengdu 610083, China
| | - Gu Gong
- Department of Anesthesiology, The General Hospital of Western Theater Command, Chengdu 610083, China
| | - Daming Sui
- Department of Pain Medicine, The General Hospital of Western Theater Command, Chengdu 610083, China
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Cao J, Tao X, Shi B, Wang J, Ma R, Zhao J, Tian J, Huang Q, Yu J, Wang L. NKD1 targeting PCM1 regulates the therapeutic effects of homoharringtonine on colorectal cancer. Mol Biol Rep 2023; 50:6543-6556. [PMID: 37338734 DOI: 10.1007/s11033-023-08572-5] [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: 03/29/2023] [Accepted: 05/31/2023] [Indexed: 06/21/2023]
Abstract
BACKGROUND Colorectal cancer (CRC) is the most common primary malignancy. Recently, antineoplastic attributes of homoharringtonine (HHT) have attracted lots of attention. This study investigated the molecular target and underlying mechanism of HHT in the CRC process by using a cellular and animal models. METHODS This study first detected the effects of HHT on the proliferation, cell cycle and apoptosis ability of CRC cells using CCK-8, Edu staining, flow cytometry and Western blotting assay. In vitro recovery experiment and in vivo tumorigenesis experiment were used to detect the targeted interaction between HHT and NKD1. After that, the downstream target and mechanism of action of HHT targeting NKD1 was determined using quantitative proteomics combined with co-immunoprecipitation/immunofluorescence assay. RESULTS HHT suppressed CRC cells proliferation by inducing cell cycle arrest and apoptosis in vitro and vivo. HHT inhibited NKD1 expression in a concentration and time dependent manner. NKD1 was overexpressed in CRC and its depletion enhanced the therapeutic sensitivity of HHT on CRC, which indicating that NKD1 plays an important role in the development of CRC as the drug delivery target of HHT. Furthermore, proteomic analysis revealed that PCM1 participated the process of NKD1-regulated cell proliferation and cell cycle. NKD1 interacted with PCM1 and promoted PCM1 degradation through the ubiquitin-proteasome pathway. The overexpression of PCM1 effectively reversed the inhibition of siNKD1 on cell cycle. CONCLUSIONS The present findings revealed that HHT blocked NKD1 expression to participate in inhibiting cell proliferation and inducing cell apoptosis, ultimately leading to obstruction of CRC development through NKD1/PCM1 dependent mechanism. Our research provide evidence for clinical application of NKD1-targeted therapy in improving HHT sensitivity for CRC treatment.
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Affiliation(s)
- Jia Cao
- Department of Beijing National Biochip Research Center Sub-Center in Ningxia, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, China
- Institute of Medical Sciences, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, China
| | - Xiang Tao
- College of Clinical Medicine, Ningxia Medical University, Yinchuan, Ningxia, China
| | - Bin Shi
- Department of Emergency, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, China
| | - Jia Wang
- Department of Beijing National Biochip Research Center Sub-Center in Ningxia, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, China
- Institute of Medical Sciences, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, China
| | - Rong Ma
- Department of Beijing National Biochip Research Center Sub-Center in Ningxia, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, China
- Institute of Medical Sciences, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, China
| | - Jufen Zhao
- College of Clinical Medicine, Ningxia Medical University, Yinchuan, Ningxia, China
| | - Jinhai Tian
- Department of Beijing National Biochip Research Center Sub-Center in Ningxia, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, China
| | - Qi Huang
- Department of Beijing National Biochip Research Center Sub-Center in Ningxia, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, China
- Institute of Medical Sciences, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, China
| | - Jingjing Yu
- Department of Beijing National Biochip Research Center Sub-Center in Ningxia, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, China
- Institute of Medical Sciences, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, China
| | - Libin Wang
- Department of Beijing National Biochip Research Center Sub-Center in Ningxia, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, China.
- College of Clinical Medicine, Ningxia Medical University, Yinchuan, Ningxia, China.
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Clinical Significance of NKD Inhibitor of WNT Signaling Pathway 1 (NKD1) in Glioblastoma. Genet Res (Camb) 2023; 2023:1184101. [PMID: 36969985 PMCID: PMC10038739 DOI: 10.1155/2023/1184101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 01/23/2023] [Accepted: 01/30/2023] [Indexed: 03/19/2023] Open
Abstract
Introduction. As the most malignant type of gliomas, glioblastoma is characterized with disappointing prognosis. Here, we aimed to investigate expression and function of NKD inhibitor of Wnt signaling pathway 1 (NKD1), an antagonist of Wnt-beta-catenin signaling pathways, in glioblastoma. Methods. The mRNA level of NKD1 was firstly retrieved from TCGA glioma dataset to evaluate its correlation with clinical characteristics and its value in prognosis prediction. Then, its protein expression level in glioblastoma was tested by immunohistochemistry staining in a retrospectively cohort collected from our medical center (n = 66). Univariate and multivariate survival analyses were conducted to assess its effect on glioma prognosis. Two glioblastoma cell lines, U87 and U251, were used to further investigate the tumor-related role of NKD1 through overexpression strategy in combination with cell proliferation assays. Immune cell enrichment in glioblastoma and its correlation with NKD1 level was finally assessed using bioinformatics analyses. Results. NKD1 shows a lower expression level in glioblastoma compared to that in the normal brain or other glioma subtypes, which is independently correlated to a worse prognosis in both the TCGA cohort and our retrospective cohort. Overexpressing NKD1 in glioblastoma cell lines can significantly attenuate cell proliferation. In addition, expression of NKD1 in glioblastoma is negatively correlated to the T cell infiltration, indicating it may have crosstalk with the tumor immune microenvironment. Conclusions. NKD1 inhibits glioblastoma progression and its downregulated expression indicates a poor prognosis.
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Zafari N, Bathaei P, Velayati M, Khojasteh-Leylakoohi F, Khazaei M, Fiuji H, Nassiri M, Hassanian SM, Ferns GA, Nazari E, Avan A. Integrated analysis of multi-omics data for the discovery of biomarkers and therapeutic targets for colorectal cancer. Comput Biol Med 2023; 155:106639. [PMID: 36805214 DOI: 10.1016/j.compbiomed.2023.106639] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/14/2023] [Accepted: 02/05/2023] [Indexed: 02/12/2023]
Abstract
The considerable burden of colorectal cancer and the rising trend in young adults emphasize the necessity of understanding its underlying mechanisms, providing new diagnostic and prognostic markers, and improving therapeutic approaches. Precision medicine is a new trend all over the world and identification of novel biomarkers and therapeutic targets is a step forward towards this trend. In this context, multi-omics data and integrated analysis are being investigated to develop personalized medicine in the management of colorectal cancer. Given the large amount of data from multi-omics approach, data integration and analysis is a great challenge. In this Review, we summarize how statistical and machine learning techniques are applied to analyze multi-omics data and how it contributes to the discovery of useful diagnostic and prognostic biomarkers and therapeutic targets. Moreover, we discuss the importance of these biomarkers and therapeutic targets in the clinical management of colorectal cancer in the future. Taken together, integrated analysis of multi-omics data has great potential for finding novel diagnostic and prognostic biomarkers and therapeutic targets, however, there are still challenges to overcome in future studies.
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Affiliation(s)
- Nima Zafari
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Parsa Bathaei
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mahla Velayati
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Fatemeh Khojasteh-Leylakoohi
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; Basic Sciences Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Majid Khazaei
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; Basic Sciences Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hamid Fiuji
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammadreza Nassiri
- Recombinant Proteins Research Group, The Research Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Seyed Mahdi Hassanian
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; Basic Sciences Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Gordon A Ferns
- Brighton & Sussex Medical School, Division of Medical Education, Falmer, Brighton, Sussex, BN1 9PH, UK
| | - Elham Nazari
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; Basic Sciences Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Amir Avan
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; Basic Sciences Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
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9
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Wang Y, Yang C, Li W, Shen Y, Deng J, Lu W, Jin J, Liu Y, Liu Q. Identification of colon tumor marker NKD1 via integrated bioinformatics analysis and experimental validation. Cancer Med 2021; 10:7383-7394. [PMID: 34547189 PMCID: PMC8525156 DOI: 10.1002/cam4.4224] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 08/07/2021] [Accepted: 08/09/2021] [Indexed: 12/15/2022] Open
Abstract
Background Colorectal cancer is an important death‐related disease in the worldwide. However, specific colon cancer tumor markers currently used for diagnosis and treatment are few. The purpose of this study is to screen the potential colon cancer markers by bioinformatics and verify the results with experiments. Methods Gene expression data were downloaded from two different databases: TCGA database and GEO datasets, which were then analyzed by two different methods (difference analysis and WGCNA method). Venn and PPI analysis obtained the potential core genes, which were then performed the GO enrichment and KEGG pathway analysis. Expressions levels of NKD1 in colon carcinoma tissues were further confirmed by immunohistochemical staining and western blot assays. Moreover, the function was measured by MTT, clone formation, and tumor transplantation experiments. Importantly, co‐immunoprecipitation, immunofluorescence, and protein stability assays were further performed to explore the underlying mechanism of NKD1 promoting cell proliferation. Results Nine potential core genes highly expressed in colon cancer samples were screened out by bioinformatics analysis. NKD1, one of the hub genes, highly expressed in the colon carcinoma tissues could enhance the proliferation of colon cancer cells. Mechanism research demonstrated that NKD1 was essential for the combination between Wnt signalosome (DVL) and β‐catenin, and that NKD1 knockout remarkably decreased the β‐catenin expression. Immunofluorescence assays further implied that NKD1 knockout significantly inhibited β‐catenin nuclear accumulation. Importantly, the stability of β‐catenin proteins was maintained by NKD1 in the colon cancer cells. Conclusion We believe that NKD1 well expressed in the colorectal carcinoma tissues can enhance the proliferation of colon cancer cells. Furthermore, the functions that NKD1 may have in colon cancer cells should be different from that NKD1 has played in the zebrafish. Thus, NKD1 could be a specific colorectal cancer marker.
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Affiliation(s)
- Yue Wang
- The Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu Province, China.,Clinical Oncology Laboratory, Changzhou Tumor Hospital Affiliated to Soochow University, Changzhou, Changzhou, China.,Department of Oncology, Wujin Hospital Affiliated with Jiangsu University, Jiangsu Province, China.,Department of Oncology, The Wujin Clinical College of Xuzhou Medical University, Jiangsu Province, China
| | - Chunxia Yang
- Department of Oncology, Wujin Hospital Affiliated with Jiangsu University, Jiangsu Province, China.,Department of Oncology, The Wujin Clinical College of Xuzhou Medical University, Jiangsu Province, China
| | - Wenjing Li
- Department of Oncology, Wujin Hospital Affiliated with Jiangsu University, Jiangsu Province, China.,Department of Oncology, The Wujin Clinical College of Xuzhou Medical University, Jiangsu Province, China
| | - Ying Shen
- Department of Oncology, Wujin Hospital Affiliated with Jiangsu University, Jiangsu Province, China.,Department of Oncology, The Wujin Clinical College of Xuzhou Medical University, Jiangsu Province, China
| | - Jianzhong Deng
- Department of Oncology, Wujin Hospital Affiliated with Jiangsu University, Jiangsu Province, China.,Department of Oncology, The Wujin Clinical College of Xuzhou Medical University, Jiangsu Province, China
| | - Wenbin Lu
- Department of Oncology, Wujin Hospital Affiliated with Jiangsu University, Jiangsu Province, China.,Department of Oncology, The Wujin Clinical College of Xuzhou Medical University, Jiangsu Province, China
| | - Jianhua Jin
- Department of Oncology, Wujin Hospital Affiliated with Jiangsu University, Jiangsu Province, China.,Department of Oncology, The Wujin Clinical College of Xuzhou Medical University, Jiangsu Province, China
| | - Yongping Liu
- The Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu Province, China.,Clinical Oncology Laboratory, Changzhou Tumor Hospital Affiliated to Soochow University, Changzhou, Changzhou, China
| | - Qian Liu
- Department of Oncology, Wujin Hospital Affiliated with Jiangsu University, Jiangsu Province, China.,Department of Oncology, The Wujin Clinical College of Xuzhou Medical University, Jiangsu Province, China
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